Three-dimensional (3D) refractive index tomography offers label-free quantitative volumetric imaging. However, existing tomography approaches are limited by optical aberrations, limited resolution, and computational complexity. To overcome these issues, we propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D refractive index distributions without iterative optimization or axial scanning. AFP employs a unique prior based on the finite sample thickness to recast the inverse scattering problem into analytically solvable linear equations. Unlike iterative methods, AFP does not require parameter tuning and computationally intensive optimizations, and can achieve efficient, robust, and generalizable image reconstructions across diverse samples and systems. We experimentally demonstrated that AFP greatly enhanced image quality and resolution under various aberration conditions across a range of applications. AFP corrected aberrations associated with 25 Zernike modes (with maximal phase difference of 2.3π and maximal Zernike coefficient value of 4), extended the synthetic numerical aperture from 0.41 to 0.99, and provided a two-fold resolution enhancement in all directions. With its simplicity, robustness, and broad applicability, AFP offers a user-friendly imaging platform for quantitative 3D analysis in biology, microbial ecology, and clinical science.
", "doi": "10.1038/s41467-025-67460-7", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2026-01-20", "volume": "17", "pages": "727" }, { "id": "authors:1b431-30035", "collection": "authors", "collection_id": "1b431-30035", "cite_using_url": "https://authors.library.caltech.edu/records/1b431-30035", "type": "article", "title": "Assessing human scalp and brain blood flow sensitivities via superficial temporal artery occlusion using speckle contrast optical spectroscopy", "author": [ { "family_name": "Huang", "given_name": "Yu Xi", "orcid": "0009-0000-0165-2084" }, { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X" }, { "family_name": "Dickson", "given_name": "Maya", "orcid": "0009-0000-8983-1190" }, { "family_name": "Abedi", "given_name": "Aidin", "orcid": "0000-0001-8243-3878" }, { "family_name": "Lo", "given_name": "Yu Tung", "orcid": "0000-0002-4234-8991" }, { "family_name": "Lyden", "given_name": "Patrick D.", "orcid": "0000-0001-6170-4042" }, { "family_name": "Russin", "given_name": "Jonathan", "orcid": "0000-0002-5304-4977" }, { "family_name": "Liu", "given_name": "Charles", "orcid": "0000-0001-6423-8577" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Cerebral blood flow is a critical metric for cerebrovascular monitoring, with applications in stroke detection, brain injury evaluation, aging, and neurological disorders. Noninvasively measuring cerebral blood dynamics is challenging due to the presence of scalp and skull, which obstruct direct brain access and contain their own blood dynamics that must be isolated. We developed an aggregated seven-channel speckle contrast optical spectroscopy (SCOS) system to measure blood flow and blood volume noninvasively. Each channel, with a distinct source-to-detector distance, targeted different depths to detect scalp and brain blood dynamics separately. By briefly occluding the superficial temporal artery, which supplies blood only to the scalp, we isolated surface blood dynamics from brain signals. Results on 20 subjects show that scalp-sensitive channels experienced significant reductions in blood dynamics during occlusion, while brain-sensitive channels experienced minimal changes. This provides experimental evidence of scalp blood flow sensitivity in diffuse optical measurements such as SCOS, highlighting optimal configuration for preferentially probing brain signals noninvasively.", "doi": "10.1063/5.0263953", "pmcid": "PMC12543367", "issn": "2473-2877", "publisher": "American Institute of Physics", "publication": "APL Bioengineering", "publication_date": "2025-12", "series_number": "4", "volume": "9", "issue": "4", "pages": "046106" }, { "id": "authors:ta6s7-wkk12", "collection": "authors", "collection_id": "ta6s7-wkk12", "cite_using_url": "https://authors.library.caltech.edu/records/ta6s7-wkk12", "type": "monograph", "title": "Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Deep Neural Network (DNN)", "author": [ { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X", "clpid": "Mahler-Simon" }, { "family_name": "Arora", "given_name": "Anika", "orcid": "0009-0003-4192-113X", "clpid": "Arora-Anika" }, { "family_name": "Readhead", "given_name": "Carol", "orcid": "0000-0003-2904-9003", "clpid": "Readhead-Carol" }, { "family_name": "Yin", "given_name": "Siyuan", "clpid": "Yi-Siyuan" }, { "family_name": "Hari", "given_name": "Surya Narayanan", "clpid": "Hari-Surya-Narayanan" }, { "family_name": "Wang", "given_name": "Ellie", "orcid": "0009-0000-1920-9582", "clpid": "Wang-Ellie-J" }, { "family_name": "Moxley", "given_name": "Cecilia I.", "clpid": "Moxley-Cecilia-I" }, { "family_name": "Adeboye", "given_name": "Abdullahi A.", "clpid": "Adeboye-Abdullahi-A" }, { "family_name": "Dong", "given_name": "Zhenyu", "orcid": "0009-0003-4507-8493", "clpid": "Dong-Zhenyu" }, { "family_name": "Zhou", "given_name": "Haowen", "clpid": "Zhou-Haowen" }, { "family_name": "Chen", "given_name": "Xi", "orcid": "0009-0007-4625-7441", "clpid": "Chen-Xi" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The ability to image blood flow in early-stage avian embryos has significant applications in developmental biology, drug and vaccine testing, as well as determining sex differentiation. In this project, we used our recently developed laser speckle contrast imaging (LSCI) system to non-invasively image extraembryonic blood vessels and used these images to attempt early sex identification of chick embryos. Specifically, we captured images of blood vessels from 1,251 living chicken embryos between day three and day four of incubation. We then applied deep neural network (DNN) models to evaluate whether it is possible to differentiate sex based on vascular patterns. Using ResNetBiT and YOLOv5 models, our results indicate that sex differentiation from extraembryonic blood vessel images was not achievable with sufficiently high accuracy or statistical significance for practical use. Specifically, ResNetBiT had a five-fold cross-validated average accuracy of 59%±5% (fold-wise p-value, p ≤ 0.3) at day 3 and 61%±3% (fold-wise, p ≤ 0.04) at day 4. YOLOv5 had a five-fold cross-validated average accuracy of 55%±3% (fold-wise, p ≤ 0.3) at day 3 and 53%±3% (fold-wise, p ≤ 0.5) at day 4. Our findings suggest that using vascular pattern imaging alone is inconclusive for reliable early sex identification in chicken embryos.
", "doi": "10.1101/2025.04.17.649355", "publisher": "BioRxiv", "publication_date": "2025-04-23" }, { "id": "authors:n0k7g-crk54", "collection": "authors", "collection_id": "n0k7g-crk54", "cite_using_url": "https://authors.library.caltech.edu/records/n0k7g-crk54", "type": "article", "title": "Dome-APIC illumination design for high space-bandwidth product analytic imaging", "author": [ { "family_name": "Lin", "given_name": "Siyu (Steven)", "orcid": "0009-0004-4985-7475", "clpid": "Lin-Steven-Siyu" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Zhao", "given_name": "Shi", "orcid": "0009-0008-4885-0473", "clpid": "Zhao-Shi" }, { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Breaking the tradeoff between resolution and field-of-view, while obtaining distortion-free images, can be achieved through computational imaging techniques. A recent approach, Angular Ptychographic Imaging with Close-form method (APIC), has showcased its capability to analytically recover both intricate aberrations and high space-bandwidth product complex optical fields with NA-matching and darkfield illuminations. However, its flat illumination setup limits its ability to efficiently reconstruct a large field-of-view simultaneously with high resolution, owing to the curvature in the wavefront from NA-matching illuminations and the finite beam angle of the Lambertian LED light source. Here, we introduce an illumination framework tailored for APIC consisting of a distant annular LED ring and an LED dome that enables the reconstruction of a larger area with an extended synthetic numerical aperture, consequently enhancing resolution. For a single set of measurements, our new prototype, termed Dome-APIC can reach 620nm resolution with a 10\u00d7/0.25 NA objective lens over a field-of-view of 450 \u00b5m x 450 \u00b5m.", "doi": "10.1364/boe.555541", "issn": "2156-7085", "publisher": "Optica Publishing Group", "publication": "Biomedical Optics Express", "publication_date": "2025-03-27", "series_number": "4", "volume": "16", "issue": "4", "pages": "1666-1677" }, { "id": "authors:tn8c2-c2q07", "collection": "authors", "collection_id": "tn8c2-c2q07", "cite_using_url": "https://authors.library.caltech.edu/records/tn8c2-c2q07", "type": "article", "title": "Automated non-invasive laser speckle imaging of the chick heart rate and extraembryonic blood vessels and their response to nifedipine and amlodipine drugs", "author": [ { "family_name": "Readhead", "given_name": "Carol", "clpid": "Readhead-Carol" }, { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X", "clpid": "Mahler-Simon" }, { "family_name": "Dong", "given_name": "Zhenyu", "orcid": "0009-0003-4507-8493", "clpid": "Dong-Zhenyu" }, { "family_name": "Sato", "given_name": "Yuki", "orcid": "0000-0001-8974-2059", "clpid": "Sato-Yuki" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" } ], "abstract": "Using our recently developed laser speckle contrast imaging (LSCI) to visualize blood vessels and monitor blood flow, we test the utility of the developing chick heart as a functional model for drug screening. To this end, we examined the effects of antihypertensive agents Nifedipine and Amlodipine, belonging to the L-type calcium channel antagonist family, on blood flow visualized noninvasively through the intact shell. Guided by the live view mode, the drugs were injected through the shell and ventral to HH16-19 chick embryos. Our results show a significant reduction in the chick's heart rate, blood flow, and vascular size within 5-20 minutes after Nifedipine or Amlodipine injection. For moderate Nifedipine concentrations, these parameters returned to initial values within 2-3 hours. Nifedipine showed a rapid reduction in heart rate and blood flow dynamics at a concentration ten times lower than Amlodipine. These findings show that our LSCI system can monitor and distinguish the chick heart's response to injected drugs from the same family. This serves as proof-of-concept, paving the way for a rapid, cost-effective, and quantitative test system for screening drugs that affect the cardiovascular system of live chick embryos. Live noninvasive imaging may also provide insights into the development and functioning of the vertebrate heart.", "doi": "10.1016/j.ydbio.2024.12.005", "issn": "0012-1606", "publisher": "Elsevier", "publication": "Developmental Biology", "publication_date": "2025-03", "volume": "519", "pages": "46-54" }, { "id": "authors:fs39e-xeb27", "collection": "authors", "collection_id": "fs39e-xeb27", "cite_using_url": "https://authors.library.caltech.edu/records/fs39e-xeb27", "type": "article", "title": "AI-based approach to dissect the variability of mouse stem cell-derived embryo models", "author": [ { "family_name": "Caldarelli", "given_name": "Paolo", "orcid": "0000-0003-4455-7778", "clpid": "Caldarelli-Paolo" }, { "family_name": "Deininger", "given_name": "Luca", "orcid": "0009-0005-5125-6422" }, { "family_name": "Zhao", "given_name": "Shi", "clpid": "Zhao-Shi" }, { "family_name": "Panda", "given_name": "Pallavi", "orcid": "0000-0001-7572-6728", "clpid": "Panda-Pallavi" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Mikut", "given_name": "Ralf", "orcid": "0000-0001-9100-5496" }, { "family_name": "Zernicka-Goetz", "given_name": "Magdalena", "orcid": "0000-0002-7004-2471", "clpid": "Zernicka-Goetz-M" } ], "abstract": "Recent advances in stem cell-derived embryo models have transformed developmental biology, offering insights into embryogenesis without the constraints of natural embryos. However, variability in their development challenges research standardization. To address this, we use deep learning to enhance the reproducibility of selecting stem cell-derived embryo models. Through live imaging and AI-based models, we classify 900 mouse post-implantation stem cell-derived embryo-like structures (ETiX-embryos) into normal and abnormal categories. Our best-performing model achieves 88% accuracy at 90 h post-cell seeding and 65% accuracy at the initial cell-seeding stage, forecasting developmental trajectories. Our analysis reveals that normally developed ETiX-embryos have higher cell counts and distinct morphological features such as larger size and more compact shape. Perturbation experiments increasing initial cell numbers further supported this finding by improving normal development outcomes. This study demonstrates deep learning’s utility in improving embryo model selection and reveals critical features of ETiX-embryo self-organization, advancing consistency in this evolving field.
", "doi": "10.1038/s41467-025-56908-5", "pmcid": "PMC11839995", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2025-02-19", "series_number": "1", "volume": "16", "issue": "1", "pages": "1772" }, { "id": "authors:f2bhd-p5111", "collection": "authors", "collection_id": "f2bhd-p5111", "cite_using_url": "https://authors.library.caltech.edu/records/f2bhd-p5111", "type": "article", "title": "Single-shot volumetric fluorescence imaging with neural fields", "author": [ { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Feng", "given_name": "Brandon Y." }, { "family_name": "Larsson", "given_name": "Elin M.", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-Elin-Maria" }, { "family_name": "Alcalde", "given_name": "Reinaldo E.", "orcid": "0000-0002-3430-5393", "clpid": "Alcalde-Reinaldo-E" }, { "family_name": "Yin", "given_name": "Siyuan", "clpid": "Yin-Siyuan" }, { "family_name": "Deng", "given_name": "Catherine", "clpid": "Deng-Catherine" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Single-shot volumetric fluorescence (SVF) imaging offers a significant advantage over traditional imaging methods that require scanning across multiple axial planes, as it can capture biological processes with high temporal resolution. The key challenges in SVF imaging include requiring sparsity constraints, eliminating depth ambiguity in the reconstruction, and maintaining high resolution across a large field of view. We introduce the QuadraPol point spread function (PSF) combined with neural fields, an approach for SVF imaging. This method utilizes a custom polarizer at the back focal plane and a polarization camera to detect fluorescence, effectively encoding the three-dimensional scene within a compact PSF without depth ambiguity. In addition, we propose a reconstruction algorithm based on the neural field technique that provides improved reconstruction quality compared with classical deconvolution methods. QuadraPol PSF, combined with neural fields, significantly reduces the acquisition time of a conventional fluorescence microscope by ∼20 times and captures a 100-mm³ cubic volume in one shot. We validate the effectiveness of both our hardware and algorithm through all-in-focus imaging of bacterial colonies on sand surfaces and visualization of plant root morphology. Our approach offers a powerful tool for advancing biological research and ecological studies.
", "doi": "10.1117/1.ap.7.2.026001", "issn": "2577-5421", "publisher": "SPIE-Intl Soc Optical Eng", "publication": "Advanced Photonics", "publication_date": "2025-02", "series_number": "02", "volume": "7", "issue": "02", "pages": "026001" }, { "id": "authors:9zmsv-3m995", "collection": "authors", "collection_id": "9zmsv-3m995", "cite_using_url": "https://authors.library.caltech.edu/records/9zmsv-3m995", "type": "article", "title": "Impact of stain variation and color normalization for prognostic predictions in pathology", "author": [ { "family_name": "Lin", "given_name": "Siyu", "clpid": "Lin-Siyu" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Watson", "given_name": "Mark" }, { "family_name": "Govindan", "given_name": "Ramaswamy" }, { "family_name": "Cote", "given_name": "Richard J." }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In recent years, deep neural networks (DNNs) have demonstrated remarkable performance in pathology applications, potentially even outperforming expert pathologists due to their ability to learn subtle features from large datasets. One complication in preparing digital pathology datasets for DNN tasks is the variation in tinctorial qualities. A common way to address this is to perform stain normalization on the images. In this study, we show that a well-trained DNN model trained on one batch of histological slides failed to generalize to another batch prepared at a different time from the same tissue blocks, even when stain normalization methods were applied. This study used sample data from a previously reported DNN that was able to identify patients with early-stage non-small cell lung cancer (NSCLC) whose tumors did and did not metastasize, with high accuracy, based on training and then testing of digital images from H&E stained primary tumor tissue sections processed at the same time. In this study, we obtained a new series of histologic slides from the adjacent recuts of the same tissue blocks processed in the same lab but at a different time. We found that the DNN trained on either batch of slides/images was unable to generalize and failed to predict progression in the other batch of slides/images (AUCcross-batch = 0.52 - 0.53 compared to AUCsame-batch = 0.74 - 0.81). The failure to generalize did not improve even when the tinctorial difference corrections were made through either traditional color-tuning or stain normalization with the help of a Cycle Generative Adversarial Network (CycleGAN) process. This highlights the need to develop an entirely new way to process and collect consistent microscopy images from histologic slides that can be used to both train and allow for the general application of predictive DNN algorithms.
", "doi": "10.1038/s41598-024-83267-w", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2025-01-18", "series_number": "1", "volume": "15", "issue": "1", "pages": "2369" }, { "id": "authors:qs0ax-h8e84", "collection": "authors", "collection_id": "qs0ax-h8e84", "cite_using_url": "https://authors.library.caltech.edu/records/qs0ax-h8e84", "type": "article", "title": "Portable six-channel laser speckle system for simultaneous measurement of cerebral blood flow and volume with potential applications in characterization of brain injury", "author": [ { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X", "clpid": "Mahler-Simon" }, { "family_name": "Huang", "given_name": "Yu Xi", "orcid": "0009-0000-0165-2084", "clpid": "Huang-Yu-Xi" }, { "family_name": "Ismagilov", "given_name": "Max" }, { "family_name": "\u00c1lvarez-Chou", "given_name": "David", "orcid": "0009-0000-5752-6706", "clpid": "\u00c1lvarez-Chou-David" }, { "family_name": "Abedi", "given_name": "Aidin" }, { "family_name": "Tyszka", "given_name": "J. Michael", "orcid": "0000-0001-9342-9014", "clpid": "Tyszka-J-M" }, { "family_name": "Lo", "given_name": "Yu Tung" }, { "family_name": "Russin", "given_name": "Jonathan" }, { "family_name": "Pantera", "given_name": "Richard L." }, { "family_name": "Liu", "given_name": "Charles" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Significance:
Cerebral blood flow (CBF) and cerebral blood volume (CBV) are key metrics for regional cerebrovascular monitoring. Simultaneous, non-invasive measurement of CBF and CBV at different brain locations would advance cerebrovascular monitoring and pave the way for brain injury detection as current brain injury diagnostic methods are often constrained by high costs, limited sensitivity, and reliance on subjective symptom reporting.
Aim:
We aim to develop a multi-channel non-invasive optical system for measuring CBF and CBV at different regions of the brain simultaneously with a cost-effective, reliable, and scalable system capable of detecting potential differences in CBF and CBV across different regions of the brain.
Approach:
The system is based on speckle contrast optical spectroscopy and consists of laser diodes and board cameras, which have been both tested and investigated for safe use on the human head. Apart from the universal serial bus connection for the camera, the entire system, including its battery power source, is integrated into a wearable headband and is powered by 9-V batteries.
Results:
The temporal dynamics of both CBF and CBV in a cohort of five healthy subjects were synchronized and exhibited similar cardiac period waveforms across all six channels. The potential use of our six-channel system for detecting the physiological sequelae of brain injury was explored in two subjects, one with moderate and one with significant structural brain damage, where the six-point CBF and CBV measurements were referenced to structural magnetic resonance imaging (MRI) scans.
Conclusions:
We pave the way for a viable multi-point optical instrument for measuring CBF and CBV. Its cost-effectiveness allows for baseline metrics to be established prior to injury in populations at risk for brain injury.
Deep learning-assisted digital pathology has demonstrated the potential to profoundly impact clinical practice, even surpassing human pathologists in performance. However, as deep neural network (DNN) architectures grow in size and complexity, their explainability decreases, posing challenges in interpreting pathology features for broader clinical insights into physiological diseases. To better assess the interpretability of digital microscopic images and guide future microscopic system design, we developed a novel method to study the predictive feature length-scale that underpins a DNN’s predictive power. We applied this method to analyze a DNN’s capability in predicting brain metastasis from early-stage non-small-cell lung cancer biopsy slides. This study quantifies DNN’s attention for brain metastasis prediction, targeting features at both the cellular scale and tissue scale in H&E-stained histological whole slide images. At the cellular scale, the predictive power of DNNs progressively increases with higher resolution and significantly decreases when the resolvable feature length exceeds 5 microns. Additionally, DNN uses more macro-scale features associated with tissue architecture and is optimized when assessing visual fields greater than 41 microns. Our study computes the length-scale requirements for optimal DNN learning on digital whole-slide microscopic images, holding the promise to guide future optical microscope designs in pathology applications and facilitating downstream deep learning analysis.
", "doi": "10.1038/s41598-024-73428-2", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2024-09-27", "series_number": "1", "volume": "14", "issue": "1", "pages": "22328" }, { "id": "authors:xb3nm-mp669", "collection": "authors", "collection_id": "xb3nm-mp669", "cite_using_url": "https://authors.library.caltech.edu/records/xb3nm-mp669", "type": "article", "title": "Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy", "author": [ { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Alcalde", "given_name": "Reinaldo E.", "orcid": "0000-0002-3430-5393", "clpid": "Alcalde-Reinalde-E" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Yin", "given_name": "Siyuan", "clpid": "Yin-Siyuan" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Microbial interactions in the rhizosphere contribute to soil health, making understanding these interactions crucial for sustainable agriculture and ecosystem management. Yet it is difficult to understand what we cannot see; among the limitations in rhizosphere imaging are challenges associated with rapidly and noninvasively imaging microbial cells over field depths relevant to plant roots. Here, we present a bimodal imaging technique called complex-field and fluorescence microscopy using the aperture scanning technique (CFAST) that addresses these limitations. CFAST integrates quantitative phase imaging using synthetic aperture imaging based on Kramers–Kronig relations, along with three-dimensional (3D) fluorescence imaging using an engineered point spread function. We showcase CFAST’s practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 μm, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane. This minimizes potential photobleaching and phototoxicity issues. Second, by leveraging CFAST’s phase sensitivity and fluorescence specificity, we track microbial growth, competition, and gene expression at early stages of colony biofilm development. Specifically, we resolve bacterial growth dynamics of mixed populations without the need for genetically labeling environmental isolates. Moreover, we find that gene expression related to phosphorus sensing and antibiotic production varies spatiotemporally within microbial populations that are surface attached and appears distinct from their expression in planktonic cultures. Together, CFAST’s attributes overcome commercial imaging platform limitations and enable insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere.
", "doi": "10.1073/pnas.2403122121", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2024-08-13", "series_number": "33", "volume": "121", "issue": "33", "pages": "e2403122121" }, { "id": "authors:84yvb-jx277", "collection": "authors", "collection_id": "84yvb-jx277", "cite_using_url": "https://authors.library.caltech.edu/records/84yvb-jx277", "type": "article", "title": "Non-invasive laser speckle contrast imaging (LSCI) of extra-embryonic blood vessels in intact avian eggs at early developmental stages", "author": [ { "family_name": "Dong", "given_name": "Zhenyu", "orcid": "0009-0003-4507-8493", "clpid": "Dong-Zhenyu" }, { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X", "clpid": "Mahler-Simon" }, { "family_name": "Readhead", "given_name": "Carol", "clpid": "Readhead-Carol" }, { "family_name": "Chen", "given_name": "Xi", "clpid": "Chen-Xi" }, { "family_name": "Dickson", "given_name": "Maya", "clpid": "Dickson-Maya" }, { "family_name": "Bronner", "given_name": "Marianne", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Imaging blood vessels in early-stage avian embryos has a wide range of practical applications for developmental biology studies, drug and vaccine testing, and early sex determination. Optical imaging, such as brightfield transmission imaging, offers a compelling solution due to its safe non-ionizing radiation, and operational benefits. However, it comes with challenges, such as eggshell opacity and light scattering. To address these, we have revisited an approach based on laser speckle contrast imaging (LSCI) and demonstrated a high-quality, comprehensive, and non-invasive visualization of blood vessels in few-days-old chicken eggs, with blood vessels as small as 100\u2005µm in diameter (with LSCI profile full-width-at-half-maximum of 275\u2005µm). We present its non-invasive use for monitoring blood flow, measuring the embryo’s heartbeat, and determining the embryo’s developmental stages using machine learning with 85% accuracy from stage HH15 to HH22. This method can potentially be used for non-invasive longitudinal studies of cardiovascular development and angiogenesis, as well as egg screening for the poultry industry.
", "doi": "10.1364/boe.530366", "issn": "2156-7085", "publisher": "Optica Publishing Group", "publication": "Biomedical Optics Express", "publication_date": "2024-08", "series_number": "8", "volume": "15", "issue": "8", "pages": "4605-4624" }, { "id": "authors:mjjn5-v2812", "collection": "authors", "collection_id": "mjjn5-v2812", "cite_using_url": "https://authors.library.caltech.edu/records/mjjn5-v2812", "type": "article", "title": "Can deep neural networks work with amplitude and phase input of defocused images?", "author": [ { "family_name": "Yin", "given_name": "Siyuan", "orcid": "0009-0009-4793-1463", "clpid": "Yin-Siyuan" }, { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Liang", "given_name": "Mingshu", "orcid": "0000-0001-7748-7652", "clpid": "Liang-Mingshu" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Deep neural network (DNN) models, particularly convolutional neural networks (CNNs), have demonstrated remarkable performance in biomedical image classification due to their ability to automatically learn features from large datasets. One common challenge in the preparation of large, microscopic datasets for DNN tasks is sample defocusing, potentially impairing the model performance. To handle defocusing, computational imaging, or specifically quantitative phase imaging (QPI), performs digital refocusing by using both the phase and the amplitude of the complex optical field. This leads us to investigate whether feeding the complex field into DNN would potentially address the defocusing problem as in-focus information is implicitly encoded in the complex field. In this paper, we assess the feasibility of employing neural networks to directly process full amplitude and phase data from a defocus plane without digital refocusing. Our specific focus lies in understanding the tolerance for defocus in image classification neural networks when amplitude and phase are taken as inputs. To accomplish this, we used Fourier ptychography microscopy (FPM) to acquire in-focus phase and amplitude images of two distinct object types – normal red blood cells and echinocytes. We then digitally propagate the complex field to generate progressively defocused images of the samples to serve as training and testing datasets for image classification neural networks. While the digitally defocused images contain sufficient information to recover the original in-focus images, we observed that current standard implementations of deep learning models are unable to effectively utilize the defocused field to distinguish between the two cell types. We conclude that the physical-model-based digital refocusing capability of QPI remains indispensable for overcoming defocusing issues in current standard DNN models.
", "doi": "10.1364/oe.527986", "issn": "1094-4087", "publisher": "Optica Publishing Group", "publication": "Optics Express", "publication_date": "2024-07-01", "series_number": "14", "volume": "32", "issue": "14", "pages": "25036-25045" }, { "id": "authors:wb048-gs927", "collection": "authors", "collection_id": "wb048-gs927", "cite_using_url": "https://authors.library.caltech.edu/records/wb048-gs927", "type": "article", "title": "Long-term imaging of three-dimensional hyphal development using the ePetri dish", "author": [ { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Dahlquist", "given_name": "Nic", "clpid": "Dahlquist-Nic" }, { "family_name": "Leete", "given_name": "Zachary", "clpid": "Leete-Zachary" }, { "family_name": "Xu", "given_name": "Michael", "clpid": "Xu-Michael" }, { "family_name": "Schneider", "given_name": "Dean", "clpid": "Schneider-Dean" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Imaging three-dimensional microbial development and behavior over extended periods is crucial for advancing microbiological studies. Here, we introduce an upgraded ePetri dish system specifically designed for extended microbial culturing and 3D imaging, addressing the limitations of existing methods. Our approach includes a sealed growth chamber to enable long-term culturing, and a multi-step reconstruction algorithm that integrates 3D deconvolution, image filtering, ridge, and skeleton detection for detailed visualization of the hyphal network. The system effectively monitored the development of Aspergillus brasiliensis hyphae over a seven-day period, demonstrating the growth medium’s stability within the chamber. The system’s 3D imaging capability was validated in a volume of 5.5 mm × 4 mm × 0.5 mm, revealing a radial growth pattern of fungal hyphae. Additionally, we show that the system can identify potential filter failures that are undetectable with 2D imaging. With these capabilities, the upgraded ePetri dish represents a significant advancement in long-term 3D microbial imaging, promising new insights into microbial development and behavior across various microbiological research areas.
", "doi": "10.1364/boe.530483", "issn": "2156-7085", "publisher": "Optica Publishing Group", "publication": "Biomedical Optics Express", "publication_date": "2024-07-01", "series_number": "7", "volume": "15", "issue": "7", "pages": "4292-4299" }, { "id": "authors:8qkyg-4p516", "collection": "authors", "collection_id": "8qkyg-4p516", "cite_using_url": "https://authors.library.caltech.edu/records/8qkyg-4p516", "type": "article", "title": "High-resolution, large field-of-view label-free imaging via aberration-corrected, closed-form complex field reconstruction", "author": [ { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Computational imaging methods empower modern microscopes to produce high-resolution, large field-of-view, aberration-free images. Fourier ptychographic microscopy can increase the space-bandwidth product of conventional microscopy, but its iterative reconstruction methods are prone to parameter selection and tend to fail under excessive aberrations. Spatial Kramers–Kronig methods can analytically reconstruct complex fields, but is limited by aberration or providing extended resolution enhancement. Here, we present APIC, a closed-form method that weds the strengths of both methods while using only NA-matching and darkfield measurements. We establish an analytical phase retrieval framework which demonstrates the feasibility of analytically reconstructing the complex field associated with darkfield measurements. APIC can retrieve complex aberrations of an imaging system with no additional hardware and avoids iterative algorithms, requiring no human-designed convergence metrics while always obtaining a closed-form complex field solution. We experimentally demonstrate that APIC gives correct reconstruction results where Fourier ptychographic microscopy fails when constrained to the same number of measurements. APIC achieves 2.8 times faster computation using image tile size of 256 (length-wise), is robust against aberrations compared to Fourier ptychographic microscopy, and capable of addressing aberrations whose maximal phase difference exceeds 3.8π when using a NA 0.25 objective in experiment.
\nBrain metastases can occur in nearly half of patients with early and locally advanced (stage I–III) non-small cell lung cancer (NSCLC). There are no reliable histopathologic or molecular means to identify those who are likely to develop brain metastases. We sought to determine if deep learning (DL) could be applied to routine H&E-stained primary tumor tissue sections from stage I–III NSCLC patients to predict the development of brain metastasis. Diagnostic slides from 158 patients with stage I–III NSCLC followed for at least 5 years for the development of brain metastases (Met+, 65 patients) versus no progression (Met−, 93 patients) were subjected to whole-slide imaging. Three separate iterations were performed by first selecting 118 cases (45 Met+, 73 Met−) to train and validate the DL algorithm, while 40 separate cases (20 Met+, 20 Met−) were used as the test set. The DL algorithm results were compared to a blinded review by four expert pathologists. The DL-based algorithm was able to distinguish the eventual development of brain metastases with an accuracy of 87% (p < 0.0001) compared with an average of 57.3% by the four pathologists and appears to be particularly useful in predicting brain metastases in stage I patients. The DL algorithm appears to focus on a complex set of histologic features. DL-based algorithms using routine H&E-stained slides may identify patients who are likely to develop brain metastases from those who will remain disease free over extended (>5 year) follow-up and may thus be spared systemic therapy.
\nIn the realm of cerebrovascular monitoring, primary metrics typically include blood pressure, which influences cerebral blood flow (CBF) and is contingent upon vessel radius. Measuring CBF non-invasively poses a persistent challenge, primarily attributed to the difficulty of accessing and obtaining signal from the brain. This study aims to introduce a compact speckle visibility spectroscopy (SVS) device designed for non-invasive CBF measurements, offering cost-effectiveness and scalability while tracking CBF with remarkable sensitivity and temporal resolution. The wearable hardware has a modular design approach consisting solely of a laser diode as the source and a meticulously selected board camera as the detector. They both can be easily placed on the head of a subject to measure CBF with no additional optical elements. The SVS device can achieve a sampling rate of 80 Hz with minimal susceptibility to external disturbances. The device also achieves better SNR compared with traditional fiber-based SVS devices, capturing about 70 times more signal and showing superior stability and reproducibility. It is designed to be paired and distributed in multiple configurations around the head, and measure signals that exceed the quality of prior optical CBF measurement techniques. Given its cost-effectiveness, scalability, and simplicity, this laser-centric tool offers significant potential in advancing non-invasive cerebral monitoring technologies.
", "doi": "10.48550/arxiv.2401.16592", "pmcid": "PMC10862935", "publication_date": "2024-01-29" }, { "id": "authors:15d9y-tkv02", "collection": "authors", "collection_id": "15d9y-tkv02", "cite_using_url": "https://authors.library.caltech.edu/records/15d9y-tkv02", "type": "article", "title": "Fourier ptychographic microscopy image stack reconstruction using implicit neural representations", "author": [ { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Feng", "given_name": "Brandon Y.", "orcid": "0000-0001-7003-9128", "clpid": "Feng-Brandon-Y" }, { "family_name": "Guo", "given_name": "Haiyun", "orcid": "0000-0001-6774-0298", "clpid": "Guo-Haiyyun" }, { "family_name": "Lin", "given_name": "Siyu (Steven)", "orcid": "0009-0004-4985-7475", "clpid": "Lin-Siyu-Steven" }, { "family_name": "Liang", "given_name": "Mingshu", "orcid": "0000-0001-7748-7652", "clpid": "Liang-Mingshu" }, { "family_name": "Metzler", "given_name": "Christopher A.", "orcid": "0000-0001-6827-7207", "clpid": "Metzler-Christopher-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Image stacks provide invaluable 3D information in various biological and pathological imaging applications. Fourier ptychographic microscopy (FPM) enables reconstructing high-resolution, wide field-of-view image stacks without z-stack scanning, thus significantly accelerating image acquisition. However, existing FPM methods take tens of minutes to reconstruct and gigabytes of memory to store a high-resolution volumetric scene, impeding fast gigapixel-scale remote digital pathology. While deep learning approaches have been explored to address this challenge, existing methods poorly generalize to novel datasets and can produce unreliable hallucinations. This work presents FPM-INR, a compact and efficient framework that integrates physics-based optical models with implicit neural representations (INRs) to represent and reconstruct FPM image stacks. FPM-INR is agnostic to system design or sample types and does not require external training data. In our experiments, FPM-INR substantially outperforms traditional FPM algorithms with up to a 25-fold increase in speed and an 80-fold reduction in memory usage for continuous image stack representations.", "doi": "10.1364/optica.505283", "issn": "2334-2536", "publisher": "Optica Publishing Group", "publication": "Optica", "publication_date": "2023-12-20", "series_number": "12", "volume": "10", "issue": "12", "pages": "1679-1687" }, { "id": "authors:vajf7-ps847", "collection": "authors", "collection_id": "vajf7-ps847", "cite_using_url": "https://authors.library.caltech.edu/records/vajf7-ps847", "type": "article", "title": "The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring", "author": [ { "family_name": "Batool", "given_name": "Syeda Maheen", "orcid": "0000-0002-3264-1182", "clpid": "Batool-Syeda-Maheen" }, { "family_name": "Yekula", "given_name": "Anudeep", "orcid": "0000-0002-0713-0292" }, { "family_name": "Khanna", "given_name": "Prerna" }, { "family_name": "Hsia", "given_name": "Tiffaney", "orcid": "0000-0003-4526-2605" }, { "family_name": "Gamblin", "given_name": "Austin S.", "orcid": "0000-0002-3615-3792" }, { "family_name": "Ekanayake", "given_name": "Emil" }, { "family_name": "Escobedo", "given_name": "Ana K.", "orcid": "0000-0001-7816-6068" }, { "family_name": "You", "given_name": "Dong Gil" }, { "family_name": "Castro", "given_name": "Cesar M.", "orcid": "0000-0002-1159-5658" }, { "family_name": "Im", "given_name": "Hyungsoon", "orcid": "0000-0002-0626-1346" }, { "family_name": "Kilic", "given_name": "Tugba", "orcid": "0000-0001-8600-0367" }, { "family_name": "Garlin", "given_name": "Michelle Andrea" }, { "family_name": "Skog", "given_name": "Johan", "orcid": "0000-0002-0926-1691" }, { "family_name": "Dinulescu", "given_name": "Daniela M.", "orcid": "0009-0003-5711-8210" }, { "family_name": "Dudley", "given_name": "Jonathan", "orcid": "0000-0002-5809-5538" }, { "family_name": "Agrawal", "given_name": "Nishant" }, { "family_name": "Cheng", "given_name": "Jordan", "orcid": "0000-0001-5352-4017" }, { "family_name": "Abtin", "given_name": "Fereidoun", "orcid": "0000-0003-2927-0883" }, { "family_name": "Aberle", "given_name": "Denise R." }, { "family_name": "Chia", "given_name": "David", "orcid": "0000-0002-0723-3670" }, { "family_name": "Elashoff", "given_name": "David", "orcid": "0000-0002-5865-8580" }, { "family_name": "Grognan", "given_name": "Tristan" }, { "family_name": "Krysan", "given_name": "Kostyantyn", "orcid": "0000-0003-0250-1346" }, { "family_name": "Oh", "given_name": "Scott S.", "orcid": "0000-0003-3993-4401" }, { "family_name": "Strom", "given_name": "Charles", "orcid": "0000-0001-9709-0724" }, { "family_name": "Tu", "given_name": "Michael", "orcid": "0000-0002-7227-4030" }, { "family_name": "Wei", "given_name": "Fang", "orcid": "0000-0002-9019-3322" }, { "family_name": "Xian", "given_name": "Rena R.", "orcid": "0000-0001-5532-6524" }, { "family_name": "Skates", "given_name": "Steven J." }, { "family_name": "Zhang", "given_name": "David Y." }, { "family_name": "Trinh", "given_name": "Thi" }, { "family_name": "Watson", "given_name": "Mark", "orcid": "0000-0002-3935-9980" }, { "family_name": "Aft", "given_name": "Rebecca", "orcid": "0000-0001-8569-7131" }, { "family_name": "Rawal", "given_name": "Siddarth" }, { "family_name": "Agarwal", "given_name": "Ashutosh" }, { "family_name": "Kesmodel", "given_name": "Susan B.", "orcid": "0000-0003-0010-6078" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Shen", "given_name": "Cheng", "clpid": "Shen-Cheng" }, { "family_name": "Hochberg", "given_name": "Fred H.", "orcid": "0000-0002-2765-8844" }, { "family_name": "Wong", "given_name": "David T.W." }, { "family_name": "Patel", "given_name": "Abhijit A." }, { "family_name": "Papadopoulos", "given_name": "Nickolas", "orcid": "0000-0001-7135-7451" }, { "family_name": "Bettegowda", "given_name": "Chetan", "orcid": "0000-0001-9991-7123" }, { "family_name": "Cote", "given_name": "Richard J." }, { "family_name": "Srivastava", "given_name": "Sudhir" }, { "family_name": "Lee", "given_name": "Hakho", "orcid": "0000-0002-0087-0909" }, { "family_name": "Carter", "given_name": "Bob S.", "orcid": "0000-0002-3586-1324" }, { "family_name": "Balaj", "given_name": "Leonora", "orcid": "0000-0003-0931-9715" } ], "abstract": "The emerging field of liquid biopsy stands at the forefront of novel diagnostic strategies for cancer and other diseases. Liquid biopsy allows minimally invasive molecular characterization of cancers for diagnosis, patient stratification to therapy, and longitudinal monitoring. Liquid biopsy strategies include detection and monitoring of circulating tumor cells, cell-free DNA, and extracellular vesicles. In this review, we address the current understanding and the role of existing liquid-biopsy-based modalities in cancer diagnostics and monitoring. We specifically focus on the technical and clinical challenges associated with liquid biopsy and biomarker development being addressed by the Liquid Biopsy Consortium, established through the National Cancer Institute. The Liquid Biopsy Consortium has developed new methods/assays and validated existing methods/technologies to capture and characterize tumor-derived circulating cargo, as well as addressed existing challenges and provided recommendations for advancing biomarker assays.
", "doi": "10.1016/j.xcrm.2023.101198", "pmcid": "PMC10591039", "issn": "2666-3791", "publisher": "Cell Press", "publication": "Cell Reports Medicine", "publication_date": "2023-10-17", "series_number": "10", "volume": "4", "issue": "10", "pages": "101198" }, { "id": "authors:ztpbv-b7e62", "collection": "authors", "collection_id": "ztpbv-b7e62", "cite_using_url": "https://authors.library.caltech.edu/records/ztpbv-b7e62", "type": "article", "title": "Interferometric speckle visibility spectroscopy (iSVS) for measuring decorrelation time and dynamics of moving samples with enhanced signal-to-noise ratio and relaxed reference requirements", "author": [ { "family_name": "Huang", "given_name": "Yu Xi", "orcid": "0009-0000-0165-2084", "clpid": "Huang-Yu-Xi" }, { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X", "clpid": "Mahler-Simon" }, { "family_name": "Mertz", "given_name": "Jerome", "orcid": "0000-0002-6343-9155", "clpid": "Mertz-Jerome" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Diffusing wave spectroscopy (DWS) is a group of techniques used to measure the dynamics of a scattering medium in a non-invasive manner. DWS methods rely on detecting the speckle light field from the moving scattering medium and measuring the speckle decorrelation time to quantify the scattering medium's dynamics. For DWS, the signal-to-noise (SNR) is determined by the ratio between measured decorrelation time to the standard error of the measurement. This SNR is often low in certain applications because of high noise variances and low signal intensity, especially in biological applications with restricted exposure and emission levels. To address this photon-limited signal-to-noise ratio problem, we investigated, theoretically and experimentally, the SNR of an interferometric speckle visibility spectroscopy (iSVS) compared to more traditional DWS methods. We found that iSVS can provide excellent SNR performance through its ability to overcome camera noise. We also proved an iSVS system has more relaxed constraints on the reference beam properties. For an iSVS system to function properly, we only require the reference beam to exhibit local temporal stability, while incident angle, reference phase and intensity uniformity do not need to be constrained. This flexibility can potentially enable more unconventional iSVS implementation schemes.", "doi": "10.1364/oe.499473", "pmcid": "PMC10545208", "issn": "1094-4087", "publisher": "Optica Publishing Group", "publication": "Optics Express", "publication_date": "2023-09-11", "series_number": "19", "volume": "31", "issue": "19", "pages": "31253-31266" }, { "id": "authors:awkca-jdb08", "collection": "authors", "collection_id": "awkca-jdb08", "cite_using_url": "https://authors.library.caltech.edu/records/awkca-jdb08", "type": "article", "title": "Assessing depth sensitivity in laser interferometry speckle visibility spectroscopy (iSVS) through source-to-detector distance variation and cerebral blood flow monitoring in humans and rabbits", "author": [ { "family_name": "Mahler", "given_name": "Simon", "orcid": "0000-0002-9761-445X" }, { "family_name": "Huang", "given_name": "Yu Xi", "orcid": "0009-0000-0165-2084" }, { "family_name": "Liang", "given_name": "Mingshu", "orcid": "0000-0001-7748-7652" }, { "family_name": "Avalos", "given_name": "Alan" }, { "family_name": "Tyszka", "given_name": "Julian M.", "orcid": "0000-0001-9342-9014", "clpid": "Tyszka-J-M" }, { "family_name": "Mertz", "given_name": "Jerome", "orcid": "0000-0002-6343-9155", "clpid": "Mertz-Jerome" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Recently, speckle visibility spectroscopy (SVS) was non-invasively applied on the head to monitor cerebral blood flow. The technique, using a multi-pixel detecting device (e.g., camera), allows the detection of a larger number of speckles, increasing the proportion of light that is detected. Due to this increase, it is possible to collect light that has propagated deeper through the brain. As a direct consequence, cerebral blood flow can be monitored. However, isolating the cerebral blood flow from the other layers, such as the scalp or skull components, remains challenging. In this paper, we report our investigations on the depth-sensitivity of laser interferometry speckle visibility spectroscopy (iSVS). Specifically, we varied the depth of penetration of the laser light into the head by tuning the source-to-detector distance, and identified the transition point at which cerebral blood flow in humans and rabbits starts to be detected.", "doi": "10.1364/boe.498815", "pmcid": "PMC10545208", "issn": "2156-7085", "publisher": "Optica Publishing Group", "publication": "Biomedical Optics Express", "publication_date": "2023-09", "series_number": "9", "volume": "14", "issue": "9", "pages": "4964-4978" }, { "id": "authors:svwq9-65433", "collection": "authors", "collection_id": "svwq9-65433", "cite_using_url": "https://authors.library.caltech.edu/records/svwq9-65433", "type": "article", "title": "Robust Kramers\u2013Kronig holographic imaging with Hilbert\u2013Huang transform", "author": [ { "family_name": "Chang", "given_name": "Xuyang", "orcid": "0000-0001-5696-0033" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Liu", "given_name": "Sitian" }, { "family_name": "Zheng", "given_name": "Dezhi", "orcid": "0000-0003-3998-5989" }, { "family_name": "Wang", "given_name": "Shuai" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Huang", "given_name": "Norden E." }, { "family_name": "Bian", "given_name": "Liheng", "orcid": "0000-0002-8016-0375" } ], "abstract": "Holography based on Kramers\u2013Kronig relations (KKR) is a promising technique due to its high-space-bandwidth product. However, the absence of an iterative process limits its noise robustness, primarily stemming from the lack of a regularization constraint. This Letter reports a generalized framework aimed at enhancing the noise robustness of KKR holography. Our proposal involves employing the Hilbert\u2013Huang transform to connect the real and imaginary parts of an analytic function. The real part is initially processed by bidimensional empirical mode decomposition into a series of intrinsic mode functions (IMFs) and a residual term. They are then selected to remove the noise and bias terms. Finally, the imaginary part can be obtained using the Hilbert transform. In this way, we efficiently suppress the noise in the synthetic complex function, facilitating high-fidelity wavefront reconstruction using \u223c20% of the exposure time required by existing methods. Our work is expected to expand the applications of KKR holography, particularly in low phototoxicity biological imaging and other related scenarios.", "doi": "10.1364/ol.495895", "issn": "0146-9592", "publisher": "Optica Publishing Group", "publication": "Optics Letters", "publication_date": "2023-08-01", "series_number": "15", "volume": "48", "issue": "15", "pages": "4161-4164" }, { "id": "authors:68h8f-74j58", "collection": "authors", "collection_id": "68h8f-74j58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230627-116746000.5", "type": "article", "title": "Automatic detection of circulating tumor cells and cancer associated fibroblasts using deep learning", "author": [ { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Rawal", "given_name": "Siddarth", "clpid": "Rawal-Siddarth" }, { "family_name": "Brown", "given_name": "Rebecca", "clpid": "Brown-Rebecca" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhao-Haowen" }, { "family_name": "Agarwal", "given_name": "Ashutosh", "clpid": "Agarwal-Ashutosh" }, { "family_name": "Watson", "given_name": "Mark A.", "orcid": "0000-0002-3935-9980", "clpid": "Watson-Mark-A" }, { "family_name": "Cote", "given_name": "Richard J.", "clpid": "Cote-Richard-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Circulating tumor cells (CTCs) and cancer-associated fibroblasts (CAFs) from whole blood are emerging as important biomarkers that potentially aid in cancer diagnosis and prognosis. The microfilter technology provides an efficient capture platform for them but is confounded by two challenges. First, uneven microfilter surfaces makes it hard for commercial scanners to obtain images with all cells in-focus. Second, current analysis is labor-intensive with long turnaround time and user-to-user variability. Here we addressed the first challenge through developing a customized imaging system and data pre-processing algorithms. Utilizing cultured cancer and CAF cells captured by microfilters, we showed that images from our custom system are 99.3% in-focus compared to 89.9% from a top-of-the-line commercial scanner. Then we developed a deep-learning-based method to automatically identify tumor cells serving to mimic CTC (mCTC) and CAFs. Our deep learning method achieved precision and recall of 94% (\u00b1\u20090.2%) and 96% (\u00b1\u20090.2%) for mCTC detection, and 93% (\u00b1\u20091.7%) and 84% (\u00b1\u20093.1%) for CAF detection, significantly better than a conventional computer vision method, whose numbers are 92% (\u00b1\u20090.2%) and 78% (\u00b1\u20090.3%) for mCTC and 58% (\u00b1\u20093.9%) and 56% (\u00b1\u20093.5%) for CAF. Our custom imaging system combined with deep learning cell identification method represents an important advance on CTC and CAF analysis.", "doi": "10.1038/s41598-023-32955-0", "pmcid": "PMC10082202", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2023-04-07", "volume": "13", "pages": "5708" }, { "id": "authors:qyzb2-abw73", "collection": "authors", "collection_id": "qyzb2-abw73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220715-744287000", "type": "article", "title": "Roadmap on wavefront shaping and deep imaging in complex media", "author": [ { "family_name": "Gigan", "given_name": "Sylvain", "orcid": "0000-0002-9914-6231", "clpid": "Gigan-Sylvain" }, { "family_name": "Katz", "given_name": "Ori", "clpid": "Katz-Ori" }, { "family_name": "de Aguiar", "given_name": "Hilton B.", "orcid": "0000-0002-2426-0371", "clpid": "de-Aguiar-Hilton-B" }, { "family_name": "Andresen", "given_name": "Esben Ravn", "clpid": "Andresen-Esben-Ravn" }, { "family_name": "Aubry", "given_name": "Alexandre", "clpid": "Aubry-Alexandre" }, { "family_name": "Bertolotti", "given_name": "Jacopo", "clpid": "Bertolotti-Jacopo" }, { "family_name": "Bossy", "given_name": "Emmanuel", "orcid": "0000-0002-8101-8290", "clpid": "Bossy-Emmanuel" }, { "family_name": "Bouchet", "given_name": "Dorian", "orcid": "0000-0002-9122-5170", "clpid": "Bouchet-Dorian" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Brasselet", "given_name": "Sophie", "clpid": "Brasselet-Sophie" }, { "family_name": "Bromberg", "given_name": "Yaron", "clpid": "Bromberg-Yaron" }, { "family_name": "Cao", "given_name": "Hui", "orcid": "0000-0002-5339-6892", "clpid": "Cao-Hui" }, { "family_name": "Chaigne", "given_name": "Thomas", "clpid": "Chaigne-Thomas" }, { "family_name": "Cheng", "given_name": "Zhongtao", "orcid": "0000-0002-9862-2873", "clpid": "Cheng-Zhongtao" }, { "family_name": "Choi", "given_name": "Wonshik", "clpid": "Choi-Wonshik" }, { "family_name": "Ci\u017em\u00e1r", "given_name": "Tom\u00e1\u0161", "clpid": "Ci\u017em\u00e1r-Tom\u00e1\u0161" }, { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Curtis", "given_name": "Vincent R.", "clpid": "Curtis-Vincent-R" }, { "family_name": "Defienne", "given_name": "Hugo", "orcid": "0000-0002-5543-2885", "clpid": "Defienne-Hugo" }, { "family_name": "Hofer", "given_name": "Matthias", "clpid": "Hofer-Matthias" }, { "family_name": "Horisaki", "given_name": "Ryoichi", "clpid": "Horisaki-Ryoichi" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Ji", "given_name": "Na", "clpid": "Ji-Na" }, { "family_name": "LaViolette", "given_name": "Aaron K.", "clpid": "LaViolette-Aaron-K" }, { "family_name": "Mertz", "given_name": "Jerome", "clpid": "Mertz-Jerome" }, { "family_name": "Moser", "given_name": "Christophe", "clpid": "Moser-Christophe" }, { "family_name": "Mosk", "given_name": "Allard P.", "orcid": "0000-0002-1140-6626", "clpid": "Mosk-Allard-P" }, { "family_name": "P\u00e9gard", "given_name": "Nicolas C.", "clpid": "P\u00e9gard-Nicolas-C" }, { "family_name": "Piestun", "given_name": "Rafael", "clpid": "Piestun-Rafael" }, { "family_name": "Popoff", "given_name": "S\u00e9bastien", "clpid": "Popoff-S\u00e9bastien" }, { "family_name": "Phillips", "given_name": "David B.", "clpid": "Phillips-David-B" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-Demetri" }, { "family_name": "Rahmani", "given_name": "Babak", "clpid": "Rahmani-Babak" }, { "family_name": "Rigneault", "given_name": "Herv\u00e9", "clpid": "Rigneault-Herv\u00e9" }, { "family_name": "Rotter", "given_name": "Stefan", "orcid": "0000-0002-4123-1417", "clpid": "Rotter-Stefan" }, { "family_name": "Tian", "given_name": "Lei", "orcid": "0000-0002-1316-4456", "clpid": "Tian-Lei" }, { "family_name": "Vellekoop", "given_name": "Ivo M.", "clpid": "Vellekoop-Ivo-M" }, { "family_name": "Waller", "given_name": "Laura", "clpid": "Waller-Laura" }, { "family_name": "Wang", "given_name": "Lihong", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong-V" }, { "family_name": "Weber", "given_name": "Timothy", "clpid": "Weber-Timothy" }, { "family_name": "Xiao", "given_name": "Sheng", "clpid": "Xiao-Sheng" }, { "family_name": "Xu", "given_name": "Chris", "orcid": "0000-0002-3493-6427", "clpid": "Xu-Chris" }, { "family_name": "Yamilov", "given_name": "Alexey", "orcid": "0000-0002-9339-6475", "clpid": "Yamilov-Alexey" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Yilmaz", "given_name": "Hasan", "orcid": "0000-0003-1889-3516", "clpid": "Yilmaz-Hasan" } ], "abstract": "The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working in this field, which has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead.", "doi": "10.1088/2515-7647/ac76f9", "issn": "2515-7647", "publisher": "IOP Publishing", "publication": "Journal of Physics: Photonics", "publication_date": "2022-10", "series_number": "4", "volume": "4", "issue": "4", "pages": "Art. No. 042501" }, { "id": "authors:yed4f-5ap40", "collection": "authors", "collection_id": "yed4f-5ap40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220909-233324000", "type": "article", "title": "Optical imaging and spectroscopy for the study of the human brain: status report", "author": [ { "family_name": "Ayaz", "given_name": "Hasan", "orcid": "0000-0001-5514-2741", "clpid": "Ayaz-Hasan" }, { "family_name": "Baker", "given_name": "Wesley B." }, { "family_name": "Blaney", "given_name": "Giles", "orcid": "0000-0003-3419-4547" }, { "family_name": "Boas", "given_name": "David A.", "orcid": "0000-0002-6709-7711" }, { "family_name": "Bortfeld", "given_name": "Heather" }, { "family_name": "Brady", "given_name": "Kenneth" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886" }, { "family_name": "Brigadoi", "given_name": "Sabrina", "orcid": "0000-0003-3032-7381" }, { "family_name": "Buckley", "given_name": "Erin M." }, { "family_name": "Carp", "given_name": "Stefan A." }, { "family_name": "Cooper", "given_name": "Robert J.", "orcid": "0000-0001-6696-8020" }, { "family_name": "Cowdrick", "given_name": "Kyle R.", "orcid": "0000-0003-2236-6137" }, { "family_name": "Culver", "given_name": "Joseph P." }, { "family_name": "Dan", "given_name": "Ippeita" }, { "family_name": "Dehghani", "given_name": "Hamid" }, { "family_name": "Devor", "given_name": "Anna" }, { "family_name": "Durduran", "given_name": "Turgut" }, { "family_name": "Eggebrecht", "given_name": "Adam T.", "orcid": "0000-0002-6320-2676" }, { "family_name": "Emberson", "given_name": "Lauren L." }, { "family_name": "Fang", "given_name": "Qianqian", "orcid": "0000-0003-0805-935X" }, { "family_name": "Fantini", "given_name": "Sergio" }, { "family_name": "Franceschini", "given_name": "Maria Angela", "orcid": "0000-0001-6758-423X" }, { "family_name": "Fischer", "given_name": "Jonas B." }, { "family_name": "Gervain", "given_name": "Judit", "orcid": "0000-0002-2125-6369" }, { "family_name": "Hirsch", "given_name": "Joy", "orcid": "0000-0002-1418-6489" }, { "family_name": "Hong", "given_name": "Keum-Shik" }, { "family_name": "Horstmeyer", "given_name": "Roarke" }, { "family_name": "Kainerstorfer", "given_name": "Jana M." }, { "family_name": "Ko", "given_name": "Tiffany S.", "orcid": "0000-0002-5113-0310" }, { "family_name": "Licht", "given_name": "Daniel J." }, { "family_name": "Liebert", "given_name": "Adam" }, { "family_name": "Luke", "given_name": "Robert", "orcid": "0000-0002-4930-8351" }, { "family_name": "Lynch", "given_name": "Jennifer M." }, { "family_name": "Mesquida", "given_name": "Jaume" }, { "family_name": "Mesquita", "given_name": "Rickson C." }, { "family_name": "Naseer", "given_name": "Noman" }, { "family_name": "Novi", "given_name": "Sergio L." }, { "family_name": "Orihuela-Espina", "given_name": "Felipe" }, { "family_name": "O'Sullivan", "given_name": "Thomas D.", "orcid": "0000-0001-8662-5121" }, { "family_name": "Peterka", "given_name": "Darcy S." }, { "family_name": "Pifferi", "given_name": "Antonio" }, { "family_name": "Pollonini", "given_name": "Luca" }, { "family_name": "Sassaroli", "given_name": "Angelo" }, { "family_name": "Sato", "given_name": "Jo\u00e3o Ricardo" }, { "family_name": "Scholkmann", "given_name": "Felix", "orcid": "0000-0002-1748-4852" }, { "family_name": "Spinelli", "given_name": "Lorenzo" }, { "family_name": "Srinivasan", "given_name": "Vivek J." }, { "family_name": "St. Lawrence", "given_name": "Keith" }, { "family_name": "Tachtsidis", "given_name": "Ilias", "orcid": "0000-0002-8125-0313" }, { "family_name": "Tong", "given_name": "Yunjie", "orcid": "0000-0001-6052-8913" }, { "family_name": "Torricelli", "given_name": "Alessandro", "orcid": "0000-0002-6878-8936" }, { "family_name": "Urner", "given_name": "Tara" }, { "family_name": "Wabnitz", "given_name": "Heidrun", "orcid": "0000-0002-3846-8659" }, { "family_name": "Wolf", "given_name": "Martin" }, { "family_name": "Wolf", "given_name": "Ursula" }, { "family_name": "Xu", "given_name": "Shiqi" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Yodh", "given_name": "Arjun G.", "orcid": "0000-0003-4744-2706" }, { "family_name": "Y\u00fccel", "given_name": "Meryem A.", "orcid": "0000-0002-4291-2847" }, { "family_name": "Zhou", "given_name": "Wenjun", "orcid": "0000-0002-6000-253X" } ], "abstract": "This report is the second part of a comprehensive two-part series aimed at reviewing an extensive and diverse toolkit of novel methods to explore brain health and function. While the first report focused on neurophotonic tools mostly applicable to animal studies, here, we highlight optical spectroscopy and imaging methods relevant to noninvasive human brain studies. We outline current state-of-the-art technologies and software advances, explore the most recent impact of these technologies on neuroscience and clinical applications, identify the areas where innovation is needed, and provide an outlook for the future directions.", "doi": "10.1117/1.nph.9.s2.s24001", "pmcid": "PMC9424749", "issn": "2329-423X", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Neurophotonics", "publication_date": "2022-08-30", "series_number": "S2", "volume": "9", "issue": "S2", "pages": "Art. No. S24001" }, { "id": "authors:agv72-2e133", "collection": "authors", "collection_id": "agv72-2e133", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220705-346652000", "type": "article", "title": "All-in-focus fine needle aspiration biopsy imaging based on Fourier ptychographic microscopy", "author": [ { "family_name": "Liang", "given_name": "Mingshu", "clpid": "Liang-Mingshu" }, { "family_name": "Bernadt", "given_name": "Cory", "orcid": "0000-0003-1540-9880", "clpid": "Bernadt-Cory" }, { "family_name": "Wong", "given_name": "Soon Boon Justin", "orcid": "0000-0002-0681-7826", "clpid": "Wong-Soon-Boon-Justin" }, { "family_name": "Choi", "given_name": "Changsoon", "orcid": "0009-0005-4037-8643", "clpid": "Choi-Changsoon" }, { "family_name": "Cote", "given_name": "Richard", "clpid": "Cote-Richard-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Context: Cytology is the study of whole cells in diagnostic pathology. Unlike standard histologic thinly sliced specimens, cytologic preparations consist of preparations of whole cells where cells commonly cluster and aggregate. As such, cytology preparations are generally much thicker than histologic slides, resulting in large patches of defocus when examined under the microscope. A diagnostic aggregate of cells often cannot be viewed in focus together, requiring pathologists to continually manipulate the focal plane, complicating the task of accurately assessing the entire cellular aggregate and thus in making a diagnosis. Further, it is extremely difficult to acquire useful uniformly in-focus digital images of cytology preparations for applications such as remote diagnostic evaluations and artificial intelligence models. The predominant current method to address this issue is to acquire digital images at multiple focal planes of the entire slide, which demands long scanning time, complex and expensive scanning systems, and huge storage capacity. \n\nAims: Here we report a unique imaging method that can acquire cytologic images efficiently and computationally render all-in-focus digital images that are highly compact. \n\nMethods and material: This method applies a metric-based digital refocusing to microscopy data collected with a Fourier ptychographic microscope (FPM). The digitally refocused patches of images are then synthesized into an all-in-focus image. \n\nResults: We report all-in-focus FPM results of thyroid fine needle aspiration (FNA) cytology samples, demonstrating our method's ability to overcome the height variance of 30\u202f\u03bcm caused by cell aggregation, and rendering images at high resolution (corresponds to a standard microscope with objective NA of 0.75) and that are all-in-focus. \n\nConclusions: This technology is applicable to standard microscopes, and we believe can have an impact on diagnostic accuracy as well as ease and speed of diagnosing challenging specimens. While we focus on cytology slides here, we anticipate this technology's advantages will translate well for histology applications. This technique also addresses the issue of remote rapid evaluation of cytology preparations. Finally, we believe that by resolving the focus heterogeneity issues in standard digital images, this technique is a critical advance for applying machine learning to cytology specimens.", "doi": "10.1016/j.jpi.2022.100119", "pmcid": "PMC9577034", "issn": "2153-3539", "publisher": "Elsevier", "publication": "Journal of Pathology Informatics", "publication_date": "2022-07-12", "volume": "13", "pages": "100119" }, { "id": "authors:7gjpw-pw604", "collection": "authors", "collection_id": "7gjpw-pw604", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220712-143800000", "type": "article", "title": "Analysis of postreconstruction digital refocusing in Fourier ptychographic microscopy", "author": [ { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhao-Haowen" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Liang", "given_name": "Mingshu", "clpid": "Liang-Mingshu" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Digital refocusing is a key feature of Fourier ptychographic microscopy (FPM). It is currently performed by determining and removing the defocus aberration during the iterative phase retrieval process. We examine the feasibility of digitally refocusing an FPM image by numerically propagating the recovered complex FPM image after the phase retrieval process has been completed \u2013 in effect, disentangling the defocus correction process from the iterative phase retrieval process. If feasible, this type of postreconstruction digital refocusing can significantly reduce the FPM computational load and provide a quick and efficient way for refocusing microscopy images on the fly. We report that such an approach is infeasible for large defocus distances because the raw FPM dataset associated with a defocused sample is illconditioned for the FPM's phase-retrieval process, and it will not output a complex-valued image that corresponds to any physically relevant image wavefront. When the defocus distance is small, the FPM can output an approximately correct image wavefront. However, this wavefront does not contain a global defocus phase term and, therefore, cannot be further focused using the digital refocusing application of a reverse global phase term. In totality, this means that postreconstruction digital refocusing does not serve a meaningful function for any defocus distance. To verify our analysis, we performed a series of experiments, and the results showed that the postreconstruction digital refocusing method is not a viable digital refocusing method.", "doi": "10.1117/1.oe.61.7.073102", "issn": "0091-3286", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Optical Engineering", "publication_date": "2022-07", "series_number": "7", "volume": "61", "issue": "7", "pages": "Art. No. 073102" }, { "id": "authors:n0st7-wqf76", "collection": "authors", "collection_id": "n0st7-wqf76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220722-768660000", "type": "article", "title": "Implementation of free-space Fourier Ptychography with near maximum system numerical aperture", "author": [ { "family_name": "Liang", "given_name": "Mingshu", "clpid": "Liang-Mingshu" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Over the past decade, the research field of Fourier Ptychographic Microscopy (FPM) has seen numerous innovative developments that significantly expands its utility. Here, we report a high numerical aperture (NA) FPM implementation that incorporates some of these innovations to achieve a synthetic NA of 1.9 \u2013 close to the maximum possible synthetic NA of 2 for a free space FPM system. At this high synthetic NA, we experimentally found that it is vital to homogenize the illumination field in order to achieve the best resolution. Our FPM implementation has a full pitch resolution of 266 nm for 465 nm light, and depth of field of 3.6 \u00b5m. In comparison, a standard transmission microscope (incoherent) with close to maximum possible NA of 0.95 has a full pitch resolution of 318 nm for 465 nm light, and depth of field of 0.65 \u00b5m. While it is generally assumed that a free-space coherent imaging system and a free-space incoherent imaging system operating at their respective maximum NA should give comparable resolution, we experimentally find that an FPM system significantly outperforms its incoherent standard microscopy counterpart in resolution by a factor of 20%. Coupled with FPM's substantially longer effective depth of field (5.5 times longer), our work indicates that, in the near-maximum NA operation regime, the FPM has significant resolution and depth of field advantages over incoherent standard microscopy.", "doi": "10.1364/oe.459833", "pmcid": "PMC9363023", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2022-06-06", "series_number": "12", "volume": "30", "issue": "12", "pages": "20321-20332" }, { "id": "authors:7ycaw-16k05", "collection": "authors", "collection_id": "7ycaw-16k05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220531-843943000", "type": "article", "title": "High-resolution non-line-of-sight imaging employing active focusing", "author": [ { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "de Goumoens", "given_name": "Frederic", "orcid": "0000-0001-7161-8762", "clpid": "de-Goumoens-Frederic" }, { "family_name": "Blochet", "given_name": "Baptiste", "orcid": "0000-0003-1457-4542", "clpid": "Blochet-Baptiste" }, { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian-EE" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Non-line-of-sight (NLOS) imaging is a rapidly developing research direction that has significant applications in autonomous vehicles, remote sensing and other areas. Existing NLOS methods primarily depend on time-gated measurements and sophisticated signal processing to extract information from scattered light. Here we introduce a method that directly manipulates light to counter the wall's scattering. This method, termed unseen non-line-of-sight casted optical aperture visibility-enhanced return (UNCOVER) focusing, operates by actively focusing light onto the hidden target using wavefront shaping. By raster scanning that focus, we can actively image the hidden object. The focus thus formed is near diffraction limited and can be substantially smaller than the object itself, thereby enabling us to perform NLOS imaging with unprecedented resolution. We demonstrate that a resolution of ~0.6\u2009mm at a distance of 0.55\u2009m is achievable in UNCOVER, giving us a distance-to-resolution ratio of ~970.", "doi": "10.1038/s41566-022-01009-8", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2022-06", "series_number": "6", "volume": "16", "issue": "6", "pages": "462-468" }, { "id": "authors:fdxqb-sqd56", "collection": "authors", "collection_id": "fdxqb-sqd56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220624-382136400", "type": "article", "title": "Neurophotonic Tools for Microscopic Measurements and Manipulation: Status Report", "author": [ { "family_name": "Abdelfattah", "given_name": "Ahmed", "clpid": "Abdelfattah-Ahmed" }, { "family_name": "Allu", "given_name": "Srinivasa Rao" }, { "family_name": "Campbell", "given_name": "Robert E." }, { "family_name": "Cheng", "given_name": "Xiaojun" }, { "family_name": "Ci\u017em\u00e1r", "given_name": "Tom\u00e1\u0161" }, { "family_name": "Costantini", "given_name": "Irene" }, { "family_name": "Emiliani", "given_name": "Valentina" }, { "family_name": "Fomin-Thunemann", "given_name": "Natalie" }, { "family_name": "Gilad", "given_name": "Ariel" }, { "family_name": "Fern\u00e1ndez Alfonso", "given_name": "Tom\u00e1s" }, { "family_name": "Ferri", "given_name": "Christopher G. L." }, { "family_name": "Harris", "given_name": "Andrew" }, { "family_name": "Hillman", "given_name": "Elizabeth M. C." }, { "family_name": "Holt", "given_name": "Matthew G." }, { "family_name": "Kili\u00e7", "given_name": "Kivilcim" }, { "family_name": "Miller", "given_name": "Evan W." }, { "family_name": "Mesquita", "given_name": "Rickson C." }, { "family_name": "Nadella", "given_name": "K. M. Naga Srinivas" }, { "family_name": "N\u00e4gerl", "given_name": "U. Valentin" }, { "family_name": "Perez Campos", "given_name": "Citlali" }, { "family_name": "Puppo", "given_name": "Francesca" }, { "family_name": "Shoham", "given_name": "Shy" }, { "family_name": "Silver", "given_name": "R. Angus" }, { "family_name": "Srinivasan", "given_name": "Vivek J." }, { "family_name": "Thunemann", "given_name": "Martin" }, { "family_name": "Tian", "given_name": "Lei" }, { "family_name": "Vinogradov", "given_name": "Sergei A." }, { "family_name": "Vitale", "given_name": "Flavia" }, { "family_name": "Uhlirova", "given_name": "Hana" }, { "family_name": "Xu", "given_name": "Chris" }, { "family_name": "Yang", "given_name": "Mu-Han" }, { "family_name": "Zhao", "given_name": "Yongxin" }, { "family_name": "Ahuja", "given_name": "Sapna" }, { "family_name": "Akkin", "given_name": "Taner" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886" }, { "family_name": "Boas", "given_name": "David A." }, { "family_name": "Buckley", "given_name": "Erin M." }, { "family_name": "Chen", "given_name": "Anderson I." }, { "family_name": "De Vittorio", "given_name": "Massimo" }, { "family_name": "Devor", "given_name": "Anna" }, { "family_name": "Doran", "given_name": "Patrick" }, { "family_name": "El Khatib", "given_name": "Mirna" }, { "family_name": "Fainman", "given_name": "Yeshaiahu" }, { "family_name": "Han", "given_name": "Xue" }, { "family_name": "Hochgeschwender", "given_name": "Ute" }, { "family_name": "Ji", "given_name": "Na" }, { "family_name": "Lake", "given_name": "Evelyn" }, { "family_name": "Li", "given_name": "Lei", "orcid": "0000-0001-6164-2646", "clpid": "Li-Lei" }, { "family_name": "Li", "given_name": "Tianqi" }, { "family_name": "Machler", "given_name": "Philipp" }, { "family_name": "Nasu", "given_name": "Yusuke" }, { "family_name": "Nimmerjahn", "given_name": "Axel", "orcid": "0000-0002-0875-7855" }, { "family_name": "Ondr\u00e1ckov\u00e1", "given_name": "Petra" }, { "family_name": "Pavone", "given_name": "Francesco S." }, { "family_name": "Peterka", "given_name": "Darcy" }, { "family_name": "Pisano", "given_name": "Filippo" }, { "family_name": "Pisanello", "given_name": "Ferruccio" }, { "family_name": "Sabatini", "given_name": "Bernardo L." }, { "family_name": "Sadegh", "given_name": "Sanaz" }, { "family_name": "Sakad\u017eic", "given_name": "Sava" }, { "family_name": "Shroff", "given_name": "Sanaya N." }, { "family_name": "Sims", "given_name": "Ruth R." }, { "family_name": "Smith", "given_name": "Spencer LaVere" }, { "family_name": "Tian", "given_name": "Lin", "orcid": "0000-0001-7012-6926" }, { "family_name": "Troxler", "given_name": "Thomas" }, { "family_name": "Valera", "given_name": "Antoine" }, { "family_name": "Vaziri", "given_name": "Alipasha" }, { "family_name": "Wang", "given_name": "Lihong V.", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Yellen", "given_name": "Gary" }, { "family_name": "Yizhar", "given_name": "Ofer", "orcid": "0000-0003-4228-1448", "clpid": "Yizhar-Ofer" } ], "abstract": "Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, in this article we review an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion article, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed and provide an outlook for the future directions.", "doi": "10.1117/1.nph.9.s1.013001", "pmcid": "PMC9047450", "issn": "2329-423X", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Neurophotonics", "publication_date": "2022-04-27", "series_number": "S1", "volume": "9", "issue": "S1", "pages": "Art. No. 013001" }, { "id": "authors:wsh2p-fqr38", "collection": "authors", "collection_id": "wsh2p-fqr38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220520-231842000", "type": "article", "title": "Speckle-resolved optical coherence tomography for mesoscopic imaging within scattering media", "author": [ { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Blochet", "given_name": "Baptiste", "orcid": "0000-0003-1457-4542", "clpid": "Blochet-Baptiste" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Light scattering poses a challenge for imaging deep in scattering media as the ballistic light exponentially attenuates with depth. In contrast to the ballistic light, the multiply scattered light penetrates deeper and also contains information about the sample. One technique to image deeper is to selectively detect only a subset of the multiply scattered light, namely the 'snake' photons, which are predominantly forward scattered and retain more direct information than the more strongly scattered light. In this work, we develop a technique, termed speckle-resolved optical coherence tomography (srOCT), for efficiently detecting these 'snake' photons to enable imaging deeper in scattering media. The system couples spatio-angular filtering with speckle-resolved interferometric detection to preferentially and efficiently detect the weakly scattered 'snake' photons. With our proof-of-concept system, we demonstrate depth-resolved imaging beyond the ballistic limit, up to a depth of 90 round-trip MFPs in a scattering phantom and a depth of 4.5 mm of chicken tissue at 0.4\u2009mm axial and lateral resolution.", "doi": "10.1364/boe.448969", "pmcid": "PMC9045937", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2022-04", "series_number": "4", "volume": "13", "issue": "4", "pages": "2068-2081" }, { "id": "authors:6cqrj-xab12", "collection": "authors", "collection_id": "6cqrj-xab12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220304-60857000", "type": "book_section", "title": "Non-line-of-sight imaging via wavefront shaping", "author": [ { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "de Goumoens", "given_name": "Frederic", "clpid": "de-Goumoens-Frederic" }, { "family_name": "Blochet", "given_name": "Baptiste", "clpid": "Blochet-Baptiste" }, { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian-EE" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Non-line-of-sight (NLOS) imaging is a rapidly developing research direction that has significant applications in autonomous vehicles, remote sensing, etc. Existing NLOS methods primarily depend on time gated measurements and/or sophisticated signal processing to extract information from the scattered light. Here, we introduce a new method that directly manipulates the light to counter the wall's scattering. This method operates by actively focusing light onto the target in a NLOS path using wavefront shaping. By raster scanning that focus, we can actively image the occluded object. The focus thus formed is near diffraction limited and can be substantially smaller than the object itself, thereby enabling us to perform NLOS imaging with unprecedented resolution. We demonstrate that a resolution of \u223c 0.6 mm at a distance of 0.55 m is achievable in our experiment.", "doi": "10.1117/12.2624775", "publisher": "Society of Photo-optical Instrumentation Engineers", "publication_date": "2022-03-02" }, { "id": "authors:tm4jg-sjf22", "collection": "authors", "collection_id": "tm4jg-sjf22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220304-60849000", "type": "book_section", "title": "Non-interferometric and non-iterative complex wave-field reconstruction based on Kramers-Kronig relations", "author": [ { "family_name": "Shen", "given_name": "Cheng", "clpid": "Shen-Cheng" }, { "family_name": "Zhou", "given_name": "Haowen", "clpid": "Zhou-Haowen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Liu", "given_name": "Yang", "orcid": "0000-0002-8155-9134", "clpid": "Liu-Yang" }, { "family_name": "Popescu", "given_name": "Gabriel", "clpid": "Popescu-Gabriel" }, { "family_name": "Park", "given_name": "YongKuen", "clpid": "Park-YongKuen" } ], "abstract": "We reported a novel non-interferometric and non-iterative computational imaging method, synthetic aperture imaging based on Kramers-Kronig relations (KKSAI), to reconstruct complex wave-field. By collecting images through a modified microscope system with pupil modulation capability, we show that the phase and amplitude profile of the sample at pupil limited resolution can be extracted from as few as two intensity images by exploiting Kramers-Kronig relations. KKSAI reconstruction is non-iterative, free of parameter tuning and applicable to a wider range of samples. Simulation and experiment results have proved that it has much lower computational burden and achieves the best reconstruction quality when compared with two existing phase imaging methods.", "doi": "10.1117/12.2608280", "publisher": "Society of Photo-optical Instrumentation Engineers", "publication_date": "2022-03-02" }, { "id": "authors:k7p4y-d6485", "collection": "authors", "collection_id": "k7p4y-d6485", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220215-496417800", "type": "article", "title": "Stain-free detection of embryo polarization using deep learning", "author": [ { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Lamba", "given_name": "Adiyant", "clpid": "Lamba-Adiyant" }, { "family_name": "Zhu", "given_name": "Meng", "orcid": "0000-0001-6157-8840", "clpid": "Zhu-Meng" }, { "family_name": "Zhang", "given_name": "Ray", "clpid": "Zhang-Ray" }, { "family_name": "Zernicka-Goetz", "given_name": "Magdalena", "orcid": "0000-0002-7004-2471", "clpid": "Zernicka-Goetz-M" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Polarization of the mammalian embryo at the right developmental time is critical for its development to term and would be valuable in assessing the potential of human embryos. However, tracking polarization requires invasive fluorescence staining, impermissible in the in vitro fertilization clinic. Here, we report the use of artificial intelligence to detect polarization from unstained time-lapse movies of mouse embryos. We assembled a dataset of bright-field movie frames from 8-cell-stage embryos, side-by-side with corresponding images of fluorescent markers of cell polarization. We then used an ensemble learning model to detect whether any bright-field frame showed an embryo before or after onset of polarization. Our resulting model has an accuracy of 85% for detecting polarization, significantly outperforming human volunteers trained on the same data (61% accuracy). We discovered that our self-learning model focuses upon the angle between cells as one known cue for compaction, which precedes polarization, but it outperforms the use of this cue alone. By compressing three-dimensional time-lapsed image data into two-dimensions, we are able to reduce data to an easily manageable size for deep learning processing. In conclusion, we describe a method for detecting a key developmental feature of embryo development that avoids clinically impermissible fluorescence staining.", "doi": "10.1038/s41598-022-05990-6", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2022-02-14", "volume": "12", "pages": "Art. No. 2404" }, { "id": "authors:56467-ekz46", "collection": "authors", "collection_id": "56467-ekz46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200624-100741522", "type": "article", "title": "Non-iterative complex wave-field reconstruction based on Kramers\u2013Kronig relations", "author": [ { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Liang", "given_name": "Mingshu", "clpid": "Liang-Mingshu" }, { "family_name": "Pan", "given_name": "An", "orcid": "0000-0001-7710-3815", "clpid": "Pan-An" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "A non-iterative and non-interferometric computational imaging method to reconstruct a complex wave field called synthetic aperture imaging based on Kramers\u2013Kronig relations (KKSAI) is reported. By collecting images through a modified microscope system with pupil modulation capability, we show that the phase and amplitude profile of the sample at pupil limited resolution can be extracted from as few as two intensity images by using Kramers\u2013Kronig (KK) relations. It is established that as long as each subaperture's edge crosses the pupil center, the collected raw images are mathematically analogous to off-axis holograms. This in turn allows us to adapt a recently reported KK-relations-based phase recovery framework in off-axis holography for use in KKSAI. KKSAI is non-iterative, free of parameter tuning, and applicable to a wider range of samples. Simulation and experiment results have proved that it has much lower computational burden and achieves the best reconstruction quality when compared with two existing phase imaging methods.", "doi": "10.1364/PRJ.419886", "issn": "2327-9125", "publisher": "Optical Society of America", "publication": "Photonics Research", "publication_date": "2021-06", "series_number": "6", "volume": "9", "issue": "6", "pages": "1003-1012" }, { "id": "authors:feyrn-1h817", "collection": "authors", "collection_id": "feyrn-1h817", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210423-121335410", "type": "article", "title": "Optical information transmission through complex scattering media with optical-channel-based intensity streaming", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian-EE" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "For the past decade, optical wavefront shaping has been the standard technique to control light through scattering media. Implicit in this dominance is the assumption that manipulating optical interference is a necessity for optical control through scattering media. In this paper, we challenge this assumption by reporting on an alternate approach for light control through a disordered scattering medium \u2013 optical-channel-based intensity streaming (OCIS). Instead of actively tuning the interference between the optical paths via wavefront shaping, OCIS controls light and transmits information through scattering media through linear intensity operations. We demonstrate a set of OCIS experiments that connect to some wavefront shaping implementations, i.e. iterative wavefront optimization, digital optical phase conjugation, image transmission through transmission matrix, and direct imaging through scattering media. We experimentally created focus patterns through scattering media on a sub-millisecond timescale. We also demonstrate that OCIS enables a scattering medium mediated secure optical communication application.", "doi": "10.1038/s41467-021-22692-1", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2021-04-23", "volume": "12", "pages": "Art. No. 2411" }, { "id": "authors:xpcdw-5m989", "collection": "authors", "collection_id": "xpcdw-5m989", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210210-120447617", "type": "article", "title": "Concept, implementations and applications of Fourier ptychography", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Jiang", "given_name": "Shaowei", "clpid": "Jiang-Shaowei" }, { "family_name": "Song", "given_name": "Pengming", "clpid": "Song-Pengming" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The competition between resolution and the imaging field of view is a long-standing problem in traditional imaging systems \u2014 they can produce either an image of a small area with fine details or an image of a large area with coarse details. Fourier ptychography (FP) is an approach for tackling this intrinsic trade-off in imaging systems. It takes the challenge of high-throughput and high-resolution imaging from the domain of improving the physical limitations of optics to the domain of computation. It also enables post-measurement computational correction of optical aberrations. We present the basic concept of FP, compare it to related imaging modalities and then discuss experimental implementations, such as aperture-scanning FP, macroscopic camera-scanning FP, reflection mode, single-shot set-up, X-ray FP, speckle-scanning scheme and deep-learning-related implementations. Various applications of FP are discussed, including quantitative phase imaging in 2D and 3D, digital pathology, high-throughput cytometry, aberration metrology, long-range imaging and coherent X-ray nanoscopy. A collection of datasets and reconstruction codes is provided for readers interested in implementing FP themselves.", "doi": "10.1038/s42254-021-00280-y", "issn": "2522-5820", "publisher": "Springer Nature", "publication": "Nature Reviews Physics", "publication_date": "2021-03", "series_number": "3", "volume": "3", "issue": "3", "pages": "207-223" }, { "id": "authors:cwpt6-wvv07", "collection": "authors", "collection_id": "cwpt6-wvv07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210217-070548457", "type": "article", "title": "Feasibility and safety study of a high resolution wide field-of-view scanning endoscope for circumferential intraluminal intestinal imaging", "author": [ { "family_name": "Lai", "given_name": "Lily L.", "clpid": "Lai-Lily-L" }, { "family_name": "Invernizzi", "given_name": "Marta", "clpid": "Invernizzi-Marta" }, { "family_name": "White", "given_name": "Michael", "clpid": "White-Michael" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Jiangtao", "given_name": "Huangfu", "clpid": "Jiangtao-Huangfu" }, { "family_name": "Lu", "given_name": "Helen", "clpid": "Lu-Helen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Lin", "given_name": "James", "clpid": "Lin-James" } ], "abstract": "Global anal cancer incidence is increasing. High resolution anoscopy (HRA) currently screens for anal cancer, although the definitive test remains unknown. To improve on intraluminal imaging of the anal canal, we conducted a first-in-human study to determine feasibility and safety of a high-resolution, wide field-of-view scanning endoscope. Fourteen patients, under an IRB-approved clinical study, underwent exam under anesthesia, HRA, and imaging with the experimental device. HRA findings were photographed using an in-line camera attached to the colposcope and compared with the scanning endoscope images. Patients were followed up within 2 weeks of the procedure. The imaging device is inserted into the anal canal and the intraluminal surface is digitally photographed in 10 s and uploaded to a computer monitor for review. Ten patients completed imaging with the device. Three patients were not imaged due to severe anal stenosis. One patient was not imaged due to technical device malfunction. The device images were compared to the HRA images. No adverse event attributable to the device was reported. The intraluminal scanning endoscope can be used for circumferential anal canal imaging and is safe for clinical use. Future clinical studies are needed to evaluate the performance of this device.", "doi": "10.1038/s41598-021-82962-2", "pmcid": "PMC7878729", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2021-02-11", "volume": "11", "pages": "Art. No. 3544" }, { "id": "authors:he0pf-p3x16", "collection": "authors", "collection_id": "he0pf-p3x16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210105-133437784", "type": "article", "title": "Diffusing wave spectroscopy: A unified treatment on temporal sampling and speckle ensemble methods", "author": [ { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian-EE" }, { "family_name": "Jahromi", "given_name": "Ali K.", "orcid": "0000-0001-9205-7853", "clpid": "Jahromi-Ali-K" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Diffusing wave spectroscopy (DWS) is a well-known set of methods to measure the temporal dynamics of dynamic samples. In DWS, dynamic samples scatter the incident coherent light, and the information of the temporal dynamics is encoded in the scattered light. To record and analyze the light signal, there exist two types of methods\u2014temporal sampling methods and speckle ensemble methods. Temporal sampling methods, including diffuse correlation spectroscopy, use one or multiple large bandwidth detectors to sample well and analyze the temporal light signal to infer the sample temporal dynamics. Speckle ensemble methods, including speckle visibility spectroscopy, use a high-pixel-count camera sensor to capture a speckle pattern and use the speckle contrast to infer sample temporal dynamics. In this paper, we theoretically and experimentally demonstrate that the decorrelation time (\u03c4) measurement accuracy or signal-to-noise ratio (SNR) of the two types of methods has a unified and similar fundamental expression based on the number of independent observables (NIO) and the photon flux. Given a time measurement duration, the NIO in temporal sampling methods is constrained by the measurement duration, while speckle ensemble methods can outperform by using simultaneous sampling channels to scale up the NIO significantly. In the case of optical brain monitoring, the interplay of these factors favors speckle ensemble methods. We illustrate that this important engineering consideration is consistent with the previous research on blood pulsatile flow measurements, where a speckle ensemble method operating at 100-fold lower photon flux than a conventional temporal sampling system can achieve a comparable SNR.", "doi": "10.1063/5.0034576", "issn": "2378-0967", "publisher": "American Institute of Physics", "publication": "APL Photonics", "publication_date": "2021-01", "series_number": "1", "volume": "6", "issue": "1", "pages": "Art. No. 016105" }, { "id": "authors:8x42h-k8m20", "collection": "authors", "collection_id": "8x42h-k8m20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201208-105038376", "type": "article", "title": "Interferometric speckle visibility spectroscopy (ISVS) for human cerebral blood flow monitoring", "author": [ { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-6036-5680", "clpid": "Xu-Jian" }, { "family_name": "Jahromi", "given_name": "Ali K.", "orcid": "0000-0001-9205-7853", "clpid": "Jahromi-Ali-K" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Robinson", "given_name": "J. Elliott", "orcid": "0000-0001-9417-3938", "clpid": "Robinson-J-Elliott" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Infrared light scattering methods have been developed and employed to non-invasively monitor human cerebral blood flow (CBF). However, the number of reflected photons that interact with the brain is low when detecting blood flow in deep tissue. To tackle this photon-starved problem, we present and demonstrate the idea of interferometric speckle visibility spectroscopy (ISVS). In ISVS, an interferometric detection scheme is used to boost the weak signal light. The blood flow dynamics are inferred from the speckle statistics of a single frame speckle pattern. We experimentally demonstrated the improvement in the measurement of fidelity by introducing interferometric detection when the signal photon number is low. We apply the ISVS system to monitor the human CBF in situations where the light intensity is \u223c100-fold less than that in common diffuse correlation spectroscopy (DCS) implementations. Due to the large number of pixels (\u223c2 \u00d7 10\u2075) used to capture light in the ISVS system, we are able to collect a similar number of photons within one exposure time as in normal DCS implementations. Our system operates at a sampling rate of 100 Hz. At the exposure time of 2 ms, the average signal photoelectron number is \u223c0.95 count/pixel, yielding a single pixel interferometric measurement signal-to-noise ratio (SNR) of \u223c0.97. The total \u223c2 \u00d7 10\u2075 pixels provide an expected overall SNR of 436. We successfully demonstrate that the ISVS system is able to monitor the human brain pulsatile blood flow, as well as the blood flow change when a human subject is doing a breath-holding task.", "doi": "10.1063/5.0021988", "issn": "2378-0967", "publisher": "American Institute of Physics", "publication": "APL Photonics", "publication_date": "2020-12", "series_number": "12", "volume": "5", "issue": "12", "pages": "Art. No. 126102" }, { "id": "authors:41jwe-p6r62", "collection": "authors", "collection_id": "41jwe-p6r62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200715-152735840", "type": "article", "title": "Method to Determine Syringe Silicone Oil Layer Heterogeneity and Investigation of its Impact on Product Particle Counts", "author": [ { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Martin", "given_name": "Daniel", "clpid": "Martin-Daniel" }, { "family_name": "Meza", "given_name": "Patricia", "clpid": "Meza-Patricia" }, { "family_name": "Torraca", "given_name": "Gianni", "clpid": "Torraca-Gianni" }, { "family_name": "Pearson", "given_name": "Thomas", "clpid": "Pearson-Thomas" }, { "family_name": "Cao", "given_name": "Shawn", "orcid": "0000-0002-4366-9965", "clpid": "Cao-Shawn" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Pre-filled syringes (PFSs) are commonly used for parenteral delivery of protein therapeutics. In PFSs, the inner surface of the syringe barrel is typically coated with silicone oil for lubrication. The total amount of silicone oil as well as its distribution can impact syringe functionality and particle formation. However, methods to non-destructively characterize the silicone oil distribution are limited. In this paper, we developed a method to visualize and quantify the relative distribution of silicone oil in unfilled syringes using a custom-built multi-color interferometric imaging system. We then applied the system in a preliminary study to investigate the impact of the silicone oil distribution on the number of particles formed in solution after filling and extrusion for two different types of syringes. The syringe type with significantly lower particle counts also exhibited significantly more homogeneous silicone oil distributions. Within syringe types, no significant association was found between silicone oil distribution and particle formation. Our method can be used in further studies that investigate the impact of syringe siliconization on PFS functionality and particle formation.", "doi": "10.1016/j.xphs.2020.07.012", "pmcid": "PMC7572663", "issn": "0022-3549", "publisher": "Elsevier", "publication": "Journal of Pharmaceutical Sciences", "publication_date": "2020-11", "series_number": "11", "volume": "109", "issue": "11", "pages": "3292-3299" }, { "id": "authors:43wg1-fmv92", "collection": "authors", "collection_id": "43wg1-fmv92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200324-095704695", "type": "article", "title": "Fluorescence imaging through dynamic scattering media with speckle-encoded ultrasound-modulated light correlation", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian" }, { "family_name": "Huang", "given_name": "Yujia", "orcid": "0000-0001-7667-8342", "clpid": "Huang-Yujia" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fluorescence imaging is indispensable to biomedical research, and yet it remains challenging to image through dynamic scattering samples. Techniques that combine ultrasound and light as exemplified by ultrasound-assisted wavefront shaping have enabled fluorescence imaging through scattering media. However, the translation of these techniques into in vivo applications has been hindered by the lack of high-speed solutions to counter the fast speckle decorrelation of dynamic tissue. Here, we report an ultrasound-enabled optical imaging method that instead leverages the dynamic nature to perform imaging. The method utilizes the correlation between the dynamic speckle-encoded fluorescence and ultrasound-modulated light signal that originate from the same location within a sample. We image fluorescent targets with an improved resolution of \u226475\u2009\u00b5m (versus a resolution of 1.3\u2009mm with direct optical imaging) within a scattering medium with 17\u2009ms decorrelation time. This new imaging modality paves the way for fluorescence imaging in highly scattering tissue in vivo.", "doi": "10.1038/s41566-020-0630-0", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2020-08", "series_number": "8", "volume": "14", "issue": "8", "pages": "511-516" }, { "id": "authors:8zsta-0rm98", "collection": "authors", "collection_id": "8zsta-0rm98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200622-104138625", "type": "article", "title": "Imaging through highly scattering human skulls with ultrasound-modulated optical tomography", "author": [ { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Advances in human brain imaging technologies are critical to understanding how the brain works and the diagnosis of brain disorders. Existing technologies have different drawbacks, and the human skull poses a great challenge for pure optical and ultrasound imaging technologies. Here we demonstrate the feasibility of using ultrasound-modulated optical tomography, a hybrid technology that combines both light and sound, to image through human skulls. Single-shot off-axis holography was used to measure the field of the ultrasonically tagged light. This Letter paves the way for imaging the brain noninvasively through the skull, with optical contrast and a higher spatial resolution than that of diffuse optical tomography.", "doi": "10.1364/ol.390920", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2020-06-01", "series_number": "11", "volume": "45", "issue": "11", "pages": "2973-2976" }, { "id": "authors:zfvxt-ccc70", "collection": "authors", "collection_id": "zfvxt-ccc70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200416-121840939", "type": "article", "title": "Single-shot surface 3D imaging by optical coherence factor", "author": [ { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian" }, { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a single-shot three-dimensional (3D) topographical imaging method, optical coherence factor (OCF) imaging, which uses optical coherence as the contrast mechanism to acquire the surface height (z-direction) information of an object. A 4-f imaging system records the light field reflected from the surface of the object. The illumination of the imaging system comes from a laser source with the optical coherence length comparable to the depth of field (DoF) of the optical system. Off-axis holographic recording is used to retrieve the coherence factor from the interference fringes, which is then converted to z-direction information. In this experiment, we validate our 3D imaging results comparing them to axial scanning full-field optical coherence tomography images. We also analyze the contrast mechanism of OCF and show that it is able to provide additional information over conventional coherent and incoherent imaging using the same imaging setup. This single-shot computationally efficient method may have potential applications in industrial quality control inspection.", "doi": "10.1364/ol.384551", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2020-04-01", "series_number": "7", "volume": "45", "issue": "7", "pages": "1734-1737" }, { "id": "authors:n4gtd-yvg15", "collection": "authors", "collection_id": "n4gtd-yvg15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200310-152644516", "type": "book_section", "title": "Single-shot surface 3-D imaging by optical coherence factor (Conference Presentation)", "book_title": "Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII", "author": [ { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian" }, { "family_name": "Cao", "given_name": "Ruizhi", "orcid": "0000-0003-3385-446X", "clpid": "Cao-Ruizhi" }, { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Brown", "given_name": "Thomas G.", "clpid": "Brown-T-G" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-Tony" }, { "family_name": "Waller", "given_name": "Laura", "clpid": "Waller-L" } ], "abstract": "We report a single-shot surface three-dimensional (3-D) imaging method that uses optical coherence as a contrast mechanism to acquire the vertical (z-direction) information of an object. The illumination of the imaging system comes from a light source with the optical coherence length similar to the depth of field (DoF) of the optical system. Holographic recording is used to retrieve the coherence visibility factor, which is then converted to z-direction information. In the experiment, we compare the imaging results of our method to conventional incoherent imaging results, showing that this contrast mechanism is able to provide additional information. We also validate our 3D imaging results by using axial scanning full-field optical coherence tomography.", "doi": "10.1117/12.2545024", "isbn": "9781510632530", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2020-03-09", "pages": "Art. No. 112450E" }, { "id": "authors:bvp7g-2h097", "collection": "authors", "collection_id": "bvp7g-2h097", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200228-130201996", "type": "article", "title": "Investigating ultrasound\u2013light interaction in scattering media", "author": [ { "family_name": "Huang", "given_name": "Yujia", "orcid": "0000-0001-7667-8342", "clpid": "Huang-Yujia" }, { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-J-H" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Significance: Ultrasound-assisted optical imaging techniques, such as ultrasound-modulated optical tomography, allow for imaging deep inside scattering media. In these modalities, a fraction of the photons passing through the ultrasound beam is modulated. The efficiency by which the photons are converted is typically referred to as the ultrasound modulation's \"tagging efficiency.\" Interestingly, this efficiency has been defined in varied and discrepant fashion throughout the scientific literature. \n\nAim: The aim of this study is the ultrasound tagging efficiency in a manner consistent with its definition and experimentally verify the contributive (or noncontributive) relationship between the mechanisms involved in the ultrasound optical modulation process.\nApproach: We adopt a general description of the tagging efficiency as the fraction of photons traversing an ultrasound beam that is frequency shifted (inclusion of all frequency-shifted components). We then systematically studied the impact of ultrasound pressure and frequency on the tagging efficiency through a balanced detection measurement system that measured the power of each order of the ultrasound tagged light, as well as the power of the unmodulated light component. \n\nResults: Through our experiments, we showed that the tagging efficiency can reach 70% in a scattering phantom with a scattering anisotropy of 0.9 and a scattering coefficient of 4\u2009\u2009mm\u207b\u00b9 for a 1-MHz ultrasound with a relatively low (and biomedically acceptable) peak pressure of 0.47 MPa. Furthermore, we experimentally confirmed that the two ultrasound-induced light modulation mechanisms, particle displacement and refractive index change, act in opposition to each other. \n\nConclusion: Tagging efficiency was quantified via simulation and experiments. These findings reveal avenues of investigation that may help improve ultrasound-assisted optical imaging techniques.", "doi": "10.1117/1.jbo.25.2.025002", "pmcid": "PMC7043283", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2020-02-26", "series_number": "2", "volume": "25", "issue": "2", "pages": "Art. No. 025002" }, { "id": "authors:v974z-zrr67", "collection": "authors", "collection_id": "v974z-zrr67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200203-082313476", "type": "monograph", "title": "In situ correction of liquid meniscus in cell culture imaging system based on parallel Fourier ptychographic microscopy (96 Eyes)", "author": [ { "family_name": "Pan", "given_name": "An", "clpid": "Pan-An" }, { "family_name": "Chan", "given_name": "Antony C. S.", "orcid": "0000-0002-5104-261X", "clpid": "Chan-Antony-C-S" }, { "family_name": "Yao", "given_name": "Baoli", "clpid": "Yao-Baoli" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We collaborated with Amgen and spent five years in designing and fabricating next generation multi-well plate imagers based on Fourier ptychographic microscopy (FPM). A 6-well imager (Emsight) and a low-cost parallel microscopic system (96 Eyes) based on parallel FPM were reported in our previous work. However, the effect of liquid meniscus on the image quality is much stronger than anticipated, introducing obvious wavevector misalignment and additional image aberration. To this end, an adaptive wavevector correction (AWC-FPM) algorithm and a pupil recovery improvement strategy are presented to solve these challenges in situ. In addition, dual-channel fluorescence excitation is added to obtain structural information for microbiologists. Experiments are demonstrated to verify their performances. The accuracy of angular resolution with our algorithm is within 0.003 rad. Our algorithms would make the FPM algorithm more robust and practical and can be extended to other FPM-based applications to overcome similar challenges.", "doi": "10.48550/arXiv.1912.00804", "publisher": "arXiv", "publication_date": "2019-11-28" }, { "id": "authors:kdfym-b3b02", "collection": "authors", "collection_id": "kdfym-b3b02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190926-144327410", "type": "article", "title": "Computational aberration correction of VIS-NIR multispectral imaging microscopy based on Fourier ptychography", "author": [ { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Chan", "given_name": "Antony Chi Shing", "clpid": "Chan-Antony-Chi-Shing" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Williams", "given_name": "D. Elliott", "clpid": "Williams-D-E" }, { "family_name": "Hajimiri", "given_name": "Ali", "orcid": "0000-0001-6736-8019", "clpid": "Hajimiri-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Due to the chromatic dispersion properties inherent in all optical materials, even the best-designed multispectral objective will exhibit residual chromatic aberration. Here, we demonstrate a multispectral microscope with a computational scheme based on the Fourier ptychographic microscopy (FPM) to correct these effects in order to render undistorted, in-focus images. The microscope consists of 4 spectral channels ranging from 405 nm to 1552 nm. After the computational aberration correction, it can achieve isotropic resolution enhancement as verified with the Siemens star sample. We image a flip-chip to show the promise of our system to conduct fault detection on silicon chips. This computational approach provides a cost-efficient strategy for high quality multispectral imaging over a broad spectral range.", "doi": "10.1364/oe.27.024923", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2019-09-02", "series_number": "18", "volume": "27", "issue": "18", "pages": "24923-24937" }, { "id": "authors:1cfpq-4sh78", "collection": "authors", "collection_id": "1cfpq-4sh78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190214-102530450", "type": "article", "title": "Parallel Fourier ptychographic microscopy for high-throughput screening with 96 cameras (96 Eyes)", "author": [ { "family_name": "Chan", "given_name": "Antony C. S.", "orcid": "0000-0002-5104-261X", "clpid": "Chan-Antony-C-S" }, { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Pan", "given_name": "An", "clpid": "Pan-An" }, { "family_name": "Xu", "given_name": "Han", "clpid": "Xu-Han" }, { "family_name": "Nojima", "given_name": "Dana", "clpid": "Nojima-Dana" }, { "family_name": "Hale", "given_name": "Christopher", "orcid": "0000-0002-2360-7759", "clpid": "Hale-C" }, { "family_name": "Wang", "given_name": "Songli", "clpid": "Wang-Songli" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of a parallel microscopy system (96 Eyes) that is capable of simultaneous imaging of all wells on a 96-well plate. The optical system consists of 96 microscopy units, where each unit is made out of a four element objective, made through a molded injection process, and a low cost CMOS camera chip. By illuminating the sample with angle varying light and applying Fourier Ptychography, we can improve the effective brightfield imaging numerical aperture of the objectives from 0.23 to 0.3, and extend the depth of field from \u00b15\u2009\u03bcm to \u00b115\u2009\u03bcm. The use of Fourier Ptychography additionally allows us to computationally correct the objectives' aberrations out of the rendered images, and provides us with the ability to render phase images. The 96 Eyes acquires raw data at a rate of 0.7\u2009frame per second (all wells) and the data are processed with 4 cores of graphical processing units (GPUs; GK210, Nvidia Tesla K80, USA). The system is also capable of fluorescence imaging (excitation\u2009=\u2009465\u2009nm, emission\u2009=\u2009510\u2009nm) at the native resolution of the objectives. We demonstrate the capability of this system by imaging S1P_1-eGFP-Human bone osteosarcoma epithelial (U2OS) cells.", "doi": "10.1038/s41598-019-47146-z", "pmcid": "PMC6668459", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2019-07-31", "volume": "9", "pages": "Art. No. 11114" }, { "id": "authors:b1v7q-aq722", "collection": "authors", "collection_id": "b1v7q-aq722", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190606-075749589", "type": "article", "title": "Computational aberration compensation by coded-aperture-based correction of aberration obtained from optical Fourier coding and blur estimation", "author": [ { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Martinez", "given_name": "Gloria W.", "clpid": "Martinez-G-W" }, { "family_name": "Lencioni", "given_name": "Karen C.", "clpid": "Lencioni-K-C" }, { "family_name": "Sadda", "given_name": "Srinivas R.", "clpid": "Sadda-S-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a novel generalized optical measurement system and computational approach to determine and correct aberrations in optical systems. The system consists of a computational imaging method capable of reconstructing an optical system's pupil function by adapting overlapped Fourier coding to an incoherent imaging modality. It recovers the high-resolution image latent in an aberrated image via deconvolution. The deconvolution is made robust to noise by using coded apertures to capture images. We term this method coded-aperture-based correction of aberration obtained from overlapped Fourier coding and blur estimation (CACAO-FB). It is well-suited for various imaging scenarios where aberration is present and where providing a spatially coherent illumination is very challenging or impossible. We report the demonstration of CACAO-FB with a variety of samples including an in vivo imaging experiment on the eye of a rhesus macaque to correct for its inherent aberration in the rendered retinal images. CACAO-FB ultimately allows for an aberrated imaging system to achieve diffraction-limited performance over a wide field of view by casting optical design complexity to computational algorithms in post-processing.", "doi": "10.1364/optica.6.000647", "pmcid": "PMC7597901", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2019-05-20", "series_number": "5", "volume": "6", "issue": "5", "pages": "647-661" }, { "id": "authors:m45qn-23c76", "collection": "authors", "collection_id": "m45qn-23c76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190522-154638477", "type": "book_section", "title": "Extending the wavelength range of multi-spectral microscope systems with Fourier ptychography", "book_title": "Label-free Biomedical Imaging and Sensing (LBIS) 2019", "author": [ { "family_name": "Chan", "given_name": "Antony Chi Shing", "clpid": "Chan-Antony-Chi-Shing" }, { "family_name": "Shen", "given_name": "Cheng", "orcid": "0000-0001-7136-4715", "clpid": "Shen-Cheng" }, { "family_name": "Williams", "given_name": "Elliot", "clpid": "Williams-E" }, { "family_name": "Lyu", "given_name": "Xiaoyu", "clpid": "Lyu-Xiaoyu" }, { "family_name": "Lu", "given_name": "Hangwen", "clpid": "Lu-Hangwen" }, { "family_name": "Ives", "given_name": "Craig", "clpid": "Ives-C-E" }, { "family_name": "Hajimiri", "given_name": "Ali", "orcid": "0000-0001-6736-8019", "clpid": "Hajimiri-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Shaked", "given_name": "Natan T.", "clpid": "Shaked-N-T" }, { "family_name": "Hayden", "given_name": "Oliver", "clpid": "Hayden-O" } ], "abstract": "Due to the chromatic dispersion properties inherent in all optical materials, even the best designed multi-spectral objective will exhibit residual chromatic aberration effect. Here we show that the aberration correction ability of Fourier Ptychographic Microscopy (FPM) is well matched and well suited for post-image acquisition correction of these effects to render in-focus images. We show that an objective with significant spectral focal shift (up to 0.02 \u03bcm/nm) and spectral field curvature (up to 0.05 \u03bcm/nm drift at off-axis position of 800\u03bcm) can be computationally corrected to render images with effectively null spectral defocus and field curvature. This approach of combining optical objective design and computational microscopy provides a good strategy for high quality multi-spectral imaging over a broad spectral range, and eliminating the need for mechanical actuation solutions.", "doi": "10.1117/12.2510875", "isbn": "9781510624221", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2019-03-25", "pages": "Art. No. 108902O" }, { "id": "authors:gjcq6-w2597", "collection": "authors", "collection_id": "gjcq6-w2597", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190404-151930944", "type": "book_section", "title": "Time-reversed ultrasonically encoded (TRUE) optical focusing through highly scattering ex vivo human cataractous lenses for congenital cataract treatment (Conference Presentation)", "book_title": "Adaptive Optics and Wavefront Control for Biological Systems V", "author": [ { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Shen", "given_name": "Yuecheng", "orcid": "0000-0003-1990-8142", "clpid": "Shen-Yuecheng" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Brodie", "given_name": "Frank L.", "clpid": "Brodie-F-L" }, { "family_name": "Wong", "given_name": "Terence T. W.", "orcid": "0000-0001-6399-758X", "clpid": "Wong-Terence-T-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wang", "given_name": "Lihong V.", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong-V" } ], "contributor": [ { "family_name": "Bifano", "given_name": "Thomas G.", "clpid": "Bifano-T-G" }, { "family_name": "Gigan", "given_name": "Sylvain", "clpid": "Gigan-S" }, { "family_name": "Ji", "given_name": "Na", "clpid": "Ji-Na" } ], "abstract": "Normal development of the visual system in infants relies on clear images being projected onto the retina, which can be disrupted by lens opacity caused by congenital cataract. This disruption, if uncorrected in early life, results in amblyopia (permanently decreased vision even after removal of the cataract). Doctors are able to prevent amblyopia by removing the cataract during the first several weeks of life, but this surgery risks a host of complications which can be equally visually disabling. Here, we investigated the feasibility of focusing light noninvasively through highly scattering cataractous lenses to stimulate the retina, thereby preventing amblyopia. This approach would allow the cataractous lens removal surgery to be delayed and hence greatly reduce the risk of complications from early surgery. Employing a wavefront shaping technique named time-reversed ultrasonically encoded (TRUE) optical focusing in reflection mode, we focused 532 nm light through a highly scattering ex vivo adult human cataractous lens of 112 mean free path thick. This work demonstrates a potential clinical application of wavefront shaping techniques.", "doi": "10.1117/12.2508994", "isbn": "9781510624146", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2019-03-04", "pages": "Art. No. 1088602" }, { "id": "authors:p9ags-fsk48", "collection": "authors", "collection_id": "p9ags-fsk48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181114-153202125", "type": "article", "title": "Wide-angular-range and high-resolution beam steering by a metasurface-coupled phased array", "author": [ { "family_name": "Xu", "given_name": "Jian", "clpid": "Xu-Jian" }, { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Zhou", "given_name": "Edward Haojiang", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Horie", "given_name": "Yu", "clpid": "Horie-Yu" }, { "family_name": "Faraon", "given_name": "Andrei", "clpid": "Faraon-A" }, { "family_name": "Yang", "given_name": "Changhuei", "clpid": "Yang-Changhuei" } ], "abstract": "Optical beam steering has broad applications in lidar, optical communications, optical interconnects, and spatially resolved optical sensors. For high-speed applications, phased-array-based beam-steering methods are favored over mechanical methods, as they are unconstrained by inertia and can inherently operate at a higher speed. However, phased-array systems exhibit a tradeoff between angular range and beam divergence, making it difficult to achieve both a large steering angle and a narrow beam divergence. Here, we present a beam-steering method based on wavefront shaping through a disorder-engineered metasurface that circumvents this range-resolution tradeoff. We experimentally demonstrate that, through this technique, one can continuously steer an optical beam within a range of 160\u00b0 (80\u00b0 from normal incidence) with an angular resolution of about 0.01\u00b0 at the cost of beam throughput.", "doi": "10.1364/ol.43.005255", "pmcid": "PMC10578143", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2018-11-01", "series_number": "21", "volume": "43", "issue": "21", "pages": "5255-5258" }, { "id": "authors:z090s-fs120", "collection": "authors", "collection_id": "z090s-fs120", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180726-140218594", "type": "article", "title": "3D imaging scanner", "author": [ { "family_name": "Wu", "given_name": "Zhouyi", "clpid": "Wu-Zhouyi" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Huangfu", "given_name": "Jiangtao", "clpid": "Huangfu-Jiangtao" } ], "abstract": "This paper proposes a multi-view three-dimensional display method based on a scanning imaging system with the light-intensity characteristic recorded by an improved flatbed scanner. Within the effective scanning depth of the imaging sensor, two transmission images are each simultaneously acquired by two linear CCD modules with different focal planes. Then the phase gradient information of the target can be obtained by an appropriate retrieval algorithm. Further, the multi-view three-dimensional effect is presented through dynamic angles of view. Theoretical analysis of this method is discussed, and experiments are carried out by building a scanner. The experiment results are presented with an algae specimen and transparent beads. We hope this method can be applied to present the three-dimensional effect of objects of flat translucent multilayer structure with a wide field of view.", "doi": "10.1364/AO.57.005399", "issn": "0003-6935", "publisher": "Optical Society of America", "publication": "Applied Optics", "publication_date": "2018-07-01", "series_number": "19", "volume": "57", "issue": "19", "pages": "5399-5404" }, { "id": "authors:afjz5-vj324", "collection": "authors", "collection_id": "afjz5-vj324", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180717-081043968", "type": "book_section", "title": "Fourier ptychography for parallel microscopy", "book_title": "High-Speed Biomedical Imaging and Spectroscopy III: Toward Big Data Instrumentation and Management", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Tsia", "given_name": "Kevin K.", "clpid": "Tsia-Kevin-K-M" }, { "family_name": "Goda", "given_name": "Keisuke", "clpid": "Goda-Keisuke" } ], "abstract": "Fourier Ptychography has shown that we can computationally correct physical aberrations. Thereby, allow us to move beyond the traditional strategy of accomplishing high quality imaging through the exacting refinement of the physical microscope system. I will report on the use of Fourier Ptychography to implement high quality parallel imaging with plastic molded lenses for 96 well plate imaging.", "doi": "10.1117/12.2292555", "isbn": "9781510614956", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2018-03-15", "pages": "Art. No. 1050502" }, { "id": "authors:fwk1q-xbm38", "collection": "authors", "collection_id": "fwk1q-xbm38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-103004538", "type": "book_section", "title": "Time-reversed ultrasonically encoded (TRUE) focusing for deep-tissue optogenetic modulation", "book_title": "Adaptive Optics and Wavefront Control for Biological Systems IV", "author": [ { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-J-H" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Robinson", "given_name": "J. Elliott", "orcid": "0000-0001-9417-3938", "clpid": "Robinson-J-E" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Bifano", "given_name": "Thomas G.", "clpid": "Bifano-T-G" }, { "family_name": "Kubby", "given_name": "Joel", "clpid": "Kubby-J" }, { "family_name": "Gigan", "given_name": "Sylvain", "clpid": "Gigan-S" } ], "abstract": "The problem of optical scattering was long thought to fundamentally limit the depth at which light could be focused through turbid media such as fog or biological tissue. However, recent work in the field of wavefront shaping has demonstrated that by properly shaping the input light field, light can be noninvasively focused to desired locations deep inside scattering media. This has led to the development of several new techniques which have the potential to enhance the capabilities of existing optical tools in biomedicine. Unfortunately, extending these methods to living tissue has a number of challenges related to the requirements for noninvasive guidestar operation, speed, and focusing fidelity. Of existing wavefront shaping methods, time-reversed ultrasonically encoded (TRUE) focusing is well suited for applications in living tissue since it uses ultrasound as a guidestar which enables noninvasive operation and provides compatibility with optical phase conjugation for high-speed operation. In this paper, we will discuss the results of our recent work to apply TRUE focusing for optogenetic modulation, which enables enhanced optogenetic stimulation deep in tissue with a 4-fold spatial resolution improvement in 800-micron thick acute brain slices compared to conventional focusing, and summarize future directions to further extend the impact of wavefront shaping technologies in biomedicine.", "doi": "10.1117/12.2288331", "isbn": "9781510614895", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2018-02-23", "pages": "Art. No. 1050210" }, { "id": "authors:jymg9-76986", "collection": "authors", "collection_id": "jymg9-76986", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170815-101915506", "type": "article", "title": "Wavefront shaping with disorder-engineered metasurfaces", "author": [ { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Horie", "given_name": "Yu", "orcid": "0000-0001-7083-1270", "clpid": "Horie-Yu" }, { "family_name": "Shibukawa", "given_name": "Atsushi", "clpid": "Shibukawa-Atsushi" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Kamali", "given_name": "Seyedeh Mahsa", "orcid": "0000-0002-6968-811X", "clpid": "Kamali-Seyedeh-Mahsa" }, { "family_name": "Arbabi", "given_name": "Amir", "orcid": "0000-0001-8831-7552", "clpid": "Arbabi-Amir" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Faraon", "given_name": "Andrei", "orcid": "0000-0002-8141-391X", "clpid": "Faraon-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Recently, wavefront shaping with disordered media has demonstrated optical manipulation capabilities beyond those of conventional optics, including extended volume, aberration-free focusing and subwavelength focusing. However, translating these capabilities to useful applications has remained challenging as the input\u2013output characteristics of the disordered media (P variables) need to be exhaustively determined via O(P) measurements. Here, we propose a paradigm shift where the disorder is specifically designed so its exact input\u2013output characteristics are known a priori and can be used with only a few alignment steps. We implement this concept with a disorder-engineered metasurface, which exhibits additional unique features for wavefront shaping such as a large optical memory effect range in combination with a wide angular scattering range, excellent stability, and a tailorable angular scattering profile. Using this designed metasurface with wavefront shaping, we demonstrate high numerical aperture (NA\u2009>\u20090.5) focusing and fluorescence imaging with an estimated ~2.2\u2009\u00d7\u200910\u2078 addressable points in an ~8\u2009mm field of view.", "doi": "10.1038/s41566-017-0078-z", "pmcid": "PMC5842956", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2018-02", "series_number": "2", "volume": "12", "issue": "2", "pages": "84-90" }, { "id": "authors:ftewx-prw03", "collection": "authors", "collection_id": "ftewx-prw03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180116-102559459", "type": "article", "title": "Time-reversed ultrasonically encoded optical focusing through highly scattering ex vivo human cataractous lenses", "author": [ { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Shen", "given_name": "Yuecheng", "orcid": "0000-0003-1990-8142", "clpid": "Shen-Yuecheng" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Brodie", "given_name": "Frank L.", "clpid": "Brodie-F-L" }, { "family_name": "Wong", "given_name": "Terence T. W.", "orcid": "0000-0001-6399-758X", "clpid": "Wong-Terence-T-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wang", "given_name": "Lihong V.", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong-V" } ], "abstract": "Normal development of the visual system in infants relies on clear images being projected onto the retina, which can be disrupted by lens opacity caused by congenital cataract. This disruption, if uncorrected in early life, results in amblyopia (permanently decreased vision even after removal of the cataract). Doctors are able to prevent amblyopia by removing the cataract during the first several weeks of life, but this surgery risks a host of complications, which can be equally visually disabling. Here, we investigated the feasibility of focusing light noninvasively through highly scattering cataractous lenses to stimulate the retina, thereby preventing amblyopia. This approach would allow the cataractous lens removal surgery to be delayed and hence greatly reduce the risk of complications from early surgery. Employing a wavefront shaping technique named time-reversed ultrasonically encoded optical focusing in reflection mode, we focused 532-nm light through a highly scattering ex vivo adult human cataractous lens. This work demonstrates a potential clinical application of wavefront shaping techniques.", "doi": "10.1117/1.JBO.23.1.010501", "pmcid": "PMC5762002", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2018-01", "series_number": "1", "volume": "23", "issue": "1", "pages": "Art. No. 010501" }, { "id": "authors:p04pt-mv098", "collection": "authors", "collection_id": "p04pt-mv098", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171107-132336726", "type": "article", "title": "Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Robinson", "given_name": "J. Elliott", "orcid": "0000-0001-9417-3938", "clpid": "Robinson-J-Elliott" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Xiao", "given_name": "Cheng", "orcid": "0000-0001-9649-7450", "clpid": "Xiao-Cheng" }, { "family_name": "Zhou", "given_name": "Chunyi", "clpid": "Zhou-Chunyi" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Noninvasive light focusing deep inside living biological tissue has long been a goal in biomedical optics. However, the optical scattering of biological tissue prevents conventional optical systems from tightly focusing visible light beyond several hundred micrometers. The recently developed wavefront shaping technique time-reversed ultrasonically encoded (TRUE) focusing enables noninvasive light delivery to targeted locations beyond the optical diffusion limit. However, until now, TRUE focusing has only been demonstrated inside nonliving tissue samples. We present the first example of TRUE focusing in 2-mm-thick living brain tissue and demonstrate its application for optogenetic modulation of neural activity in 800-\u03bcm-thick acute mouse brain slices at a wavelength of 532 nm. We found that TRUE focusing enabled precise control of neuron firing and increased the spatial resolution of neuronal excitation fourfold when compared to conventional lens focusing. This work is an important step in the application of TRUE focusing for practical biomedical uses.", "doi": "10.1126/sciadv.aao5520", "pmcid": "PMC5722648", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2017-12", "series_number": "12", "volume": "3", "issue": "12", "pages": "Art. No. eaao5520" }, { "id": "authors:595k8-ysd50", "collection": "authors", "collection_id": "595k8-ysd50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171211-091117607", "type": "article", "title": "Focusing light inside scattering media with magnetic-particle-guided wavefront shaping", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Haber", "given_name": "Tom", "clpid": "Haber-Tom" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Kim", "given_name": "Jinho", "orcid": "0000-0001-8711-960X", "clpid": "Kim-Jinho" }, { "family_name": "Berlin", "given_name": "Jacob M.", "orcid": "0000-0001-7498-766X", "clpid": "Berlin-Jacob-M" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optical scattering has traditionally limited the ability to focus light inside scattering media such as biological tissue. Recently developed wavefront shaping techniques promise to overcome this limit by tailoring an optical wavefront to constructively interfere at a target location deep inside scattering media. To find such a wavefront solution, a \"guidestar\" mechanism is required to identify the target location. However, developing guidestars of practical usefulness is challenging, especially in biological tissue, which hinders the translation of wavefront shaping techniques. Here, we demonstrate a guidestar mechanism that relies on magnetic modulation of small particles. This guidestar method features an optical modulation efficiency of 29% and enables micrometer-scale focusing inside biological tissue with a peak intensity-to-background ratio (PBR) of 140; both numbers are one order of magnitude higher than those achieved with the ultrasound guidestar, a popular guidestar method. We also demonstrate that light can be focused on cells labeled with magnetic particles, and to different target locations by magnetically controlling the position of a particle. Since magnetic fields have a large penetration depth even through bone structures like the skull, this optical focusing method holds great promise for deep-tissue applications such as optogenetic modulation of neurons, targeted light-based therapy, and imaging.", "doi": "10.1364/OPTICA.4.001337", "pmcid": "PMC5881932", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2017-11-20", "series_number": "11", "volume": "4", "issue": "11", "pages": "1337-1343" }, { "id": "authors:my3wd-7zq33", "collection": "authors", "collection_id": "my3wd-7zq33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171117-083356029", "type": "article", "title": "In vivo study of optical speckle decorrelation time across depths in the mouse brain", "author": [ { "family_name": "Qureshi", "given_name": "Muhammad Mohsin", "orcid": "0000-0003-0362-0144", "clpid": "Qureshi-Muhammad-Mohsin" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Jeon", "given_name": "Hee-Jae", "clpid": "Jeon-Hee-Jae" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Safi", "given_name": "Abdul Mohaimen", "orcid": "0000-0003-1117-0286", "clpid": "Safi-Abdul-Mohaimen" }, { "family_name": "Eom", "given_name": "Tae Joong", "orcid": "0000-0003-0556-4027", "clpid": "Eom-Tae-Joong" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Chung", "given_name": "Euiheon", "orcid": "0000-0002-3326-6927", "clpid": "Chung-Euiheon" } ], "abstract": "The strong optical scattering of biological tissue confounds our ability to focus light deeply into the brain beyond depths of a few hundred microns. This challenge can be potentially overcome by exploiting wavefront shaping techniques which allow light to be focused through or inside scattering media. However, these techniques require the scattering medium to be static, as changes in the arrangement of the scatterers between the wavefront recording and playback steps reduce the fidelity of the focus that is formed. Furthermore, as the thickness of the scattering medium increases, the influence of the dynamic nature becomes more severe due to the growing number of scattering events experienced by each photon. In this paper, by examining the scattering dynamics in the mouse brain in vivo via multispeckle diffusing wave spectroscopy (MSDWS) using a custom fiber probe that simulates a point-like source within the brain, we investigate the relationship between this decorrelation time and the depth of the point-like light source inside the living mouse brain at depths up to 3.2 mm.", "doi": "10.1364/BOE.8.004855", "pmcid": "PMC5695936", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2017-11-01", "series_number": "11", "volume": "8", "issue": "11", "pages": "4855-4864" }, { "id": "authors:8mkxm-d1538", "collection": "authors", "collection_id": "8mkxm-d1538", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171117-082155006", "type": "article", "title": "Focusing light through scattering media by transmission matrix inversion", "author": [ { "family_name": "Xu", "given_name": "Jian", "orcid": "0000-0002-4743-2471", "clpid": "Xu-Jian" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Liu", "given_name": "Yan", "orcid": "0000-0002-5837-4908", "clpid": "Liu-Yan" }, { "family_name": "Zhou", "given_name": "Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Focusing light through scattering media has broad applications in optical imaging, manipulation and therapy. The contrast of the focus can be quantified by peak-to-background intensity ratio (PBR). Here, we theoretically and numerically show that by using a transmission matrix inversion method to achieve focusing, within a limited field of view and under a low noise condition in transmission matrix measurements, the PBR of the focus can be higher than that achieved by conventional methods such as optical phase conjugation or feedback-based wavefront shaping. Experimentally, using a phase-modulation spatial light modulator, we increase the PBR by 66% over that achieved by conventional methods based on phase conjugation. In addition, we demonstrate that, within a limited field of view and under a low noise condition in transmission matrix measurements, our matrix inversion method enables light focusing to multiple foci with greater fidelity than those of conventional methods.", "doi": "10.1364/OE.25.027234", "pmcid": "PMC5941990", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2017-10-30", "series_number": "22", "volume": "25", "issue": "22", "pages": "27234-27246" }, { "id": "authors:ajwe5-wbj73", "collection": "authors", "collection_id": "ajwe5-wbj73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170821-084016652", "type": "book_section", "title": "Fourier Ptychographic Microscopy for Rapid, High-Resolution Imaging of Circulating Tumor Cells Enriched by Microfiltration", "book_title": "Circulating Tumor Cells", "author": [ { "family_name": "Williams", "given_name": "Anthony", "clpid": "Williams-A-J" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Cote", "given_name": "Richard J.", "clpid": "Cote-R-J" } ], "contributor": [ { "family_name": "Magbanua", "given_name": "Mark Jesus M.", "clpid": "Magbanua-M-J-M" }, { "family_name": "Park", "given_name": "John W.", "clpid": "Park-J-W" } ], "abstract": "Examining the hematogenous compartment for evidence of metastasis has increased significantly within the oncology research community in recent years, due to the development of technologies aimed at the enrichment of circulating tumor cells (CTCs), the subpopulation of primary tumor cells that gain access to the circulatory system and are responsible for colonization at distant sites. In contrast to other technologies, filtration-based CTC enrichment, which exploits differences in size between larger tumor cells and surrounding smaller, non-tumor blood cells, has the potential to improve CTC characterization through isolation of tumor cell populations with greater molecular heterogeneity. However, microscopic analysis of uneven filtration surfaces containing CTCs is laborious, time-consuming, and inconsistent, preventing widespread use of filtration-based enrichment technologies. Here, integrated with a microfiltration-based CTC and rare cell enrichment device we have previously described, we present a protocol for Fourier Ptychographic Microscopy (FPM), a method that, unlike many automated imaging platforms, produces high-speed, high-resolution images that can be digitally refocused, allowing users to observe objects of interest present on multiple focal planes within the same image frame. The development of a cost-effective and high-throughput CTC analysis system for filtration-based enrichment technologies could have profound clinical implications for improved CTC detection and analysis.", "doi": "10.1007/978-1-4939-7144-2_8", "isbn": "978-1-4939-7143-5", "publisher": "Humana Press", "place_of_publication": "New York, NY", "publication_date": "2017-08-18", "pages": "107-117" }, { "id": "authors:jqzsa-a8b53", "collection": "authors", "collection_id": "jqzsa-a8b53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180717-083621756", "type": "book_section", "title": "Magnetic guidestar assisted light focusing through scattering media", "book_title": "Adaptive Optics and Wavefront Control for Biological Systems III", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-J-H" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Bifano", "given_name": "Thomas G.", "clpid": "Bifano-T-G" }, { "family_name": "Kubby", "given_name": "Joel", "clpid": "Kubby-J" }, { "family_name": "Gigan", "given_name": "Sylvain", "clpid": "Gigan-S" } ], "abstract": "Optical scattering of biological tissue limits the working depth of conventional biomedical optics, which relies on the detection of ballistic photons. Recent developed optical phase conjugation (OPC) technique breaks through this depth limit by harnessing the scattered photons and shaping an optical wavefront that can \"undo\" the optical scattering. The OPC system measures the complex light field exiting the tissue and reconstructs a phase conjugated copy of the measured wavefront, which propagates in the reversed direction to the source of the light. To focus light inside a scattering medium, an embedded light source or \"guidestar\" is often required. Therefore, developing guidestar mechanisms plays an important role in advancing the OPC technique for deep tissue optical focusing and imaging. In addition to having strong optical modulation efficiency and compact size, a favorable guidestar for biomedical applications should also have good biocompatibility, fast response time, and be noninvasive or require only minimally invasive procedure. While a number of guidestar mechanisms have been developed and showed promising for various biomedical applications, they all have their own limitations. We have been developing new guidestars and tailoring them to meet the need for biomedical imaging and therapies. We are going to present our recent progress in novel guidestar development, compare them with established guidestar mechanisms, and discuss their potential in biomedical applications.", "doi": "10.1117/12.2252997", "isbn": "9781510605879", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2017-04-24", "pages": "Art. No. 100730I" }, { "id": "authors:10mz7-aft37", "collection": "authors", "collection_id": "10mz7-aft37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180717-082347539", "type": "book_section", "title": "Quantitative phase imaging by pupil modulation different phase contrast (PMDPC)", "book_title": "Quantitative Phase Imaging III", "author": [ { "family_name": "Lu", "given_name": "Hangwen", "clpid": "Lu-Hangwen" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Popescu", "given_name": "Gabriel", "clpid": "Popescu-G" }, { "family_name": "Park", "given_name": "YongKeun", "clpid": "Park-YongKeun" } ], "abstract": "Differential phase contrast (DPC) is a non-interference quantitative phase imaging method achieved by asymmetric optical systems. Quantitative DPC images are achieved previously with asymmetric illumination systems. However, it works well for on-focus thin samples only. Considering the limitation, we develop a pupil modulation differential phase contrast (PMDPC) imaging method. Instead of modulating the illumination, we use a spatial light modulator (SLM) to modulate a 4f imaging system's pupil plane. When half of the pupil plane is blocked by the SLM, a phase gradient image forms on the image plane. Using two such phase gradient images captured separately by applying complementary half-circle pupils on SLM, a DPC image can be constructed that carries the sample's phase information. A quantitative phase image of the sample can be reconstructed after a deconvolution procedure. Further, we are able to combine this quantitative phase with the sample's intensity image to obtain the complete complex object field which then allows us to post-process the image. We report experimentally that aberrations arising from the optical elements in the system can be corrected by deconvolving the reconstructed image with a pre-calibrated pupil function. We can also digitally extend the depth of field using angular spectrum propagation algorithm. With our PMDPC imaging setup where NA equals to 0.36, a quantitative phase image with periodic resolution of 1.73\u00b5m is obtained. The depth of field for a 20x, 0.4NA objective is extended digitally by 20 times to -50~50 micrometers.", "doi": "10.1117/12.2252576", "isbn": "9781510605893", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2017-04-24", "pages": "Art. No. 100740P" }, { "id": "authors:57jyj-3p616", "collection": "authors", "collection_id": "57jyj-3p616", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170831-081004023", "type": "book_section", "title": "Incubator embedded cell culture imaging system (EmSight) based on Fourier ptychographic microscopy", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XV", "author": [ { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Henley", "given_name": "Beverley M.", "clpid": "Henley-Beverley-M" }, { "family_name": "Kim", "given_name": "Charlene H.", "clpid": "Kim-Charlene-H" }, { "family_name": "Lester", "given_name": "Henry A.", "orcid": "0000-0002-5470-5255", "clpid": "Lester-H-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-Daniuel-L" }, { "family_name": "Nicolau", "given_name": "D. V.", "clpid": "Nicolau-D-V" }, { "family_name": "Leif", "given_name": "R. C.", "clpid": "Leif-R-C" } ], "abstract": "Multi-day tracking of cells in culture systems can provide valuable information in bioscience experiments. We report the development of a cell culture imaging system, named EmSight, which incorporates multiple compact Fourier ptychographic microscopes with a standard multiwell imaging plate. The system is housed in an incubator and presently incorporates six microscopes, imaging an ANSI standard 6-well plate at the same time. By using the same low magnification objective lenses (NA of 0.1) as the objective and the tube lens, the EmSight is configured as a 1:1 imaging system that, providing large field-of-view (FOV) imaging (5.7 mm \u00d7 4.3 mm) onto a low-cost CMOS imaging sensor. The EmSight improves the image resolution by capturing a series of images of the sample at varying illumination angles; the instrument reconstructs a higher-resolution image by using the iterative Fourier ptychographic algorithm. In addition to providing high-resolution brightfield and phase imaging, the EmSight is also capable of fluorescence imaging at the native resolution of the objectives. We characterized the system using a phase Siemens star target, and show four-fold improved coherent resolution (synthetic NA of 0.42) and a depth of field of 0.2 mm. To conduct live, long-term dopaminergic neuron imaging, we cultured ventral midbrain from mice driving eGFP from the tyrosine hydroxylase promoter. The EmSight system tracks movements of dopaminergic neurons over a 21 day period.", "doi": "10.1117/12.2249906", "isbn": "9781510605770", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2017-04-24", "pages": "Art. No. 100680X" }, { "id": "authors:0r6an-sqe75", "collection": "authors", "collection_id": "0r6an-sqe75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170303-084226860", "type": "article", "title": "Optical Phase Conjugation with Less Than a Photon per Degree of Freedom", "author": [ { "family_name": "Jang", "given_name": "M.", "clpid": "Jang-M" }, { "family_name": "Yang", "given_name": "C.", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Vellekoop", "given_name": "I. M.", "clpid": "Vellekoop-I-M" } ], "abstract": "We demonstrate experimentally that optical phase conjugation can be used to focus light through strongly scattering media even when far less than a photon per optical degree of freedom is detected. We found that the best achievable intensity contrast is equal to the total number of detected photons, as long as the resolution of the system is high enough. Our results demonstrate that phase conjugation can be used even when the photon budget is extremely low, such as in high-speed focusing through dynamic media or imaging deep inside tissue.", "doi": "10.1103/PhysRevLett.118.093902", "pmcid": "PMC5508849", "issn": "0031-9007", "publisher": "American Physical Society", "publication": "Physical Review Letters", "publication_date": "2017-03-03", "series_number": "9", "volume": "118", "issue": "9", "pages": "Art. No. 093902" }, { "id": "authors:qhx9y-5jw27", "collection": "authors", "collection_id": "qhx9y-5jw27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170420-082230274", "type": "article", "title": "Imaging moving targets through scattering media", "author": [ { "family_name": "Cua", "given_name": "Michelle", "clpid": "Cua-Michelle" }, { "family_name": "Zhou", "given_name": "Edward Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optical microscopy in complex, inhomogeneous media is challenging due to the presence of multiply scattered light that limits the depths at which diffraction-limited resolution can be achieved. One way to circumvent the degradation in resolution is to use speckle- correlation-based imaging (SCI) techniques, which permit imaging of objects inside scattering media at diffraction-limited resolution. However, SCI methods are currently limited to imaging sparsely tagged objects in a dark-field scenario. In this work, we demonstrate the ability to image hidden, moving objects in a bright-field scenario. By using a deterministic phase modulator to generate a spatially incoherent light source, the background contribution can be kept constant between acquisitions and subtracted out. In this way, the signal arising from the object can be isolated, and the object can be reconstructed with high fidelity. With the ability to effectively isolate the object signal, our work is not limited to imaging bright objects in the dark-field case, but also works in bright-field scenarios, with non-emitting objects.", "doi": "10.1364/OE.25.003935", "pmcid": "PMC5772388", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2017-02-20", "series_number": "4", "volume": "25", "issue": "4", "pages": "3935-3945" }, { "id": "authors:wenz3-ztk36", "collection": "authors", "collection_id": "wenz3-ztk36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161202-113920973", "type": "article", "title": "Motion-corrected Fourier ptychography", "author": [ { "family_name": "Bian", "given_name": "Liheng", "orcid": "0000-0002-8016-0375", "clpid": "Bian-Liheng" }, { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Guo", "given_name": "Kaikai", "clpid": "Guo-Kaikai" }, { "family_name": "Suo", "given_name": "Jinli", "clpid": "Suo-Jinli" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Chen", "given_name": "Feng", "clpid": "Chen-Feng" }, { "family_name": "Dai", "given_name": "Qionghai", "orcid": "0000-0001-7043-3061", "clpid": "Dai-Qionghai" } ], "abstract": "Fourier ptychography (FP) is a recently proposed computational imaging technique for high space-bandwidth product imaging. In real setups such as endoscope and transmission electron microscope, the common sample motion largely degrades the FP reconstruction and limits its practicability. In this paper, we propose a novel FP reconstruction method to efficiently correct for unknown sample motion. Specifically, we adaptively update the sample's Fourier spectrum from low spatial-frequency regions towards high spatial-frequency ones, with an additional motion recovery and phase-offset compensation procedure for each sub-spectrum. Benefiting from the phase retrieval redundancy theory, the required large overlap between adjacent sub-spectra offers an accurate guide for successful motion recovery. Experimental results on both simulated data and real captured data show that the proposed method can correct for unknown sample motion with its standard deviation being up to 10% of the field-of-view scale. We have released our source code for non-commercial use, and it may find wide applications in related FP platforms such as endoscopy and transmission electron microscopy.", "doi": "10.1364/BOE.7.004543", "pmcid": "PMC5119594", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2016-11-01", "series_number": "11", "volume": "7", "issue": "11", "pages": "4543-4553" }, { "id": "authors:gqp46-7p531", "collection": "authors", "collection_id": "gqp46-7p531", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160919-122718840", "type": "article", "title": "Wide-field Fourier ptychographic microscopy using laser illumination source", "author": [ { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Lu", "given_name": "Hangwen", "clpid": "Lu-Hangwen" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Zhou", "given_name": "Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fourier ptychographic (FP) microscopy is a coherent imaging method that can synthesize an image with a higher bandwidth using multiple low-bandwidth images captured at different spatial frequency regions. The method's demand for multiple images drives the need for a brighter illumination scheme and a high-frame-rate camera for a faster acquisition. We report the use of a guided laser beam as an illumination source for an FP microscope. It uses a mirror array and a 2-dimensional scanning Galvo mirror system to provide a sample with plane-wave illuminations at diverse incidence angles. The use of a laser presents speckles in the image capturing process due to reflections between glass surfaces in the system. They appear as slowly varying background fluctuations in the final reconstructed image. We are able to mitigate these artifacts by including a phase image obtained by differential phase contrast (DPC) deconvolution in the FP algorithm. We use a 1-Watt laser configured to provide a collimated beam with 150 mW of power and beam diameter of 1 cm to allow for the total capturing time of 0.96 seconds for 96 raw FPM input images in our system, with the camera sensor's frame rate being the bottleneck for speed. We demonstrate a factor of 4 resolution improvement using a 0.1 NA objective lens over the full camera field-of-view of 2.7 mm by 1.5 mm.", "doi": "10.1364/BOE.7.004787", "pmcid": "PMC5119616", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2016-11-01", "series_number": "11", "volume": "7", "issue": "11", "pages": "4787-4802" }, { "id": "authors:1vssz-6g398", "collection": "authors", "collection_id": "1vssz-6g398", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161222-112221157", "type": "article", "title": "Quantitative phase imaging and complex field reconstruction by pupil modulation differential phase contrast", "author": [ { "family_name": "Lu", "given_name": "Hangwen", "clpid": "Lu-Hangwen" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Differential phase contrast (DPC) is a non-interferometric quantitative phase imaging method achieved by using an asymmetric imaging procedure. We report a pupil modulation differential phase contrast (PMDPC) imaging method by filtering a sample's Fourier domain with half-circle pupils. A phase gradient image is captured with each half-circle pupil, and a quantitative high resolution phase image is obtained after a deconvolution process with a minimum of two phase gradient images. Here, we introduce PMDPC quantitative phase image reconstruction algorithm and realize it experimentally in a 4f system with an SLM placed at the pupil plane. In our current experimental setup with the numerical aperture of 0.36, we obtain a quantitative phase image with a resolution of 1.73\u03bcm after computationally removing system aberrations and refocusing. We also extend the depth of field digitally by 20 times to \u00b150\u03bcm with a resolution of 1.76\u03bcm.", "doi": "10.1364/OE.24.025345", "pmcid": "PMC5234501", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2016-10-31", "series_number": "22", "volume": "24", "issue": "22", "pages": "25345-25361" }, { "id": "authors:zzsww-f2n17", "collection": "authors", "collection_id": "zzsww-f2n17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161010-124426959", "type": "article", "title": "Glare suppression by coherence gated negation", "author": [ { "family_name": "Zhou", "given_name": "Edward Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Shibukawa", "given_name": "Atsushi", "clpid": "Shibukawa-Atsushi" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Imaging of a weak target hidden behind a scattering medium can be significantly confounded by glare. We report a method, termed coherence gated negation (CGN), that uses destructive optical interference to suppress glare and allow improved imaging of a weak target. As a demonstration, we show that by permuting through a set range of amplitude and phase values for a reference beam interfering with the optical field from the glare and target reflection, we can suppress glare by an order of magnitude, even when the optical wavefront is highly disordered. This strategy significantly departs from conventional coherence gating methods in that CGN actively \"gates out\" the unwanted optical contributions while conventional methods \"gate in\" the target optical signal. We further show that the CGN method can outperform conventional coherence gating image quality in certain scenarios by more effectively rejecting unwanted optical contributions.", "doi": "10.1364/OPTICA.3.001107", "pmcid": "PMC5509221", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2016-10", "series_number": "10", "volume": "3", "issue": "10", "pages": "1107-1113" }, { "id": "authors:je69j-s5c48", "collection": "authors", "collection_id": "je69j-s5c48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160801-135931634", "type": "article", "title": "Incubator embedded cell culture imaging system (EmSight) based on Fourier ptychographic microscopy", "author": [ { "family_name": "Kim", "given_name": "Jinho", "orcid": "0000-0001-8711-960X", "clpid": "Kim-Jinho" }, { "family_name": "Henley", "given_name": "Beverley M.", "orcid": "0000-0002-6211-2433", "clpid": "Henley-Beverley-M" }, { "family_name": "Kim", "given_name": "Charlene H.", "clpid": "Kim-Charlene-H" }, { "family_name": "Lester", "given_name": "Henry A.", "orcid": "0000-0002-5470-5255", "clpid": "Lester-H-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Multi-day tracking of cells in culture systems can provide valuable information in bioscience experiments. We report the development of a cell culture imaging system, named EmSight, which incorporates multiple compact Fourier ptychographic microscopes with a standard multiwell imaging plate. The system is housed in an incubator and presently incorporates six microscopes. By using the same low magnification objective lenses as the objective and the tube lens, the EmSight is configured as a 1:1 imaging system that, providing large field-of-view (FOV) imaging onto a low-cost CMOS imaging sensor. The EmSight improves the image resolution by capturing a series of images of the sample at varying illumination angles; the instrument reconstructs a higher-resolution image by using the iterative Fourier ptychographic algorithm. In addition to providing high-resolution brightfield and phase imaging, the EmSight is also capable of fluorescence imaging at the native resolution of the objectives. We characterized the system using a phase Siemens star target, and show four-fold improved coherent resolution (synthetic NA of 0.42) and a depth of field of 0.2 mm. To conduct live, long-term dopaminergic neuron imaging, we cultured ventral midbrain from mice driving eGFP from the tyrosine hydroxylase promoter. The EmSight system tracks movements of dopaminergic neurons over a 21 day period.", "doi": "10.1364/BOE.7.003097", "pmcid": "PMC4986817", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2016-08-01", "series_number": "8", "volume": "7", "issue": "8", "pages": "3097-3110" }, { "id": "authors:1hh0s-eee29", "collection": "authors", "collection_id": "1hh0s-eee29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160930-124858247", "type": "article", "title": "Diffraction tomography with Fourier ptychography", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first captures a sequence of intensity-only images of a sample under angularly varying illumination. Then, using principles from ptychography and diffraction tomography, it computationally solves for the sample structure in three dimensions. The experimental microscope demonstrates a lateral spatial resolution of 0.39 \u03bcm and an axial resolution of 3.7 \u03bcm at the Nyquist\u2013Shannon sampling limit (0.54 and 5.0 \u03bcm at the Sparrow limit, respectively) across a total imaging depth of 110 \u03bcm. Unlike competing methods, this technique quantitatively measures the volumetric refractive index of primarily transparent and contiguous sample features without the need for interferometry or any moving parts. Wide field-of-view reconstructions of thick biological specimens suggest potential applications in pathology and developmental biology.", "doi": "10.1364/OPTICA.3.000827", "pmcid": "PMC5521281", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2016-08", "series_number": "8", "volume": "3", "issue": "8", "pages": "827-835" }, { "id": "authors:n2zb4-bkb68", "collection": "authors", "collection_id": "n2zb4-bkb68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160729-151210898", "type": "article", "title": "Aperture scanning Fourier ptychographic microscopy", "author": [ { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fourier ptychographic microscopy (FPM) is implemented through aperture scanning by an LCOS spatial light modulator at the back focal plane of the objective lens. This FPM configuration enables the capturing of the complex scattered field for a 3D sample both in the transmissive mode and the reflective mode. We further show that by combining with the compressive sensing theory, the reconstructed 2D complex scattered field can be used to recover the 3D sample scattering density. This implementation expands the scope of application for FPM and can be beneficial for areas such as tissue imaging and wafer inspection.", "doi": "10.1364/BOE.7.003140", "pmcid": "PMC4986821", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2016-08", "series_number": "8", "volume": "7", "issue": "8", "pages": "3140-3150" }, { "id": "authors:rvzpp-abq39", "collection": "authors", "collection_id": "rvzpp-abq39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160620-080444939", "type": "article", "title": "Fourier ptychographic reconstruction using Poisson maximum likelihood and truncated Wirtinger gradient", "author": [ { "family_name": "Bian", "given_name": "Liheng", "orcid": "0000-0002-8016-0375", "clpid": "Bian-Liheng" }, { "family_name": "Suo", "given_name": "Jinli", "clpid": "Suo-Jinli" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Chen", "given_name": "Feng", "clpid": "Chen-Feng" }, { "family_name": "Dai", "given_name": "Qionghai", "orcid": "0000-0001-7043-3061", "clpid": "Dai-Qionghai" } ], "abstract": "Fourier ptychographic microscopy (FPM) is a novel computational coherent imaging technique for high space-bandwidth product imaging. Mathematically, Fourier ptychographic (FP) reconstruction can be implemented as a phase retrieval optimization process, in which we only obtain low resolution intensity images corresponding to the sub-bands of the sample's high resolution (HR) spatial spectrum, and aim to retrieve the complex HR spectrum. In real setups, the measurements always suffer from various degenerations such as Gaussian noise, Poisson noise, speckle noise and pupil location error, which would largely degrade the reconstruction. To efficiently address these degenerations, we propose a novel FP reconstruction method under a gradient descent optimization framework in this paper. The technique utilizes Poisson maximum likelihood for better signal modeling, and truncated Wirtinger gradient for effective error removal. Results on both simulated data and real data captured using our laser-illuminated FPM setup show that the proposed method outperforms other state-of-the-art algorithms. Also, we have released our source code for non-commercial use.", "doi": "10.1038/srep27384", "pmcid": "PMC4901273", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2016-06-10", "volume": "6", "pages": "Art. No. 27384" }, { "id": "authors:msy6h-5ha02", "collection": "authors", "collection_id": "msy6h-5ha02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160804-095326080", "type": "book_section", "title": "Simultaneous fluorescence and high-resolution bright-field imaging with aberration correction over a wide field-of-view with Fourier ptychographic microscopy (FPM)", "book_title": "Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIII", "author": [ { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Brown", "given_name": "Thomas G.", "clpid": "Brown-T-G" }, { "family_name": "Cogswell", "given_name": "Carol J.", "clpid": "Cogswell-C-J" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-Tony" } ], "abstract": "We present a method to acquire both fluorescence and high-resolution bright-field images with correction for the spatially varying aberrations over a microscope's wide field-of-view (FOV). First, the procedure applies Fourier ptychographic microscopy (FPM) to retrieve the amplitude and phase of a sample, at a resolution that significantly exceeds the cutoff frequency of the microscope objective lens. At the same time, FPM algorithm is able to leverage on the redundancy within the set of acquired FPM bright-field images to estimate the microscope aberrations, which usually deteriorate in regions further away from the FOV's center. Second, the procedure acquires a raw wide-FOV fluorescence image within the same setup. Lack of moving parts allows us to use the FPM-estimated aberration map to computationally correct for the aberrations in the fluorescence image through deconvolution. Overlaying the aberration-corrected fluorescence image on top of the high-resolution bright-field image can be done with accurate spatial correspondence. This can provide means to identifying fluorescent regions of interest within the context of the sample's bright-field information. An experimental demonstration successfully improves the bright-field resolution of fixed, stained and fluorescently tagged HeLa cells by a factor of 4.9, and reduces the error caused by aberrations in a fluorescence image by 31%, over a field of view of 6.2 mm by 9.3 mm. For optimal deconvolution, we show the fluorescence image needs to have a signal-to-noise ratio of ~18.", "doi": "10.1117/12.2211974", "isbn": "978-1-62841-947-4", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2016-04-27", "pages": "Art. No. 97130I" }, { "id": "authors:1era7-0kz80", "collection": "authors", "collection_id": "1era7-0kz80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170109-143310163", "type": "book_section", "title": "Focusing light in deep tissue with time-reversed ultrasound microbubble encoded light (Conference Presentation)", "book_title": "Adaptive Optics and Wavefront Control for Biological Systems II", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Bifano", "given_name": "Thomas G.", "clpid": "Bifano-T-G" }, { "family_name": "Kubby", "given_name": "Joel", "clpid": "Kubby-J" }, { "family_name": "Gigan", "given_name": "Sylvain", "clpid": "Gigan-S" } ], "abstract": "Optical scattering of biological tissue limits the penetration depth of conventional optical techniques, which rely on the detection of ballistic photons. Recent developed optical phase conjugation (OPC) technique breaks through this depth limit by shaping an optical wavefront that can \"undo\" the optical scattering. Assisted with an ultrasound focus, this technique enables optical focusing inside biological tissue in a freely addressable fashion. However, ultrasound modulation efficiency is low and the focusing resolution is limited by the ultrasound. Here we present a new technique, time-reversed ultrasound microbubble encoded (TRUME) optical focusing, which is able to provide high focusing efficiency and sub-ultrasound resolution. This technique achieves the wavefront solution by taking the difference of the optical fields captured outside the sample before and after ultrasound-driven microbubble destruction. A conjugated wavefront was then reconstructed and sent back to the sample to form a focus at the site of microbubble destruction. We experimentally demonstrate that a focus with ~2 um size was formed through a 2-mm thick biological tissue using this method. While the size the microbubble sets the resolution of an individual focus, the scale of the ultrasound focus limits the focusing addressability of this technique. Importantly, by utilizing the nonlinear destruction of microbubbles, the TRUME technique breaks the addressable focus resolution barrier imposed by the ultrasound focus. We experimentally demonstrate a 2-fold improvement in addressability using this effect. Since microbubbles are widely used as ultrasound contrast agents in human, this technique provides a promising solution for focusing light deep inside biological tissue.", "doi": "10.1117/12.2212042", "isbn": "978-1-62841-951-1", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2016-04-27", "pages": "Art. No. 97171K" }, { "id": "authors:fgdfm-fys41", "collection": "authors", "collection_id": "fgdfm-fys41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160728-145043078", "type": "book_section", "title": "The relationship between decorrelation time and sample thickness in acute rat brain tissue slices (Conference Presentation)", "book_title": "Dynamics and Fluctuations in Biomedical Photonics XIII", "author": [ { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-J-H" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Larin", "given_name": "Kirill V.", "clpid": "Larin-K-V" }, { "family_name": "Leahy", "given_name": "Martin J.", "clpid": "Leahy-M-J" }, { "family_name": "Wang", "given_name": "Ruikang K.", "clpid": "Wang-Ruikang-K" } ], "abstract": "The optical opacity of biological tissue has long been a challenge in biomedical optics due to the strong scattering\nnature of tissue in the optical regime. While most conventional optical techniques attempt to gate out multiply\nscattered light and use only unscattered light, new approaches in the field of wavefront shaping exploit the time\nreversible symmetry of optical scattering in order to focus light inside or through scattering media. While these\napproaches have been demonstrated effectively on static samples, it has proven difficult to apply them to dynamic\nbiological samples since even small changes in the relative positions of the scatterers within will cause the time\nsymmetry that wavefront shaping relies upon to decorrelate. In this paper we investigate the decorrelation curves of\nacute rat brain slices for thicknesses in the range 1-3 mm (1/e decorrelation time on the order of seconds) using\nmulti-speckle diffusing wave spectroscopy (MSDWS) and compare the results with theoretical predictions. The\nresults of this study demonstrate that the 1/L^2 relationship between decorrelation time and thickness predicted by\ndiffusing wave spectroscopy provides a good rule of thumb for estimating how the decorrelation of a sample will\nchange with increasing thickness. Understanding this relationship will provide insight to guide the future\ndevelopment of biophotonic wavefront shaping tools by giving an estimate of how fast wavefront shaping systems\nneed to operate to overcome the dynamic nature of biological samples.", "doi": "10.1117/12.2208972", "isbn": "978-1-62841-941-2", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2016-04-26", "pages": "Art. No. 97070U" }, { "id": "authors:tkpvd-7r641", "collection": "authors", "collection_id": "tkpvd-7r641", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160429-135633578", "type": "article", "title": "Optical phase conjugation assisted scattering lens: variable focusing and 3D patterning", "author": [ { "family_name": "Ryu", "given_name": "Jihee", "orcid": "0000-0003-2444-4493", "clpid": "Ryu-Jihee" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Eom", "given_name": "Tae Joong", "orcid": "0000-0003-0556-4027", "clpid": "Eom-Tae-Joong" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Chung", "given_name": "Euiheon", "orcid": "0000-0002-3326-6927", "clpid": "Chung-Euiheon" } ], "abstract": "Variable light focusing is the ability to flexibly select the focal distance of a lens. This feature presents technical challenges, but is significant for optical interrogation of three-dimensional objects. Numerous lens designs have been proposed to provide flexible light focusing, including zoom, fluid, and liquid-crystal lenses. Although these lenses are useful for macroscale applications, they have limited utility in micron-scale applications due to restricted modulation range and exacting requirements for fabrication and control. Here, we present a holographic focusing method that enables variable light focusing without any physical modification to the lens element. In this method, a scattering layer couples low-angle (transverse wave vector) components into a full angular spectrum, and a digital optical phase conjugation (DOPC) system characterizes and plays back the wavefront that focuses through the scattering layer. We demonstrate micron-scale light focusing and patterning over a wide range of focal distances of 22\u201351\u2009mm. The interferometric nature of the focusing scheme also enables an aberration-free scattering lens. The proposed method provides a unique variable focusing capability for imaging thick specimens or selective photoactivation of neuronal networks.", "doi": "10.1038/srep23494", "pmcid": "PMC4877672", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2016-04-06", "volume": "6", "pages": "Art. No. 23494" }, { "id": "authors:awp3m-dpp59", "collection": "authors", "collection_id": "awp3m-dpp59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160218-123702274", "type": "article", "title": "Analyzing the relationship between decorrelation time and tissue thickness in acute rat brain slices using multispeckle diffusing wave spectroscopy", "author": [ { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Novel techniques in the field of wavefront shaping have enabled light to be focused deep inside or through scattering media such as biological tissue. However, most of these demonstrations have been limited to thin, static samples since these techniques are very sensitive to changes in the arrangement of the scatterers within. As the samples of interest get thicker, the influence of the dynamic nature of the sample becomes even more pronounced and the window of time in which the wavefront solutions remain valid shrinks further. In this paper, we examine the time scales upon which this decorrelation happens in acute rat brain slices via multispeckle diffusing wave spectroscopy and investigate the relationship between this decorrelation time and the thickness of the sample using diffusing wave spectroscopy theory and Monte Carlo photon transport simulation.", "doi": "10.1364/JOSAA.33.000270", "pmcid": "PMC4783160", "issn": "1084-7529", "publisher": "Optical Society of America", "publication": "Journal of the Optical Society of America A", "publication_date": "2016-02-01", "series_number": "2", "volume": "33", "issue": "2", "pages": "270-275" }, { "id": "authors:ev2ma-6zj91", "collection": "authors", "collection_id": "ev2ma-6zj91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160225-134254700", "type": "article", "title": "Wide field-of-view fluorescence image deconvolution with aberration-estimation from Fourier ptychography", "author": [ { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Kim", "given_name": "Jinho", "orcid": "0000-0001-8711-960X", "clpid": "Kim-Jinho" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "This paper presents a method to simultaneously acquire an aberration-corrected, wide field-of-view fluorescence image and a high-resolution coherent bright-field image using a computational microscopy method. First, the procedure applies Fourier ptychographic microscopy (FPM) to retrieve the amplitude and phase of a sample, at a resolution that significantly exceeds the cutoff spatial frequency of the microscope objective lens. At the same time, redundancy within the set of acquired FPM bright-field images offers a means to estimate microscope aberrations. Second, the procedure acquires an aberrated fluorescence image, and computationally improves its resolution through deconvolution with the estimated aberration map. An experimental demonstration successfully improves the bright-field resolution of fixed, stained and fluorescently tagged HeLa cells by a factor of 4.9, and reduces the error caused by aberrations in a fluorescence image by up to 31%, over a field of view of 6.2 mm by 9.3 mm. For optimal deconvolution, we show the fluorescence image needs to have a signal-to-noise ratio of at least ~18.", "doi": "10.1364/BOE.7.000352", "pmcid": "PMC4771454", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2016-02-01", "series_number": "2", "volume": "7", "issue": "2", "pages": "352-368" }, { "id": "authors:0b0cg-rkc20", "collection": "authors", "collection_id": "0b0cg-rkc20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-092710093", "type": "article", "title": "Standardizing the resolution claims for coherent microscopy", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Heintzmann", "given_name": "Rainer", "clpid": "Heintzmann-R" }, { "family_name": "Popescu", "given_name": "Gabriel", "clpid": "Popescu-G" }, { "family_name": "Waller", "given_name": "Laura", "clpid": "Waller-L" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The definition and reporting of spatial resolution for coherent imaging methods varies widely in the imaging community. We advocate the use of a standard spoke-pattern imaging target and the mandatory inclusion of information about underlying a priori assumptions.", "doi": "10.1038/nphoton.2015.279", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2016-02", "series_number": "2", "volume": "10", "issue": "2", "pages": "68-71" }, { "id": "authors:kxmha-27510", "collection": "authors", "collection_id": "kxmha-27510", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151124-095652864", "type": "article", "title": "Optical focusing inside scattering media with time-reversed ultrasound microbubble encoded light", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Focusing light inside scattering media in a freely addressable fashion is challenging, as the wavefront of the scattered light is highly disordered. Recently developed ultrasound-guided wavefront shaping methods are addressing this challenge, albeit with relatively low modulation efficiency and resolution limitations. In this paper, we present a new technique, time-reversed ultrasound microbubble encoded (TRUME) optical focusing, which can focus light with improved efficiency and sub-ultrasound wavelength resolution. This method ultrasonically destroys microbubbles, and measures the wavefront change to compute and render a suitable time-reversed wavefront solution for focusing. We demonstrate that the TRUME technique can create an optical focus at the site of bubble destruction with a size of ~2\u2009\u03bcm. We further demonstrate a twofold enhancement in addressable focus resolution in a microbubble aggregate target by exploiting the nonlinear pressure-to-destruction response of the microbubbles. The reported technique provides a deep tissue-focusing solution with high efficiency, resolution, and specificity.", "doi": "10.1038/ncomms9968", "pmcid": "PMC4673873", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2015-11-24", "volume": "6", "pages": "Art. No. 8968" }, { "id": "authors:a8grg-t1m64", "collection": "authors", "collection_id": "a8grg-t1m64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201019-081605033", "type": "book_section", "title": "Fluorescence chip-scale microscope for point of care detection and analysis", "author": [ { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "[no abstract]", "publisher": "Curran Associates", "publication_date": "2015-10" }, { "id": "authors:max14-4va71", "collection": "authors", "collection_id": "max14-4va71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150909-110929870", "type": "article", "title": "Guidestar-assisted wavefront-shaping methods for focusing light into biological tissue", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In the field of biomedical optics, optical scattering has traditionally limited the range of imaging within tissue to a depth of one millimetre. A recently developed class of wavefront-shaping techniques now aims to overcome this limit and achieve diffraction-limited control of light beyond one centimetre. By manipulating the spatial profile of an optical field before it enters a scattering medium, it is possible to create a micrometre-scale focal spot deep within tissue. To successfully operate in vivo, these wavefront-shaping techniques typically require feedback from within the biological sample. This Review summarizes recently developed 'guidestar' mechanisms that provide feedback for intra-tissue focusing. Potential applications of guidestar-assisted focusing include optogenetic control over neurons, targeted photodynamic therapy and deep tissue imaging.", "doi": "10.1038/NPHOTON.2015.140", "pmcid": "PMC4900467", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2015-09", "series_number": "9", "volume": "9", "issue": "9", "pages": "563-571" }, { "id": "authors:yjxzc-ca061", "collection": "authors", "collection_id": "yjxzc-ca061", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150924-074000986", "type": "article", "title": "Focusing through dynamic tissue with millisecond digital optical phase conjugation", "author": [ { "family_name": "Wang", "given_name": "Daifa", "orcid": "0000-0003-3977-3206", "clpid": "Wang-Daifa" }, { "family_name": "Zhou", "given_name": "Edward Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Brake", "given_name": "Joshua", "orcid": "0000-0002-5113-6886", "clpid": "Brake-Joshua-H" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Digital optical phase conjugation (DOPC) is a new technique employed in wavefront shaping and phase conjugation for focusing light through or within scattering media such as biological tissues. DOPC is particularly attractive as it intrinsically achieves a high fluence reflectivity in comparison to nonlinear optical approaches. However, the slow refresh rate of liquid crystal spatial light modulators and limitations imposed by computer data transfer speeds have thus far made it difficult for DOPC to achieve a playback latency of shorter than \u223c200\u2009\u2009ms and, therefore, prevented DOPC from being practically applied to thick living samples. In this paper, we report a novel DOPC system that is capable of 5.3 ms playback latency. This speed improvement of almost 2 orders of magnitude is achieved by using a digital micromirror device, field programmable gate array (FPGA) processing, and a single-shot binary phase retrieval technique. With this system, we are able to focus through 2.3 mm living mouse skin with blood flowing through it (decorrelation time \u223c30\u2009\u2009ms) and demonstrate that the focus can be maintained indefinitely\u2014an important technological milestone that has not been previously reported, to the best of our knowledge.", "doi": "10.1364/OPTICA.2.000728", "pmcid": "PMC4677392", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2015-08-20", "series_number": "8", "volume": "2", "issue": "8", "pages": "728-735" }, { "id": "authors:6erj6-gcq91", "collection": "authors", "collection_id": "6erj6-gcq91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150518-120647295", "type": "article", "title": "Translation correlations in anisotropically scattering media", "author": [ { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Vellekoop", "given_name": "Ivo M.", "clpid": "Vellekoop-I-M" }, { "family_name": "Papadopoulos", "given_name": "Ioannis N.", "clpid": "Papadopoulos-I-N" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Controlling light propagation across scattering media by wavefront shaping holds great promise for a wide range of communications and imaging applications. But, finding the right shape for the wavefront is a challenge when the mapping between input and output scattered wavefronts (that is, the transmission matrix) is not known. Correlations in transmission matrices, especially the so-called memory effect, have been exploited to address this limitation. However, the traditional memory effect applies to thin scattering layers at a distance from the target, which precludes its use within thick scattering media, such as fog and biological tissue. Here, we theoretically predict and experimentally verify new transmission matrix correlations within thick anisotropically scattering media, with important implications for biomedical imaging and adaptive optics.", "doi": "10.1038/NPHYS3373", "issn": "1745-2473", "publisher": "Nature Publishing Group", "publication": "Nature Physics", "publication_date": "2015-08", "series_number": "8", "volume": "11", "issue": "8", "pages": "684-689" }, { "id": "authors:05sd6-3fh97", "collection": "authors", "collection_id": "05sd6-3fh97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150813-123734254", "type": "article", "title": "Counting White Blood Cells from a Blood Smear Using Fourier Ptychographic Microscopy", "author": [ { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Kulkarni", "given_name": "Rajan P.", "clpid": "Kulkarni-R-P" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "White blood cell (WBC) count is a valuable metric for assisting with diagnosis or prognosis of various diseases such as coronary heart disease, type 2 diabetes, or infection. Counting WBCs can be done either manually or automatically. Automatic methods are capable of counting a large number of cells to give a statistically more accurate reading of the WBC count of a sample, but the specialized equipment tends to be expensive. Manual methods are inexpensive since they only involve a conventional light microscope setup. However, it is more laborious and error-prone because the small field-of-view (FOV) of the microscope necessitates mechanical scanning of a specimen for counting an adequate number of WBCs. Here, we investigate the use of Fourier ptychographic microscopy (FPM) to bypass these issues of the manual methods. With a 2x objective, FPM can provide a FOV of 120 mm^2 with enhanced resolution comparable to that of a 20x objective, which is adequate for non-differentially counting WBCs in just one FOV. A specialist was able to count the WBCs in FPM images with 100% accuracy compared to the count as determined from conventional microscope images. An automatic counting algorithm was also developed to identify WBCs from FPM's captured images with 95% accuracy, paving the way for a cost-effective WBC counting setup with the advantages of both the automatic and manual counting methods.", "doi": "10.1371/journal.pone.0133489", "pmcid": "PMC4506059", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLOS ONE", "publication_date": "2015-07-17", "series_number": "7", "volume": "10", "issue": "7", "pages": "Art. No. e0133489" }, { "id": "authors:chfmc-83e85", "collection": "authors", "collection_id": "chfmc-83e85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141211-154256164", "type": "article", "title": "Digital pathology with Fourier ptychography", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Willems", "given_name": "Phil", "clpid": "Willems-P" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fourier ptychographic microscopy (FPM) is a recently introduced method of acquiring high-resolution, wide field of view (FOV) giga-pixel histology images. The FPM procedure first acquires a sequence of low-resolution images of a sample under variable-angle illumination. It then combines these images using a novel phase retrieval algorithm to improve the employed microscope's resolution beyond its conventional limit. Here, we first describe how FPM's resolution improvement can enhance wide FOV histology imaging. Second, we show that FPM also records a thin sample's optical phase, which can help pathologists digitally extract as much information as possible from a given histology slide.", "doi": "10.1016/j.compmedimag.2014.11.005", "pmcid": "PMC4369155", "issn": "0895-6111", "publisher": "Elsevier", "publication": "Computerized Medical Imaging and Graphics", "publication_date": "2015-06", "volume": "42", "pages": "38-43" }, { "id": "authors:kkrzr-gnz69", "collection": "authors", "collection_id": "kkrzr-gnz69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150619-160809918", "type": "article", "title": "Solving ptychography with a convex relaxation", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Chen", "given_name": "Richard Y.", "clpid": "Chen-Richard-Y" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Ames", "given_name": "Brendan", "clpid": "Ames-Brendan-P-W" }, { "family_name": "Tropp", "given_name": "Joel A.", "orcid": "0000-0003-1024-1791", "clpid": "Tropp-J-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Ptychography is a powerful computational imaging technique that transforms a collection of low-resolution images into a high-resolution sample reconstruction. Unfortunately, algorithms that currently solve this reconstruction problem lack stability, robustness, and theoretical guarantees. Recently, convex optimization algorithms have improved the accuracy and reliability of several related reconstruction efforts. This paper proposes a convex formulation of the ptychography problem. This formulation has no local minima, it can be solved using a wide range of algorithms, it can incorporate appropriate noise models, and it can include multiple a priori constraints. The paper considers a specific algorithm, based on low-rank factorization, whose runtime and memory usage are near-linear in the size of the output image. Experiments demonstrate that this approach offers a 25% lower background variance on average than alternating projections, the ptychographic reconstruction algorithm that is currently in widespread use.", "doi": "10.1088/1367-2630/17/5/053044", "pmcid": "PMC4486359", "issn": "1367-2630", "publisher": "IOP", "publication": "New Journal of Physics", "publication_date": "2015-05-27", "series_number": "5", "volume": "17", "issue": "5", "pages": "Art. No. 053044" }, { "id": "authors:6zf4t-qbz79", "collection": "authors", "collection_id": "6zf4t-qbz79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150720-103926731", "type": "book_section", "title": "Physically secure and fully reconfigurable data storage using optical scattering", "book_title": "2015 IEEE International Symposium on Hardware Oriented Security and Trust (HOST)", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Assawaworrarit", "given_name": "Sid", "clpid": "Assawaworrarit-S" }, { "family_name": "Ruhrmair", "given_name": "Ulrich", "clpid": "Ruhrmair-U" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "This paper presents an optical method of storing random cryptographic keys within a reconfigurable volume of polymer-dispersed liquid crystal (PDLC). We suggest a PDLC-based device that functions as an integrated optical physical unclonable function (PUF). Our device can selectively access a dense set (up to 10 Gb/mm^3 in theory) of non-electronically saved random bits. Furthermore, this optical PUF can fully erase and transform these bits into a new random configuration in less than one second, via a simple electrical signal. When a short voltage spike is applied across the PDLC film interface, its optical scattering potential completely decorrelates. We confirm this phenomenon with detailed experiments on a proof-of-concept device, thereby suggesting the security use of a new class of optical materials as (i) securely and efficiently reconfigurable PUFs, and (ii) an erasable storage medium for random cryptographic keys. Our work can eventually help address the challenge of quickly and completely erasing sensitive digital electronic memory and/or key material. It also establishes a new and hopefully fruitful connection between security questions and the material sciences.", "doi": "10.1109/HST.2015.7140255", "isbn": "978-1-4673-7420-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-05", "pages": "157-162" }, { "id": "authors:k4mbn-q2w02", "collection": "authors", "collection_id": "k4mbn-q2w02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150410-093758340", "type": "article", "title": "Optofluidic ultrahigh-throughput detection of fluorescent drops", "author": [ { "family_name": "Kim", "given_name": "Minkyu", "clpid": "Kim-Minkyu" }, { "family_name": "Pan", "given_name": "Ming", "clpid": "Pan-Ming" }, { "family_name": "Gai", "given_name": "Ya", "clpid": "Gai-Ya" }, { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Tang", "given_name": "Sindy K. Y.", "clpid": "Tang-Sindy-K-Y" } ], "abstract": "This paper describes an optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254000 drops per second. To our knowledge, this rate is the highest interrogation rate published thus far. Our device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view in conventional microscopy. The interrogation rate of our device is currently limited by the acquisition speed of CMOS sensor, and is expected to increase further as high-speed sensors become increasingly available.", "doi": "10.1039/c4lc01465k", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2015-03-21", "series_number": "6", "volume": "15", "issue": "6", "pages": "1417-1423" }, { "id": "authors:x7g88-dx609", "collection": "authors", "collection_id": "x7g88-dx609", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150323-111739047", "type": "article", "title": "High numerical aperture Fourier ptychography: principle, implementation and characterization", "author": [ { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-Roarke" }, { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fourier ptychography (FP) utilizes illumination control and computational post-processing to increase the resolution of bright-field microscopes. In effect, FP extends the fixed numerical aperture (NA) of an objective lens to form a larger synthetic system NA. Here, we build an FP microscope (FPM) using a 40X 0.75NA objective lens to synthesize a system NA of 1.45. This system achieved a two-slit resolution of 335 nm at a wavelength of 632 nm. This resolution closely adheres to theoretical prediction and is comparable to the measured resolution (315 nm) associated with a standard, commercially available 1.25 NA oil immersion microscope. Our work indicates that Fourier ptychography is an attractive method to improve the resolution-versus-NA performance, increase the working distance, and enlarge the field-of-view of high-resolution bright-field microscopes by employing lower NA objectives.", "doi": "10.1364/OE.23.003472", "pmcid": "PMC5802253", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2015-02-09", "series_number": "3", "volume": "23", "issue": "3", "pages": "3472-3491" }, { "id": "authors:1j4zm-61e16", "collection": "authors", "collection_id": "1j4zm-61e16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150313-124847798", "type": "article", "title": "A wide field-of-view scanning endoscope for whole anal canal imaging", "author": [ { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Huangfu", "given_name": "Jiangtao", "clpid": "Huangfu-Jiangtao" }, { "family_name": "Lai", "given_name": "Lily L.", "clpid": "Lai-Lily-L" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a novel wide field-of-view (FOV) scanning endoscope, the AnCam, which is based on contact image sensor (CIS) technology used in commercialized business card scanners. The AnCam can capture the whole image of the anal canal within 10 seconds with a resolution of 89 \u03bcm, a maximum FOV of 100 mm \u00d7 120 mm, and a depth-of-field (DOF) of 0.65 mm at 5.9 line pairs per mm (lp/mm). We demonstrate the performance of the AnCam by imaging the entire anal canal of pigs and tracking the dynamics of acetowhite testing. We believe the AnCam can potentially be a simple and convenient solution for screening of the anal canal for dysplasia and for surveillance in patients following treatment for anal cancer.", "doi": "10.1364/BOE.6.000607", "pmcid": "PMC4354600", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2015-02-01", "series_number": "2", "volume": "6", "issue": "2", "pages": "607-614" }, { "id": "authors:2rdt6-4w497", "collection": "authors", "collection_id": "2rdt6-4w497", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150206-114208650", "type": "article", "title": "Relation between speckle decorrelation and optical phase conjugation (OPC)-based turbidity suppression through dynamic scattering media: a study on in vivo mouse skin", "author": [ { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Vellekoop", "given_name": "Ivo M.", "orcid": "0000-0002-9674-7592", "clpid": "Vellekoop-I-M" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "orcid": "0000-0002-8570-3869", "clpid": "Judkewitz-B" }, { "family_name": "Chung", "given_name": "Euiheon", "orcid": "0000-0002-3326-6927", "clpid": "Chung-Euiheon" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Light scattering in biological tissue significantly limits the accessible depth for localized optical interrogation and deep-tissue optical imaging. This challenge can be overcome by exploiting the time-reversal property of optical phase conjugation (OPC) to reverse multiple scattering events or suppress turbidity. However, in living tissue, scatterers are highly movable and the movement can disrupt time-reversal symmetry when there is a latency in the OPC playback. In this paper, we show that the motion-induced degradation of the OPC turbidity-suppression effect through a dynamic scattering medium shares the same decorrelation time constant as that determined from speckle intensity autocorrelation \u2013 a popular conventional measure of scatterer movement. We investigated this decorrelation characteristic time through a 1.5-mm-thick dorsal skin flap of a living mouse and found that it ranges from 50 ms to 2.5 s depending on the level of immobilization. This study provides information on relevant time scales for applying OPC to living tissues.", "doi": "10.1364/BOE.6.000072", "pmcid": "PMC4317115", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2015-01-01", "series_number": "1", "volume": "6", "issue": "1", "pages": "72-85" }, { "id": "authors:2tynn-xe535", "collection": "authors", "collection_id": "2tynn-xe535", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150108-153546749", "type": "article", "title": "Iterative Time-Reversed Ultrasonically Encoded Light Focusing in Backscattering Mode", "author": [ { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "orcid": "0000-0002-8570-3869", "clpid": "Judkewitz-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The Time-Reversed Ultrasound-Encoded (TRUE) light technique enables noninvasive focusing deep inside scattering media. However, the time-reversal procedure usually has a low signal-to-noise ratio because the intensity of ultrasound-encoded light is intrinsically low. Consequently, the contrast and resolution of TRUE focus is far from ideal, especially in the backscattering geometry, which is more practical in many biomedical applications. To improve the light intensity and resolution of TRUE focus, we developed an iterative TRUE (iTRUE) light focusing technique that employs the TRUE focus itself as a signal source (rather than diffused light) for subsequent TRUE procedures. Importantly, this iTRUE technique enables light focusing in backscattering mode. Here, we demonstrate the concept by focusing light in between scattering layers in a backscattering configuration and show that the light intensity at the focus is progressively enhanced by a factor of ~20. By scanning across a fluorescent bead between these two scattering layers, the focusing resolution in the ultrasound axial and lateral directions was improved ~2-fold and ~3-fold, respectively. We further explored the application of iTRUE in biological samples by focusing light between 1 mm thick chicken tissue and cartilage, and light intensity enhancements of the same order were also observed.", "doi": "10.1038/srep07156", "pmcid": "PMC4239564", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2014-11-21", "series_number": "11", "volume": "4", "issue": "11", "pages": "Art. No. 7156" }, { "id": "authors:jsbhp-08337", "collection": "authors", "collection_id": "jsbhp-08337", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140811-084244344", "type": "article", "title": "Microfluidic-integrated laser-controlled microactuators with on-chip microscopy imaging functionality", "author": [ { "family_name": "Jung", "given_name": "Jae Hee", "clpid": "Jung-Jae-Hee" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The fabrication of a novel microfluidic system, integrated with a set of laser-controlled microactuators on an ePetri on-chip microscopy platform, is presented in this paper. In the fully integrated microfluidic system, a set of novel thermally actuated paraffin-based microactuators, precisely controlled by programmed laser optics, was developed to regulate flow and to provide pumping of liquid solutions without external connections. The microfluidic chip was fabricated on a complementary metal\u2013oxide\u2013semiconductor (CMOS)-imaging sensor chip on an ePetri platform; this configuration provided real-time, wide field-of-view, high-resolution imaging using a sub-pixel sweeping microscopy technique. The system of microactuators, which consisted of microvalves and a micropump, operated well in the microfluidic channel with a focused near-infrared laser beam providing the actuation control. As a demonstration, we used our prototype to assess cell\u2013drug interactions and to monitor cell growth directly within an incubator in real time. The powerful combination of laser-actuated microfluidics and chip-scale microscopy techniques represents a significant step forward in terms of a simple, robust, high-throughput, and highly compact analysis system for biomedical and bioscience applications.", "doi": "10.1039/C4LC00790E", "pmcid": "PMC4153594", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2014-10-07", "series_number": "19", "volume": "14", "issue": "19", "pages": "3781-3789" }, { "id": "authors:qf64s-19824", "collection": "authors", "collection_id": "qf64s-19824", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141106-135056845", "type": "article", "title": "Overlapped Fourier coding for optical aberration removal", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present an imaging procedure that simultaneously optimizes a camera's resolution and retrieves a sample's phase over a sequence of snapshots. The technique, termed overlapped Fourier coding (OFC), first digitally pans a small aperture across a camera's pupil plane with a spatial light modulator. At each aperture location, a unique image is acquired. The OFC algorithm then fuses these low-resolution images into a full-resolution estimate of the complex optical field incident upon the detector. Simultaneously, the algorithm utilizes redundancies within the acquired dataset to computationally estimate and remove unknown optical aberrations and system misalignments via simulated annealing. The result is an imaging system that can computationally overcome its optical imperfections to offer enhanced resolution, at the expense of taking multiple snapshots over time.", "doi": "10.1364/OE.22.024062", "pmcid": "PMC4247187", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-10-06", "series_number": "20", "volume": "22", "issue": "20", "pages": "24062-24080" }, { "id": "authors:k2q1k-1we42", "collection": "authors", "collection_id": "k2q1k-1we42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150112-090251876", "type": "book_section", "title": "Rethinking Microscopy", "book_title": "2014 IEEE Photonics Conference", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "I will discuss my group's recent work on rethinking microscopy from the ground up. I will report on a self-imaging petri dish technology (ePetri) which is capable of streaming microscopy-level live cell culture images directly out of the incubator. I will also discuss our recent work on Fourier Ptychographic Microscopy which enables a standard microscope to push past its physical optical limitations to provide gigapixel imaging ability and to outperform the best available high-performance optical microscope.", "doi": "10.1109/IPCon.2014.6994959", "isbn": "978-1-4577-1504-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-10", "pages": "1-2" }, { "id": "authors:88jqk-bf851", "collection": "authors", "collection_id": "88jqk-bf851", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150427-132705735", "type": "article", "title": "Focusing on moving targets through scattering samples", "author": [ { "family_name": "Zhou", "given_name": "Edward Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "orcid": "0000-0002-8570-3869", "clpid": "Judkewitz-B" } ], "abstract": "Focusing light through scattering media has been a longstanding goal of biomedical optics. While wavefront shaping and optical time-reversal techniques can in principle be used to focus light across scattering media, achieving this within a scattering medium with a noninvasive and efficient reference beacon, or guide star, remains an important challenge. Here, we show optical time-reversal focusing using a new technique termed Time Reversal by Analysis of Changing wavefronts from Kinetic targets (TRACK). By taking the difference between time-varying scattering fields caused by a moving object and applying optical time reversal, light can be focused back to the location previously occupied by the object. We demonstrate this approach with discretely moved objects as well as with particles in an aqueous flow, and obtain a focal peak-to-background strength of 204 in our demonstration experiments. We further demonstrate that the generated focus can be used to noninvasively count particles in a flow-cytometry configuration\u2014even when the particles are hidden behind a strong diffuser. By achieving optical time reversal and focusing noninvasively without any external guide stars, using just the intrinsic characteristics of the sample, this work paves the way to a range of scattering media imaging applications, including underwater and atmospheric focusing as well as noninvasive in vivo flow cytometry.", "doi": "10.1364/OPTICA.1.000227", "pmcid": "PMC4301445", "issn": "2334-2536", "publisher": "Optical Society of America", "publication": "Optica", "publication_date": "2014-10", "series_number": "4", "volume": "1", "issue": "4", "pages": "227-232" }, { "id": "authors:eaznb-hpr78", "collection": "authors", "collection_id": "eaznb-hpr78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140821-083207520", "type": "article", "title": "A smartphone-based chip-scale microscope using ambient illumination", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Portable chip-scale microscopy devices can potentially address various imaging needs in mobile healthcare and environmental monitoring. Here, we demonstrate the adaptation of a smartphone's camera to function as a compact lensless microscope. Unlike other chip-scale microscopy schemes, this method uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is based on the shadow imaging technique where the sample is placed on the surface of the image sensor, which captures direct shadow images under illumination. To improve the image resolution beyond the pixel size, we perform pixel super-resolution reconstruction with multiple images at different angles of illumination, which are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. The lensless imaging scheme allows for sub-micron resolution imaging over an ultra-wide field-of-view (FOV). Image acquisition and reconstruction are performed on the device using a custom-built Android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.", "doi": "10.1039/c4lc00523f", "pmcid": "PMC4124038", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2014-08-21", "series_number": "16", "volume": "14", "issue": "16", "pages": "3056-3063" }, { "id": "authors:xy9cd-j9762", "collection": "authors", "collection_id": "xy9cd-j9762", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140321-141005322", "type": "article", "title": "Viral plaque analysis on a wide field-of-view, time-lapse, on-chip imaging platform", "author": [ { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The observation of viral plaques is the standard method for determining the viral titer and understanding the behaviors of viruses. Here, we report the application of a wide field-of-view (FOV), time-lapse, on-chip imaging platform, termed the ePetri, for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm \u00d7 4 mm. As demonstration, we captured high-resolution time-lapse images of MNV-1-infected cells at 30 min intervals. We implemented a customized image-processing program containing a density-based clustering algorithm to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. By using the results in a viral titer count format, we showed that our approach gives results that are comparable to conventional plaque assays. We further showed that the extra information collected by the ePetri can be used to monitor the dynamics of plaque formation and growth. Finally, we performed a demonstration experiment to show the relevance of such an experimental format for viral inhibitor study. We believe the ePetri is a simple and compact solution for the automation of viral plaque assays, plaque behavior analysis, and antiviral drug discovery and study.", "doi": "10.1039/c3an02323k", "pmcid": "PMC4077935", "issn": "0003-2654", "publisher": "Royal Society of Chemistry", "publication": "Analyst", "publication_date": "2014-08-07", "series_number": "15", "volume": "139", "issue": "15", "pages": "3727-3734" }, { "id": "authors:9abz5-20y30", "collection": "authors", "collection_id": "9abz5-20y30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140527-110620702", "type": "article", "title": "A high-efficiency microfluidic device for size-selective trapping and sorting", "author": [ { "family_name": "Kim", "given_name": "Jinho", "clpid": "Kim-Jinho" }, { "family_name": "Erath", "given_name": "Jessey", "clpid": "Erath-J" }, { "family_name": "Rodriguez", "given_name": "Ana", "clpid": "Rodriguez-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the development of a simple poly(dimethylsiloxane) microfluidic device for high-efficiency trapping and sorting of micron-size particles. In this device, hydrodynamic fluid flow through the sieve-like microfluidic channel sequentially fills the trap positions with particles of the trap size, and particles smaller than the trap size pass through the sieve and are trapped by smaller traps downstream. By incorporating side channels alongside the main channel, we were able to decouple the fluidic flow in one stage from the flows in the other stages. This decoupling allows us to modularize each stage of the device regardless of the size of the entire device. In our demonstration experiment with the prototype, we showed that more than 85% of the polystyrene microspheres (of sizes 15 \u03bcm, 6 \u03bcm and 4 \u03bcm) were sorted in the correct segment of the device that targets their respective sizes. Moreover, this high-efficiency device was able to trap all microspheres which were introduced into the device. Finally, we tested the device's ability to trap and sort three different species of waterborne parasites (Entamoeba, Giardia, and Cryptosporidium) and obtained excellent sorting performance.", "doi": "10.1039/C4LC00219A", "pmcid": "PMC4073585", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2014-07-21", "series_number": "14", "volume": "14", "issue": "14", "pages": "2480-2490" }, { "id": "authors:x4npg-27t82", "collection": "authors", "collection_id": "x4npg-27t82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140912-103400081", "type": "article", "title": "Fourier ptychographic microscopy for filtration-based circulating tumor cell enumeration and analysis", "author": [ { "family_name": "Williams", "given_name": "Anthony", "clpid": "Williams-Anthony-J" }, { "family_name": "Chung", "given_name": "Jaebum", "orcid": "0000-0003-3932-8428", "clpid": "Chung-Jaebum" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Rawal", "given_name": "Siddharth", "clpid": "Rawal-Siddharth" }, { "family_name": "Ao", "given_name": "Zheng", "clpid": "Ao-Zheng" }, { "family_name": "Datar", "given_name": "Ram", "clpid": "Datar-Ram-H" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Cote", "given_name": "Richard", "clpid": "Cote-Richard-J" } ], "abstract": "Circulating tumor cells (CTCs) are recognized as a candidate biomarker with strong prognostic and predictive potential in metastatic disease. Filtration-based enrichment technologies have been used for CTC characterization, and our group has previously developed a membrane microfilter device that demonstrates efficacy in model systems and clinical blood samples. However, uneven filtration surfaces make the use of standard microscopic techniques a difficult task, limiting the performance of automated imaging using commercially available technologies. Here, we report the use of Fourier ptychographic microscopy (FPM) to tackle this challenge. Employing this method, we were able to obtain high-resolution color images, including amplitude and phase, of the microfilter samples over large areas. FPM's ability to perform digital refocusing on complex images is particularly useful in this setting as, in contrast to other imaging platforms, we can focus samples on multiple focal planes within the same frame despite surface unevenness. In model systems, FPM demonstrates high image quality, efficiency, and consistency in detection of tumor cells when comparing corresponding microfilter samples to standard microscopy with high correlation (R^2=0.99932). Based on these results, we believe that FPM will have important implications for improved, high throughput, filtration-based CTC analysis, and, more generally, image analysis of uneven surfaces.", "doi": "10.1117/1.JBO.19.6.066007", "pmcid": "PMC4572097", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2014-06-20", "series_number": "6", "volume": "19", "issue": "6", "pages": "Art. No. 066007" }, { "id": "authors:gkse4-vsq67", "collection": "authors", "collection_id": "gkse4-vsq67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140801-072531278", "type": "article", "title": "Method for auto-alignment of digital optical phase conjugation systems based on digital propagation", "author": [ { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Zhou", "given_name": "Haojiang", "orcid": "0000-0001-7020-9502", "clpid": "Zhou-Edward-Haojiang" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "orcid": "0000-0002-8570-3869", "clpid": "Judkewitz-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5\u2009cm, rotation and tip/tilt of ~5\u2218, and in-plane displacement of ~5\u2009mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30\u2009% of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems.", "doi": "10.1364/OE.22.014054", "pmcid": "PMC4083057", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-06-16", "series_number": "12", "volume": "22", "issue": "12", "pages": "14054-14071" }, { "id": "authors:ptwgm-w1z14", "collection": "authors", "collection_id": "ptwgm-w1z14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140605-130038426", "type": "article", "title": "Axial standing-wave illumination frequency-domain imaging (SWIF)", "author": [ { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Despite their tremendous contribution to biomedical research and diagnosis, conventional spatial sampling techniques such as wide-field, point scanning or selective plane illumination microscopy face inherent limiting trade-offs between spatial resolution, field-of-view, phototoxicity and recording speed. Several of these trade-offs are the result of spatial sampling with diffracting beams. Here, we introduce a new strategy for fluorescence imaging, SWIF, which instead encodes the axial profile of a sample in the Fourier domain. We demonstrate how this can be achieved with propagation-invariant illumination patterns that extend over several millimeters and robustly propagate through layers of varying refractive index. This enabled us to image a lateral field-of-view of 0.8 mm x 1.5 mm with an axial resolution of 2.4 \u00b5m \u2013 greatly exceeding the lateral field-of-view of conventional illumination techniques (~100 \u00b5m) at comparable resolution. Thus, SWIF allowed us to surpass the limitations of diffracting illumination beams and untangle lateral field-of-view from resolution.", "doi": "10.1364/OE.22.011001", "pmcid": "PMC4083045", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-05-05", "series_number": "9", "volume": "22", "issue": "9", "pages": "11001-11010" }, { "id": "authors:vcbqh-agg77", "collection": "authors", "collection_id": "vcbqh-agg77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-104521720", "type": "book_section", "title": "A model for ultrasound modulated light in a turbid medium", "book_title": "Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXI", "author": [ { "family_name": "Hollmann", "given_name": "Joseph L.", "clpid": "Hollmann-J-L" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "DiMarzio", "given_name": "Charles A.", "clpid": "DiMarzio-C-A" } ], "contributor": [ { "family_name": "Brown", "given_name": "Thomas G.", "clpid": "Brown-T-G" }, { "family_name": "Cogswell", "given_name": "Carol J.", "clpid": "Cogswell-C-J" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-T" } ], "abstract": "The ability to focus light in most tissue degrades quickly with depth due to high optical scattering. Researchers have investigated using both ultrasound (US) and light synergistically to overcome this difficulty. Ultrasound has been utilized to modulated light within tissue to create a diffusive wave at that is modulated at the US frequency. Recently, there has been interest in the modulated sidebands which reside at optical frequency plus or minus the US frequency. This paper will discuss a model for US-light interactions in a scattering medium. We will use this model to relate the radiance in the probe beam to the radiance in the diffusive wave. We will then employ the P-1 approximation to the radiative transport equation to find the fluence and flux of the modulated wave. We will use these parameters to write a diffusion equation for the modulated wave that can be described in terms of the incoming optical power, and the US intensity and geometry.", "doi": "10.1117/12.2041179", "isbn": "0819498629", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2014-03-12", "pages": "Art. No. 89490U" }, { "id": "authors:fptx0-ee160", "collection": "authors", "collection_id": "fptx0-ee160", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140516-083523368", "type": "article", "title": "Model for estimating the penetration depth limit of the time-reversed ultrasonically encoded optical focusing technique", "author": [ { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Ruan", "given_name": "Haowen", "orcid": "0000-0002-4917-4509", "clpid": "Ruan-Haowen" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "orcid": "0000-0002-8570-3869", "clpid": "Judkewitz-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The time-reversed ultrasonically encoded (TRUE) optical focusing technique is a method that is capable of focusing light deep within a scattering medium. This theoretical study aims to explore the depth limits of the TRUE technique for biological tissues in the context of two primary constraints \u2013 the safety limit of the incident light fluence and a limited TRUE's recording time (assumed to be 1 ms), as dynamic scatterer movements in a living sample can break the time-reversal scattering symmetry. Our numerical simulation indicates that TRUE has the potential to render an optical focus with a peak-to-background ratio of ~2 at a depth of ~103 mm at wavelength of 800 nm in a phantom with tissue scattering characteristics. This study sheds light on the allocation of photon budget in each step of the TRUE technique, the impact of low signal on the phase measurement error, and the eventual impact of the phase measurement error on the strength of the TRUE optical focus.", "doi": "10.1364/OE.22.005787", "pmcid": "PMC4086332", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-03-10", "series_number": "5", "volume": "22", "issue": "5", "pages": "5787-5807" }, { "id": "authors:6swan-td176", "collection": "authors", "collection_id": "6swan-td176", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140409-124558217", "type": "monograph", "title": "Reconfigurable random bit storage using polymer-dispersed liquid crystal", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Assawaworrarit", "given_name": "Sid", "clpid": "Assawaworrarit-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present an optical method of storing random cryptographic keys, at high densities, within an electronically reconfigurable volume of polymer-dispersed liquid crystal (PDLC) film. We demonstrate how temporary application of a voltage above PDLC's saturation threshold can completely randomize (i.e., decorrelate) its optical scattering potential in less than a second. A unique optical setup is built around this resettable PDLC film to non-electronically save many random cryptographic bits, with minimal error, over a period of one day. These random bits, stored at an unprecedented density (10 Gb/mm^3), can then be erased and transformed into a new random key space in less than one second. Cryptographic applications of such a volumetric memory device include use as a crypto-currency wallet and as a source of resettable \"fingerprints\" for time-sensitive authentication.", "doi": "10.48550/arXiv.1403.2419", "publication_date": "2014-03-10" }, { "id": "authors:11n04-3yw28", "collection": "authors", "collection_id": "11n04-3yw28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140515-133137601", "type": "article", "title": "Embedded pupil function recovery for Fourier ptychographic microscopy", "author": [ { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We develop and test a pupil function determination algorithm, termed embedded pupil function recovery (EPRY), which can be incorporated into the Fourier ptychographic microscopy (FPM) algorithm and recover both the Fourier spectrum of sample and the pupil function of imaging system simultaneously. This EPRY-FPM algorithm eliminates the requirement of the previous FPM algorithm for a priori knowledge of the aberration in the imaging system to reconstruct a high quality image. We experimentally demonstrate the effectiveness of this algorithm by reconstructing high resolution, large field-of-view images of biological samples. We also illustrate that the pupil function we retrieve can be used to study the spatially varying aberration of a large field-of-view imaging system. We believe that this algorithm adds more flexibility to FPM and can be a powerful tool for the characterization of an imaging system's aberration.", "doi": "10.1364/OE.22.004960", "pmcid": "PMC4086333", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-03-10", "series_number": "5", "volume": "22", "issue": "5", "pages": "4960-4972" }, { "id": "authors:61vt2-bnw94", "collection": "authors", "collection_id": "61vt2-bnw94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140620-095257730", "type": "book_section", "title": "Time-Reversal Optical Focusing for Biophotonics Applications", "book_title": "MEMS Adaptive Optics VIII", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "I will discuss our recent work on the use of digital optical phase conjugation and ultrasound tagging to accomplish time-reversal\ndeep tissue optical focusing for fluorescence imaging and other applications.", "doi": "10.1117/12.2042406", "isbn": "9780819498915", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2014-03-07", "pages": "Art. No. 89780K" }, { "id": "authors:ez0bk-rgy80", "collection": "authors", "collection_id": "ez0bk-rgy80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140731-094446383", "type": "article", "title": "Diffusion model for ultrasound-modulated light", "author": [ { "family_name": "Hollmann", "given_name": "Joseph L.", "clpid": "Hollmann-J-L" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "DiMarzio", "given_name": "Charles A.", "clpid": "DiMarzio-C-A" } ], "abstract": "Researchers use ultrasound (US) to modulate diffusive light in a highly scattering medium like tissue. This paper analyzes the US\u2013optical interaction in the scattering medium and derives an expression for the US-modulated optical radiance. The diffusion approximation to the radiative transport equation is employed to develop a Green's function for US-modulated light. The predicted modulated fluence and flux are verified using finite-difference time-domain simulations. The Green's function is then utilized to illustrate the modulated reflectance as the US\u2013optical interaction increases in depth. The intent of this paper is to focus on high US frequencies necessary for high-resolution imaging because they are of interest for applications such as phase conjugation.", "doi": "10.1117/1.JBO.19.3.035005", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2014-03", "series_number": "3", "volume": "19", "issue": "3", "pages": "Art. No. 035005" }, { "id": "authors:w5pca-g8824", "collection": "authors", "collection_id": "w5pca-g8824", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140411-140804984", "type": "article", "title": "Imaging and Identification of Waterborne Parasites Using a Chip-Scale Microscope", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Erath", "given_name": "Jessey", "clpid": "Erath-J" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Willems", "given_name": "Phil", "clpid": "Willems-P" }, { "family_name": "Eichinger", "given_name": "Daniel", "clpid": "Eichinger-D" }, { "family_name": "Rodriguez", "given_name": "Ana", "clpid": "Rodriguez-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate a compact portable imaging system for the detection of waterborne parasites in resource-limited settings. The previously demonstrated sub-pixel sweeping microscopy (SPSM) technique is a lens-less imaging scheme that can achieve high-resolution (<1 \u00b5m) bright-field imaging over a large field-of-view (5.7 mm\u00d74.3 mm). A chip-scale microscope system, based on the SPSM technique, can be used for automated and high-throughput imaging of protozoan parasite cysts for the effective diagnosis of waterborne enteric parasite infection. We successfully imaged and identified three major types of enteric parasite cysts, Giardia, Cryptosporidium, and Entamoeba, which can be found in fecal samples from infected patients. We believe that this compact imaging system can serve well as a diagnostic device in challenging environments, such as rural settings or emergency outbreaks.", "doi": "10.1371/journal.pone.0089712", "pmcid": "PMC3935895", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2014-02-26", "series_number": "2", "volume": "9", "issue": "2", "pages": "Art. No. e89712" }, { "id": "authors:m2e00-mgy46", "collection": "authors", "collection_id": "m2e00-mgy46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140317-082342071", "type": "article", "title": "Advances in optics for biotechnology, medicine and surgery", "author": [ { "family_name": "Fitzmaurice", "given_name": "Maryann", "clpid": "Fitzmaurice-M" }, { "family_name": "Pogue", "given_name": "Brian W.", "clpid": "Pogue-B-W" }, { "family_name": "Tearney", "given_name": "Guillermo J.", "clpid": "Tearney-G-J" }, { "family_name": "Tunnell", "given_name": "James W.", "clpid": "Tunnell-J-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The guest editors introduce a Biomedical Optics Express feature issue that includes contributions from participants at the 2013 conference on Advances in Optics for Biotechnology, Medicine and Surgery XIII.", "doi": "10.1364/BOE.5.000560", "pmcid": "PMC3920884", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2014-02-01", "series_number": "2", "volume": "5", "issue": "2", "pages": "560-561" }, { "id": "authors:7zm73-p8844", "collection": "authors", "collection_id": "7zm73-p8844", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140307-103704952", "type": "article", "title": "A phase space model of Fourier ptychographic microscopy", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "A new computational imaging technique, termed Fourier ptychographic microscopy (FPM), uses a sequence of low-resolution images captured under varied illumination to iteratively converge upon a high-resolution complex sample estimate. Here, we propose a mathematical model of FPM that explicitly connects its operation to conventional ptychography, a common procedure applied to electron and X-ray diffractive imaging. Our mathematical framework demonstrates that under ideal illumination conditions, conventional ptychography and FPM both produce datasets that are mathematically linked by a linear transformation. We hope this finding encourages the future cross-pollination of ideas between two otherwise unconnected experimental imaging procedures. In addition, the coherence state of the illumination source used by each imaging platform is critical to successful operation, yet currently not well understood. We apply our mathematical framework to demonstrate that partial coherence uniquely alters both conventional ptychography's and FPM's captured data, but up to a certain threshold can still lead to accurate resolution-enhanced imaging through appropriate computational post-processing. We verify this theoretical finding through simulation and experiment.", "doi": "10.1364/OE.22.000338", "pmcid": "PMC3926543", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2014-01-13", "series_number": "1", "volume": "22", "issue": "1", "pages": "338-358" }, { "id": "authors:0wes0-5dg92", "collection": "authors", "collection_id": "0wes0-5dg92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140203-113756615", "type": "article", "title": "0.5 gigapixel microscopy using a flatbed scanner", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "orcid": "0000-0002-4268-2690", "clpid": "Zheng-Guoan" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The capability to perform high-resolution, wide field-of-view (FOV) microscopy imaging is highly sought after in biomedical applications. In this paper, we report a wide FOV microscopy system that uses a closed-circuit-television (CCTV) lens for image relay and a flatbed scanner for data acquisition. We show that such an imaging system is capable of capturing a 10 mm \u00d7 7.5 mm FOV image with 0.78 \u00b5m resolution, resulting in more than 0.5 billion pixels across the entire image. The resolution and field curve of the proposed system were characterized by imaging a USAF resolution target and a hole-array target. To demonstrate its application, 0.5 gigapixel images of histology slides were acquired using this system.", "doi": "10.1364/BOE.5.000001", "pmcid": "PMC3891323", "issn": "2156-7085", "publisher": "Optical Society of America", "publication": "Biomedical Optics Express", "publication_date": "2014-01-01", "series_number": "1", "volume": "5", "issue": "1", "pages": "1-8" }, { "id": "authors:1ehxz-10b95", "collection": "authors", "collection_id": "1ehxz-10b95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140116-132831677", "type": "article", "title": "Physical key-protected one-time pad", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "Vellekoop", "given_name": "Ivo M.", "clpid": "Vellekoop-I-M" }, { "family_name": "Assawaworrarit", "given_name": "Sid", "clpid": "Assawaworrarit-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We describe an encrypted communication principle that forms a secure link between two parties without\nelectronically saving either of their keys. Instead, random cryptographic bits are kept safe within the unique\nmesoscopic randomness of two volumetric scattering materials. We demonstrate how a shared set of\npatterned optical probes can generate 10 gigabits of statistically verified randomness between a pair of\nunique 2 mm^3 scattering objects. This shared randomness is used to facilitate information-theoretically\nsecure communication following a modified one-time pad protocol. Benefits of volumetric physical storage\nover electronic memory include the inability to probe, duplicate or selectively reset any bits without\nfundamentally altering the entire key space. Our ability to securely couple the randomness contained within\ntwo unique physical objects can extend to strengthen hardware required by a variety of cryptographic\nprotocols, which is currently a critically weak link in the security pipeline of our increasingly mobile\ncommunication culture.", "doi": "10.1038/srep03543", "pmcid": "PMC3866593", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2013-12-18", "volume": "3", "pages": "Art. No. 3543" }, { "id": "authors:yt00b-kym74", "collection": "authors", "collection_id": "yt00b-kym74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131224-100217865", "type": "article", "title": "Quantitative phase imaging via Fourier ptychographic microscopy", "author": [ { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" } ], "abstract": "Fourier ptychographic microscopy (FPM) is a recently developed imaging modality that uses angularly varying illumination to extend a system's performance beyond the limit defined by its optical components. The FPM technique applies a novel phase-retrieval procedure to achieve resolution enhancement and complex image recovery. In this Letter, we compare FPM data to theoretical prediction and phase-shifting digital holography measurement to show that its acquired phase maps are quantitative and artifact-free. We additionally explore the relationship between the achievable spatial and optical thickness resolution offered by a reconstructed FPM phase image. We conclude by demonstrating enhanced visualization and the collection of otherwise unobservable sample information using FPM's quantitative phase.", "doi": "10.1364/OL.38.004845", "pmcid": "PMC4277232", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2013-11-15", "series_number": "22", "volume": "38", "issue": "22", "pages": "4845-4848" }, { "id": "authors:0hccr-s0w89", "collection": "authors", "collection_id": "0hccr-s0w89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141212-093902623", "type": "book_section", "title": "On-Chip Fluorescence Microscopy for Wide Field-of-View High-Throughput Phynotype Screening of Caenorhabditis elegans", "book_title": "17th International Conference on Miniaturized Systems for Chemistry and Life Sciences", "author": [ { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Kato", "given_name": "Mihoko", "orcid": "0000-0003-3827-8879", "clpid": "Kato-Mihoko" }, { "family_name": "Sternberg", "given_name": "Paul", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We developed a low-cost compact on-chip fluorescence imaging platform, termed the Fluorescence Talbot\nMicroscopy (FTM), which utilizes the Talbot self-imaging effect to enable efficient fluorescence imaging over a large\nand directly-scalable field-of-view (FOV). The FTM prototype has a resolution of 1.2 \u03bcm and an FOV of 3.9\u00d73.5mm^2. We demonstrate the use of the FTM prototype in performing high-throughput imaging of live Caenorhabditis elegans (C. elegans), and RNA interference (RNAi) phenotyping of distal tip cell (DTC) migration defects in C. elegans.", "isbn": "978-0-9798064-6-9", "publisher": "Caltech Library", "publication_date": "2013-10", "pages": "257-259" }, { "id": "authors:gy8xc-c8w78", "collection": "authors", "collection_id": "gy8xc-c8w78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130808-111715101", "type": "article", "title": "Wide-field, high-resolution Fourier ptychographic microscopy", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report an imaging method, termed Fourier ptychographic microscopy (FPM), which iteratively stitches together a\nnumber of variably illuminated, low-resolution intensity images in Fourier space to produce a wide-field, high-resolution\ncomplex sample image. By adopting a wavefront correction strategy, the FPM method can also correct for aberrations and\ndigitally extend a microscope's depth of focus beyond the physical limitations of its optics. As a demonstration, we built a\nmicroscope prototype with a resolution of 0.78 \u00b5m, a field of view of \u223c120 mm^2 and a resolution-invariant depth of focus\nof 0.3 mm (characterized at 632 nm). Gigapixel colour images of histology slides verify successful FPM operation. The\nreported imaging procedure transforms the general challenge of high-throughput, high-resolution microscopy from one\nthat is coupled to the physical limitations of the system's optics to one that is solvable through computation.", "doi": "10.1038/nphoton.2013.187", "pmcid": "PMC4169052", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2013-09", "series_number": "9", "volume": "7", "issue": "9", "pages": "739-745" }, { "id": "authors:bhzcp-0h923", "collection": "authors", "collection_id": "bhzcp-0h923", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131121-132206912", "type": "article", "title": "Characterization of Talbot pattern illumination for scanning optical microscopy", "author": [ { "family_name": "Liu", "given_name": "Guangshuo", "clpid": "Liu-Guangshuo" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" } ], "abstract": "We studied the use of Talbot pattern illumination in scanning optical microscopy (SOM). Unlike conventional illumination spots used in SOM, the focal spots in Talbot pattern are more complicated and do not have a simple Gaussian intensity distribution. To find out the resolution of SOM using Talbot pattern, we characterized the evolution of the full-width-at-half-maximum spot size of the Talbot focal spots by computer simulation. We then simulated the SOM imaging under Talbot pattern illumination using the razor blade and the U.S. Air Force target as the sample objects, and compared the results with those performed with Gaussian spots as illumination. Using several foci searching algorithms, the optimal focal distances were found to be shorter than the theoretical Talbot distances. The simulation results were consistent with the experiment results published previously. We then provide a practical guidance for searching for optimal focal distances in the SOM based on these studies.", "doi": "10.1117/1.OE.52.9.091714", "issn": "0091-3286", "publisher": "International Society for Optical Engineering", "publication": "Optical Engineering", "publication_date": "2013-09", "series_number": "9", "volume": "52", "issue": "9", "pages": "Art. No. 091714" }, { "id": "authors:v12fc-v8697", "collection": "authors", "collection_id": "v12fc-v8697", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130815-084711799", "type": "article", "title": "Characterization of spatially varying aberrations for wide field-of-view microscopy", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We describe a simple and robust approach for characterizing the spatially varying pupil aberrations of microscopy systems. In our demonstration with a standard microscope, we derive the location-dependent pupil transfer functions by first capturing multiple intensity images at different defocus settings. Next, a generalized pattern search algorithm is applied to recover the complex pupil functions at ~350 different spatial locations over the entire field-of-view. Parameter fitting transforms these pupil functions into accurate 2D aberration maps. We further demonstrate how these aberration maps can be applied in a phase-retrieval based microscopy setup to compensate for spatially varying aberrations and to achieve diffraction-limited performance over the entire field-of-view. We believe that this easy-to-use spatially-varying pupil characterization method may facilitate new optical imaging strategies for a variety of wide field-of-view imaging platforms.", "doi": "10.1364/OE.21.015131", "pmcid": "PMC3724395", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2013-07-01", "series_number": "13", "volume": "21", "issue": "13", "pages": "15131-15143" }, { "id": "authors:dvv2j-4j844", "collection": "authors", "collection_id": "dvv2j-4j844", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130805-103927291", "type": "article", "title": "Wide field-of-view Talbot grid-based microscopy for multicolor fluorescence imaging", "author": [ { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Erath", "given_name": "Jessey", "clpid": "Erath-J" }, { "family_name": "Rodriguez", "given_name": "Ana", "clpid": "Rodriguez-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The capability to perform multicolor, wide field-of-view (FOV) fluorescence microscopy imaging is important in screening and pathology applications. We developed a microscopic slide-imaging system that can achieve multicolor, wide FOV, fluorescence imaging based on the Talbot effect. In this system, a light-spot grid generated by the Talbot effect illuminates the sample. By tilting the excitation beam, the Talbot-focused spot scans across the sample. The images are reconstructed by collecting the fluorescence emissions that correspond to each focused spot with a relay optics arrangement. The prototype system achieved an FOV of 12 \u00d7 10 mm^2 at an acquisition time as fast as 23 s for one fluorescence channel. The resolution is fundamentally limited by spot size, with a demonstrated full-width at half-maximum spot diameter of 1.2 \u03bcm. The prototype was used to nimage green fluorescent beads, double-stained human breast cancer SK-BR-3 cells, Giardia lamblia cysts, and the Cryptosporidium parvum oocysts. This imaging method is scalable and simple for implementation of high-speed wide FOV fluorescence microscopy.", "doi": "10.1364/OE.21.014555", "pmcid": "PMC3726246", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2013-06-17", "series_number": "12", "volume": "21", "issue": "12", "pages": "14555-14565" }, { "id": "authors:75chw-t2f58", "collection": "authors", "collection_id": "75chw-t2f58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130715-100248148", "type": "article", "title": "Chip-scale fluorescence microscope based on a silo-filter complementary metal-oxide semiconductor image sensor", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Lee", "given_name": "J. Eugene", "clpid": "Lee-J-Eugene" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate a silo-filter (SF) complementary metal-oxide semiconductor (CMOS) image sensor for a chip-scale fluorescence microscope. The extruded pixel design with metal walls between neighboring pixels guides fluorescence emission through the thick absorptive filter to the photodiode of a pixel. Our prototype device achieves 13 \u03bcm resolution over a wide field of view (4.8\u2009\u2009mm \u00d7 4.4\u2009\u2009mm). We demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.", "doi": "10.1364/OL.38.001817", "pmcid": "PMC3740726", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2013-06-01", "series_number": "11", "volume": "38", "issue": "11", "pages": "1817-1819" }, { "id": "authors:kmxs4-4vr29", "collection": "authors", "collection_id": "kmxs4-4vr29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130802-101105632", "type": "article", "title": "Optofluidics 2013", "author": [ { "family_name": "Liu", "given_name": "Ai-Qun", "clpid": "Liu-Ai-Qun" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optofluidics is broadly defined as the fusion of optics and microfluidics. The\nterm optofluidics was coined less than a decade ago. Yet, the term and the\nconcept it encapsulates have pervaded through a significant fraction of the\nminiature system research community. Optofluidic research continues to\ngrow in unanticipated directions. The Second International Conference on\nOptofluidics (Optofluidics-2012) showcased some of these developments.\nThe conference was first organized by Xi'an Jiaotong University in 2011 and\nthen Suzhou University, Institute of Nanotechnology, Xi'an Jiaotong\nUniversity and Suzhou Industrial Park where it was proudly hosted as a\nsummit conference of the CHInano conference in Suzhou on 13\u201315 Sep\n2012. We are happy that Lab on a Chip, a major publication venue for\noptofluidic research has scheduled this themed issue.", "doi": "10.1039/c3lc90054a", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2013-05-30", "series_number": "14", "volume": "13", "issue": "14", "pages": "2673-2674" }, { "id": "authors:j19fp-pqw74", "collection": "authors", "collection_id": "j19fp-pqw74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130524-100820411", "type": "article", "title": "Optical phase conjugation (OPC)-assisted isotropic focusing", "author": [ { "family_name": "Jang", "given_name": "Mooseok", "orcid": "0000-0003-1977-9539", "clpid": "Jang-Mooseok" }, { "family_name": "Sentenac", "given_name": "Anne", "clpid": "Sentenac-Anne" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Isotropic optical focusing \u2013 the focusing of light with axial confinement that matches its lateral confinement, is important for a broad range of applications. Conventionally, such focusing is achieved by overlapping the focused beams from a pair of opposite-facing microscope objective lenses. However the exacting requirements for the alignment of the objective lenses and the method's relative intolerance to sample turbidity have significantly limited its utility. In this paper, we present an optical phase conjugation (OPC)-assisted isotropic focusing method that can address both challenges. We exploit the time-reversal nature of OPC playback to naturally guarantee the overlap of the two focused beams even when the objective lenses are significantly misaligned (up to 140 microns transversely and 80 microns axially demonstrated). The scattering correction capability of OPC also enabled us to accomplish isotropic focusing through thick scattering samples (demonstrated with samples of ~7 scattering mean free paths). This method can potentially improve 4Pi microscopy and 3D microstructure patterning.", "doi": "10.1364/OE.21.008781", "pmcid": "PMC3641024", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2013-04-08", "series_number": "7", "volume": "21", "issue": "7", "pages": "8781-8792" }, { "id": "authors:wy90v-srh46", "collection": "authors", "collection_id": "wy90v-srh46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130429-111649331", "type": "article", "title": "Speckle-scale focusing in the diffusive regime with time reversal of variance-encoded light (TROVE)", "author": [ { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Mathy", "given_name": "Alexandre", "clpid": "Mathy-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Focusing of light in the diffusive regime inside scattering media has long been considered impossible. Recently, this limitation has been overcome with time reversal of ultrasound-encoded light (TRUE), but the resolution of this approach is fundamentally limited by the large number of optical modes within the ultrasound focus. Here, we introduce a new approach, time reversal of variance-encoded light (TROVE), which demixes these spatial modes by variance encoding to break the resolution barrier imposed by the ultrasound. By encoding individual spatial modes inside the scattering sample with unique variances, we effectively uncouple the system resolution from the size of the ultrasound focus. This enables us to demonstrate optical focusing and imaging with diffuse light at an unprecedented, speckle-scale lateral resolution of ~5 \u00b5m.", "doi": "10.1038/NPHOTON.2013.31", "pmcid": "PMC3692396", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2013-04", "series_number": "4", "volume": "7", "issue": "4", "pages": "300-305" }, { "id": "authors:jdzej-y4305", "collection": "authors", "collection_id": "jdzej-y4305", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130325-083959903", "type": "article", "title": "Wide Field-of-View On-Chip Talbot Fluorescence Microscopy for Longitudinal Cell Culture Monitoring from within the Incubator", "author": [ { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Bower", "given_name": "Danielle V.", "orcid": "0000-0002-4469-4855", "clpid": "Bower-D-V" }, { "family_name": "Yiu", "given_name": "Patrick", "clpid": "Yiu-Patrick" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Time-lapse or longitudinal fluorescence microscopy is broadly used in cell biology. However, current available time-lapse fluorescence microscopy systems are bulky and costly. The limited field-of-view (FOV) associated with the microscope objective necessitates mechanical scanning if a larger FOV is required. Here we demonstrate a wide FOV time-lapse fluorescence self-imaging Petri dish system, termed the Talbot Fluorescence ePetri, which addresses these issues. This system's imaging is accomplished through the use of the Fluorescence Talbot Microscopy (FTM). By incorporating a microfluidic perfusion subsystem onto the platform, we can image cell cultures directly from within an incubator. Our prototype has a resolution limit of 1.2 \u03bcm and an FOV of 13 mm^2. As demonstration, we obtained time-lapse images of HeLa cells expressing H2B-eGFP. We also employed the system to analyze the cells' dynamic response to an anticancer drug, camptothecin (CPT). This method can provide a compact and simple solution for automated fluorescence imaging of cell cultures in incubators.", "doi": "10.1021/ac303356v", "pmcid": "PMC3587116", "issn": "0003-2700", "publisher": "American Chemical Society", "publication": "Analytical Chemistry", "publication_date": "2013-02-19", "series_number": "4", "volume": "85", "issue": "4", "pages": "2356-2360" }, { "id": "authors:3qjqz-m9325", "collection": "authors", "collection_id": "3qjqz-m9325", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130326-091254901", "type": "article", "title": "Analysis and modeling of an ultrasound-modulated guide star to increase the depth of focusing in a turbid medium", "author": [ { "family_name": "Hollmann", "given_name": "Joseph L.", "clpid": "Hollmann-J-L" }, { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "DiMarzio", "given_name": "Charles A.", "clpid": "DiMarzio-C-A" } ], "abstract": "The effects of strong scattering in tissue limit the depth to which light may be focused. However, it has been shown that scattering may be reduced utilizing adaptive optics with a focused ultrasound (US) beam guidestar. The optical signal traveling through the US beam waist is frequency shifted and may be isolated with demodulation. This paper utilizes a multiphysics simulation to model the optical and US interactions in both synthetic tissue and random scattering media. The results illustrate that optical energy may be focused within a turbid medium utilizing a US guidestar. The results also suggest that optical energy travels preferentially along optical channels within a turbid medium.", "doi": "10.1117/1.JBO.18.2.025004", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2013-02", "series_number": "2", "volume": "18", "issue": "2", "pages": "Art. No. 025004" }, { "id": "authors:xdex8-t5s39", "collection": "authors", "collection_id": "xdex8-t5s39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130107-153250959", "type": "article", "title": "Wide and scalable field-of-view Talbot-grid-based fluorescence microscopy", "author": [ { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Kato", "given_name": "Mihoko", "orcid": "0000-0003-3827-8879", "clpid": "Kato-Mihoko" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Here we report a low-cost and simple wide field-of-view (FOV) on-chip fluorescence-imaging platform, termed fluorescence Talbot microscopy (FTM), which utilizes the Talbot self-imaging effect to enable efficient fluorescence imaging over a large and directly scalable FOV. The FTM prototype has a resolution of 1.2 \u03bcm and an FOV of 3.9\u2009\u2009mm\u00d73.5\u2009\u2009mm. We demonstrate the imaging capability of FTM on fluorescently labeled breast cancer cells (SK-BR-3) and human embryonic kidney 293 (HEK) cells expressing green fluorescent protein.", "doi": "10.1364/OL.37.005018", "pmcid": "PMC3718313", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2012-12-01", "series_number": "23", "volume": "37", "issue": "23", "pages": "5018-5020" }, { "id": "authors:84kdy-z6r64", "collection": "authors", "collection_id": "84kdy-z6r64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130118-151818356", "type": "article", "title": "Markov speckle for efficient random bit generation", "author": [ { "family_name": "Horstmeyer", "given_name": "Roarke", "orcid": "0000-0002-2480-9141", "clpid": "Horstmeyer-R" }, { "family_name": "Chen", "given_name": "Richard Y.", "clpid": "Chen-Richard-Y" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optical speckle is commonly observed in measurements using coherent radiation. While lacking experimental validation, previous work has often assumed that speckle's random spatial pattern follows a Markov process. Here, we present a derivation and experimental confirmation of conditions under which this assumption holds true. We demonstrate that a detected speckle field can be designed to obey the first-order Markov property by using a Cauchy attenuation mask to modulate scattered light. Creating Markov speckle enables the development of more accurate and efficient image post-processing algorithms, with applications including improved de-noising, segmentation and super-resolution. To show its versatility, we use the Cauchy mask to maximize the entropy of a detected speckle field with fixed average speckle size, allowing cryptographic applications to extract a maximum number of useful random bits from speckle images.", "doi": "10.1364/OE.20.026394", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2012-11-19", "series_number": "24", "volume": "20", "issue": "24", "pages": "26394-26410" }, { "id": "authors:xskqp-rje18", "collection": "authors", "collection_id": "xskqp-rje18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121016-132439545", "type": "book_section", "title": "Digital Petri dish for on-chip cell monitoring", "book_title": "2012 Conference on Lasers and Electro-Optics", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a digital Petri dish platform for on-chip cell monitoring. We demonstrate the ability to image confluent cell cultures with 6 mm \u00d7 4 mm filed-of-view and \u223c0.7 \u03bcm resolution by using the proposed platform.", "isbn": "978-1-4673-1839-6", "publisher": "Optical Society of America", "place_of_publication": "Washington, DC", "publication_date": "2012-10-17", "pages": "1-2" }, { "id": "authors:10jjw-m5y42", "collection": "authors", "collection_id": "10jjw-m5y42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121017-091324926", "type": "book_section", "title": "Towards giga-pixel microscopy", "book_title": "2012 Conference on Lasers and Electro-Optics", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Ou", "given_name": "Xiaoze", "clpid": "Ou-Xiaoze" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a wide field-of-view (FOV) microscopy imaging system that is capable to capture a 10 mm \u2217 7.5 mm FOV image with submicron resolution, resulting in 0.54 giga-pixels across the entire image.", "isbn": "978-1-4673-1839-6", "publisher": "Optical Society of America", "place_of_publication": "Washington, DC", "publication_date": "2012-10-17", "pages": "1-2" }, { "id": "authors:3bb2d-5fb79", "collection": "authors", "collection_id": "3bb2d-5fb79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121005-104644595", "type": "article", "title": "Digital optical phase conjugation of fluorescence in turbid tissue", "author": [ { "family_name": "Vellekoop", "given_name": "Ivo M.", "clpid": "Vellekoop-I-M" }, { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate a method for phase conjugating fluorescence. Our method, called reference free digital optical phase conjugation, can conjugate extremely weak, incoherent optical signals. It was used to phase conjugate fluorescent light originating from a bead covered with 0.5\u2009mm of light-scattering tissue. The phase conjugated beam refocuses onto the bead and causes a local increase of over two orders of magnitude in the light intensity. Potential applications are in imaging, optical trapping, and targeted photochemical activation inside turbid tissue.", "doi": "10.1063/1.4745775", "pmcid": "PMC3436909", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2012-08-20", "series_number": "8", "volume": "101", "issue": "8", "pages": "Art. No. 081108" }, { "id": "authors:n4mcx-9fy41", "collection": "authors", "collection_id": "n4mcx-9fy41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121001-144745910", "type": "article", "title": "Themed issue: Optofluidics", "author": [ { "family_name": "Liu", "given_name": "Ai-Qun", "clpid": "Liu-Ai-Qun" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The term optofluidics defines a growing\nresearch area that integrates optics and\nmicrofluidics in ways that enable unique\nstrengths and advantages for a broad range\nof applications. The First International\nConference on Optofluidics (Optofluidics-\n2011) organized by Xi'an Jiaotong\nUniversity and Lab on a Chip on 11\u201312\nDecember 2011 featured work in this field,\nwith an exciting two-day program of presentations\nand discussions. We are happy\nthat Lab on a Chip, a major publication\ndestination for optofluidic research, has\nscheduled this themed issue on Optofluidics.\nWe are especially heartened that the optofluidics\ncommunity has responded enthusiastically\nwith a large number of excellent\nmanuscript submissions.", "doi": "10.1039/c2lc90086f", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2012-08-16", "series_number": "19", "volume": "12", "issue": "19", "pages": "3539-3539" }, { "id": "authors:v3dq0-n1x69", "collection": "authors", "collection_id": "v3dq0-n1x69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120626-124726276", "type": "article", "title": "Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light", "author": [ { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Judkewitz", "given_name": "Benjamin", "clpid": "Judkewitz-B" }, { "family_name": "DiMarzio", "given_name": "Charles A.", "clpid": "DiMarzio-C-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Fluorescence imaging is one of the most important research tools in biomedical sciences. However, scattering of light severely impedes imaging of thick biological samples beyond the ballistic regime. Here we directly show focusing and high-resolution fluorescence imaging deep inside biological tissues by digitally time-reversing ultrasound-tagged light with high optical gain (~5\u00d710^5). We confirm the presence of a time-reversed optical focus along with a diffuse background\u2014a corollary of partial phase conjugation\u2014and develop an approach for dynamic background cancellation. To illustrate the potential of our method, we image complex fluorescent objects and tumour microtissues at an unprecedented depth of 2.5 mm in biological tissues at a lateral resolution of 36 \u03bcm\u00d752 \u03bcm and an axial resolution of 657 \u03bcm. Our results set the stage for a range of deep-tissue imaging applications in biomedical research and medical diagnostics.", "doi": "10.1038/ncomms1925", "pmcid": "PMC3621452", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2012-06-26", "series_number": "928", "volume": "3", "issue": "928", "pages": "1-8" }, { "id": "authors:s9kzy-9g445", "collection": "authors", "collection_id": "s9kzy-9g445", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120621-135552222", "type": "article", "title": "On-chip continuous monitoring of motile microorganisms on an ePetri platform", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Mukherjee", "given_name": "Nandini", "clpid": "Mukherjee-N" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Self-imaging Petri dish platforms with microscopy resolution, which we term 'ePetri', can significantly streamline cell cultures and/or other longitudinal biological studies. In this paper, we demonstrate high-resolution imaging and long-term culture of motile microorganisms in a specialized ePetri platform by taking advantage of the inherent motion. By applying a super-resolution algorithm to a set of low-resolution images of the microorganisms as they move across the sensing area of a complementary metal oxide semiconductor (CMOS) image sensor chip, we can render an improved-resolution image of the microorganisms. We perform a longitudinal study of Euglena gracilis cultured in an ePetri platform, and image-based analysis on the motion and morphology of the cells. As a miniaturized and automated culture monitoring platform, this ePetri technology can greatly improve studies and experiments with motile microorganisms.", "doi": "10.1039/C2LC40090A", "pmcid": "PMC3371133", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2012-06-06", "series_number": "13", "volume": "12", "issue": "13", "pages": "2385-2390" }, { "id": "authors:w1fmj-hv062", "collection": "authors", "collection_id": "w1fmj-hv062", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120224-151606385", "type": "article", "title": "Quantitative surface normal measurement by a wavefront camera", "author": [ { "family_name": "Ren", "given_name": "Jian", "clpid": "Ren-Jian" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "A compact wavefront camera that allows users to quantitatively measure the intensity and wavefront at a remote object plane is reported. The camera is built from a chip-scale wavefront sensor that we previously developed. By measuring the wavefront of the image and calibrating the wavefront relationship between the image and object planes, the wavefront at the object plane can be computed and the surface normal of the object can be derived. We built a prototype camera and calibrated the wavefront relationship. In a proof-of-concept experiment, a set of concave mirrors with different focal lengths (50\u2013200 mm), were imaged. The results agree well with their expected values. To demonstrate the application of the camera, we applied this method to measure the deformation of a microfluidic channel under pressure.", "doi": "10.1364/OL.37.000199", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2012-01-15", "series_number": "2", "volume": "37", "issue": "2", "pages": "199-201" }, { "id": "authors:rb2dn-00131", "collection": "authors", "collection_id": "rb2dn-00131", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110930-090239172", "type": "article", "title": "Fluorescence microscopy imaging with a Fresnel zone plate array based optofluidic microscope", "author": [ { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Han", "given_name": "Chao", "clpid": "Han-Chao" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of an on-chip microscope system, termed fluorescence optofluidic microscope (FOFM), which is capable of fluorescence microscopy imaging of samples in fluid media. The FOFM employs an array of Fresnel zone plates (FZP) to generate an array of focused light spots within a microfluidic channel. As a sample flows through the channel and across the array of focused\nlight spots, the fluorescence emissions are collected by a filter-coated CMOS sensor, which serves as the channel's floor. The collected data can then be processed to render fluorescence microscopy images at a resolution determined by the focused light spot size (experimentally measured as 0.65 mm FWHM). In our experiments, our established resolution was 1.0 mm due to Nyquist criterion consideration. As a demonstration, we show that such a system can be used to image the cell nuclei stained by Acridine Orange and cytoplasm labeled by Qtracker.", "doi": "10.1039/c1lc20654k", "pmcid": "PMC3710399", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2011-11-07", "series_number": "21", "volume": "2011", "issue": "21", "pages": "3698-3702" }, { "id": "authors:1521t-ww309", "collection": "authors", "collection_id": "1521t-ww309", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111129-093810678", "type": "article", "title": "Microscopy refocusing and dark-field imaging by using a simple LED array", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Kolner", "given_name": "Christopher", "clpid": "Kolner-C" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The condenser is one of the main components in most transmitted light compound microscopes. In this Letter, we show that such a condenser can be replaced by a programmable LED array to achieve greater imaging flexibility and functionality. Without mechanically scanning the sample or changing the microscope setup, the proposed approach can be used for dark-field imaging, bright-field imaging, microscopy sectioning, and digital refocusing. Images of a starfish embryo were acquired by using such an approach for demonstration.", "doi": "10.1364/OL.36.003987", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2011-10-15", "series_number": "20", "volume": "36", "issue": "20", "pages": "3987-3989" }, { "id": "authors:p5kjq-wec04", "collection": "authors", "collection_id": "p5kjq-wec04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111108-160027564", "type": "article", "title": "The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM)", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Antebi", "given_name": "Yaron", "clpid": "Antebi-Y" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a chip-scale lensless wide-field-of-view microscopy imaging technique, subpixel perspective sweeping microscopy, which can render microscopy images of growing or confluent cell cultures autonomously. We demonstrate that this technology can be used to build smart Petri dish platforms, termed ePetri, for cell culture experiments. This technique leverages the recent broad and cheap availability of high performance image sensor chips to provide a low-cost and automated microscopy solution. Unlike the two major classes of lensless microscopy methods, optofluidic microscopy and digital in-line holography microscopy, this new approach is fully capable of working with cell cultures or any samples in which cells may be contiguously connected. With our prototype, we demonstrate the ability to image samples of area 6 mm \u00d7 4 mm at 660-nm resolution. As a further demonstration, we showed that the method can be applied to image color stained cell culture sample and to image and track cell culture growth directly within an incubator. Finally, we showed that this method can track embryonic stem cell differentiations over the entire sensor surface. Smart Petri dish based on this technology can significantly streamline and improve cell culture experiments by cutting down on human labor and contamination risks.", "doi": "10.1073/pnas.1110681108", "pmcid": "PMC3193234", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2011-10-11", "series_number": "41", "volume": "108", "issue": "41", "pages": "16889-16894" }, { "id": "authors:15pjb-3yd28", "collection": "authors", "collection_id": "15pjb-3yd28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111207-094726805", "type": "article", "title": "Color Capable Sub-Pixel Resolving Optofluidic Microscope and Its Application to Blood Cell Imaging for Malaria Diagnosis", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Leitao", "given_name": "Ricardo", "clpid": "Leitao-R" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Rodriguez", "given_name": "Ana", "clpid": "Rodriguez-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Miniaturization of imaging systems can significantly benefit clinical diagnosis in challenging environments, where access to physicians and good equipment can be limited. Sub-pixel resolving optofluidic microscope (SROFM) offers high-resolution imaging in the form of an on-chip device, with the combination of microfluidics and inexpensive CMOS image sensors. In this work, we report on the implementation of color SROFM prototypes with a demonstrated optical resolution of 0.66 \u00b5m at their highest acuity. We applied the prototypes to perform color imaging of red blood cells (RBCs) infected with Plasmodium falciparum, a particularly harmful type of malaria parasites and one of the major causes of death in the developing world.", "doi": "10.1371/journal.pone.0026127", "pmcid": "PMC3191177", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2011-10-11", "series_number": "10", "volume": "6", "issue": "10", "pages": "Art. No. e26127" }, { "id": "authors:bpw2p-mr364", "collection": "authors", "collection_id": "bpw2p-mr364", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141125-080704287", "type": "book_section", "title": "Color sub-pixel resolving optofluidic microscope and its application to blood cell imaging for malaria diagnosis", "book_title": "15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011", "author": [ { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Leitao", "given_name": "Ricardo", "clpid": "Leitao-R" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Rodriguez", "given_name": "Ana", "clpid": "Rodriguez-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Landers", "given_name": "James P.", "clpid": "Landers-J-P" } ], "abstract": "We report on the implementation of color sub-pixel resolving optofluidic microscope (SROFM), a high resolution (HR) on-chip\nimaging system for diagnostic applications in rural regions. With the combination of microfluidics and inexpensive\ncomplementary metal oxide semiconductor (CMOS) image sensors, we demonstrate optical resolution of 0.66 \u00b5m at the\nhighest acuity. We applied the prototypes to perform color imaging of red blood cells (RBCs) infected with Plasmodium falciparum\n(P. falciparum), a particularly harmful type of malaria parasites and one of the major causes of death in the developing\nworld.", "isbn": "9781618395955", "publisher": "Curran Associates, Inc.", "place_of_publication": "San Diego, CA", "publication_date": "2011-10", "pages": "1947-1949" }, { "id": "authors:5g64k-vft82", "collection": "authors", "collection_id": "5g64k-vft82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110707-084249160", "type": "article", "title": "Focal plane tuning in wide-field-of-view microscope\n with Talbot pattern illumination", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Li", "given_name": "Zheng", "clpid": "Li-Zheng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We have developed a focal plane tuning technique for use in focus-grid-based wide-field-of-view microscopy (WFM). In WFM, the incidence of a collimated beam on a mask with a two-dimensional grid of aperture produced the Talbot images of the aperture grid. The Talbot pattern functioned as a focus grid and was used to illuminate the sample. By scanning the sample across the focus grid and collecting the transmission, we can generate a microscopy image of the sample. By tuning the wavelength of the laser, we can tune the focal plane of the WFM and acquire images of different depth into the sample. Images of a green algae microscope slide were acquired at different focal planes for demonstration.", "doi": "10.1364/OL.36.002179", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2011-06-15", "series_number": "12", "volume": "36", "issue": "12", "pages": "2179-2181" }, { "id": "authors:hx6t4-ztz49", "collection": "authors", "collection_id": "hx6t4-ztz49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110802-105801657", "type": "article", "title": "Ex Vivo Optical Coherence Tomography Imaging of\n Collector Channels with a Scanning Endoscopic Probe", "author": [ { "family_name": "Ren", "given_name": "Jian", "clpid": "Ren-Jian" }, { "family_name": "Gille", "given_name": "Henrick K.", "clpid": "Gille-H-K" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Purpose. To achieve high-fidelity optical coherence tomography (OCT) imaging of ex vivo collector channels (CCs) exiting Schlemm's canal (SC) using a paired-angle rotating scanning endoscopic probe.\nMethods. An endoscopic probe was developed to guide an OCT laser beam onto human cadaver eye tissue samples to detect CCs. The prototype probe consisted of two gradient-index (GRIN) lenses that were housed in two stainless steel needles, respectively. The probe scanned the laser beam across a fan shape area by rotating the two GRIN lenses. The authors built a swept source OCT system to provide the depth scans. Human cadaver eye tissue was prepared for imaging. OCT images were acquired while the wall of SC was scanned. After successfully locating the opening of a CC on the SC wall from the OCT images, the authors applied scanning electron microscopy (SEM) to image the sample for comparison.\nResults. The prototype probe focused the laser beam to a working distance of approximately 1.4 mm (in air), with spot sizes ranging from 12 to 14 \u03bcm. The fan shape scan area had a radius of 3 mm and an arc angle of approximately 40\u00b0. Acquired OCT images clearly showed a CC opening on the wall of SC with the channel going into the sclera, from which quantitative measurements were made. Results from OCT and SEM show good agreement with each other.\nConclusions. The resolving power of the scanning endoscopic probe is sufficient to locate CCs and to observe their shape.", "doi": "10.1167/iovs.10-6744", "issn": "0146-0404", "publisher": "Association for Research in Vision and Ophthalmology", "publication": "Investigative Ophthalmology and Visual Science", "publication_date": "2011-06", "series_number": "7", "volume": "52", "issue": "7", "pages": "3921-3925" }, { "id": "authors:55xja-zcz02", "collection": "authors", "collection_id": "55xja-zcz02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120416-084201133", "type": "book_section", "title": "Subpixel resolving optofluidic microscope based on super resolution algorithm", "book_title": "2011 IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of a fully on-chip, lensless, sub-pixel resolving optofluidic microscope (SROFM) based on the super resolution algorithm. The device utilizes microfluidic flow to deliver specimens directly across a complementary metal oxide semiconductor (CMOS) sensor to generate a sequence of low-resolution (LR) projection images, where resolution is limited by the sensor's pixel size. This image sequence is then processed with a pixel super-resolution algorithm to reconstruct a single high resolution (HR) image, where features beyond the Nyquist rate of the LR images are resolved. We demonstrate the device's capabilities by imaging red blood cell, microspheres, protist Euglena gracilis, and Entamoeba invadens cysts with sub-cellular resolution. We also demonstrate the capability of SROFM for malaria infected red blood cell diagnostics.", "doi": "10.1109/ISBI.2011.5872653", "isbn": "978-1-4244-4127-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-04", "pages": "1362-1365" }, { "id": "authors:jt7nx-wjc32", "collection": "authors", "collection_id": "jt7nx-wjc32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-105623020", "type": "book_section", "title": "Boosting detection sensitivity by using a surface-wave-enabled darkfield aperture (SWEDA)", "book_title": "Plasmonics in Biology and Medicine VIII", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Vo-Dinh", "given_name": "Tuan", "clpid": "Vo-Dinh-Tuan" }, { "family_name": "Lakowicz", "given_name": "Joseph R.", "clpid": "Lakowicz-J-R" } ], "abstract": "The on-chip detection of a weak optical signal in biological experiments can easily be complicated by the presence of an overwhelming background signal, and as such, pre-detection background suppression is substantively important for weak signal detection. In this paper, we report a structure that can be directly incorporated onto optical sensors to accomplish background suppression prior to detection. This structure, termed surface-wave-enabled darkfield aperture (SWEDA), consists of a central sub-wavelength hole surrounded by concentric grooves that are milled onto a gold layer. Incoming light can be collected and converted into surface waves (SW) by the concentric grooves and then be recoupled into propagating light through the central hole. We show that the SW-assisted optical component and the direct transmission component of the central hole can cancel each other, resulting in near-zero transmission under uniform illumination (observed suppression factor of 1230). This structure can therefore be used to suppress a light field's bright background and allow sensitive detection of localized light field non-uniformity (observed image contrast enhancement of 27dB). We also show that under a coherent background illumination, a CMOS pixel patterned with the proposed structure achieves better SNR performance than an un-patterned single pixel.", "doi": "10.1117/12.871044", "isbn": "9780819484482", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2011-02-11", "pages": "Art. No. 79110X" }, { "id": "authors:v9v4k-a5278", "collection": "authors", "collection_id": "v9v4k-a5278", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120406-105928613", "type": "book_section", "title": "Boosting Detection Sensitivity by Using a Surface-Wave-Enabled\n Darkfield Aperture (SWEDA)", "book_title": "Plasmonics in Biology and Medicine VIII", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Vo-Dinh", "given_name": "Tuan", "clpid": "Vo-Dinh-T" }, { "family_name": "Lakowicz", "given_name": "Joseph R.", "clpid": "Lakowicz-J-R" } ], "abstract": "The on-chip detection of a weak optical signal in biological experiments can easily be complicated by the presence of an overwhelming background signal, and as such, pre-detection background suppression is substantively important for weak signal detection. In this paper, we report a structure that can be directly incorporated onto optical sensors to accomplish background suppression prior to detection. This structure, termed surface-wave-enabled darkfield aperture (SWEDA), consists of a central sub-wavelength hole surrounded by concentric grooves that are milled onto a gold layer. Incoming light can be collected and converted into surface waves (SW) by the concentric grooves and then be recoupled into propagating light through the central hole. We show that the SW-assisted optical component and the direct transmission component of the central hole can cancel each other, resulting in near-zero transmission under uniform illumination (observed suppression factor of 1230). This structure can therefore be used to suppress a light field's bright background and allow sensitive detection of localized light field non-uniformity (observed image contrast enhancement of 27dB). We also show that under a coherent background illumination, a CMOS pixel patterned with the proposed structure achieves better SNR performance than an un-patterned single pixel.", "doi": "10.1117/12.871044", "isbn": "978-0-8194-8448-2", "publisher": "SPIE", "place_of_publication": "Bellingham, WA", "publication_date": "2011-02-11", "pages": "Art. No. 79110X" }, { "id": "authors:026cq-6r596", "collection": "authors", "collection_id": "026cq-6r596", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110401-104659519", "type": "book_section", "title": "Deep tissue imaging by time-reversal optical phase conjugation techniques", "book_title": "23rd Annual Meeting of the IEEE Photonics Society", "author": [ { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We recently demonstrated that it is possible to use optical phase conjugation as a means to\ntime reverse the scattering of light through biological tissue 1. This newly observed phenomenon,\ntermed turbidity suppression by optical phase conjugation (TSOPC), can potentially be adapted\nfor numerous biophotonics applications, such as coherent deep optical imaging of tissue,\nenhanced light delivery for photodynamic therapy and high sensitivity absorption spectrum\nmeasurements. In this talk, we shall report on our recent findings and discuss the potential\napplications.", "doi": "10.1109/PHOTONICS.2010.5698867", "isbn": "978-1-4244-5368-9", "publisher": "IEEE", "publication_date": "2010-11", "pages": "278-278" }, { "id": "authors:cd43n-pgm98", "collection": "authors", "collection_id": "cd43n-pgm98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100830-134234366", "type": "article", "title": "Pixel level optical-transfer-function design based on the surface-wave-interferometry aperture", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The design of optical transfer function (OTF) is of significant importance for optical information processing in various imaging and vision systems. Typically, OTF design relies on sophisticated bulk optical arrangement in the light path of the optical systems. In this letter, we demonstrate a surface-wave-interferometry aperture (SWIA) that can be directly incorporated onto optical sensors to accomplish OTF design on the pixel level. The whole aperture design is based on the bull's eye structure. It composes of a central hole (diameter of 300 nm) and periodic groove (period of 560 nm) on a 340 nm thick gold layer. We show, with both simulation and experiment, that different types of optical transfer functions (notch, highpass and lowpass filter) can be achieved by manipulating the interference between the direct transmission of the central hole and the surface wave (SW) component induced from the periodic groove. Pixel level OTF design provides a low-cost, ultra robust, highly compact method for numerous applications such as optofluidic microscopy, wavefront detection, darkfield imaging, and computational photography.", "doi": "10.1364/OE.18.016499", "pmcid": "PMC3408955", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2010-08-02", "series_number": "16", "volume": "18", "issue": "16", "pages": "16499-16506" }, { "id": "authors:x9qsy-0br53", "collection": "authors", "collection_id": "x9qsy-0br53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100830-091946797", "type": "article", "title": "Wavefront image sensor chip", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Ren", "given_name": "Jian", "clpid": "Ren-Jian" }, { "family_name": "Tearney", "given_name": "Guillermo J.", "clpid": "Tearney-G-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of an image sensor chip, termed wavefront image sensor chip (WIS), that can measure both intensity/amplitude and phase front variations of a light wave separately and quantitatively. By monitoring the tightly confined transmitted light spots through a circular aperture grid in a high Fresnel number regime, we can measure both intensity and phase front variations with a high sampling density (11 \u00b5m) and high sensitivity (the sensitivity of normalized phase gradient measurement is 0.1 mrad under the typical working condition). By using WIS in a standard microscope, we can collect both bright-field (transmitted light intensity) and normalized phase gradient images. Our experiments further demonstrate that the normalized phase gradient images of polystyrene microspheres, unstained and stained starfish embryos, and strongly birefringent potato starch granules are improved versions of their corresponding differential interference contrast (DIC) microscope images in that they are artifact-free and quantitative. Besides phase microscopy, WIS can benefit machine recognition, object ranging, and texture assessment for a variety of applications.", "doi": "10.1364/OE.18.016685", "pmcid": "PMC3408896", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2010-08-02", "series_number": "16", "volume": "18", "issue": "16", "pages": "16685-16701" }, { "id": "authors:9zabh-5kj74", "collection": "authors", "collection_id": "9zabh-5kj74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100817-110023102", "type": "article", "title": "Improving weak-signal identification via predetection background suppression by a pixel-level, surface-wave enabled dark-field aperture", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the successful implementation of a surface-wave enabled dark-field aperture (SWEDA) directly on a complementary metal-oxide semiconductor sensor pixel (2.2\u03bcm). This SWEDA pixel allows predetection cancellation of a uniform coherent background. We show that the signal-to-noise ratio (SNR) of the SWEDA pixel is better than that of a single undressed pixel over a significant range of signal-to-background ratio (SBR). For a small SBR value (SBR=0.001, background intensity=3.96W/m^2, integration time=5ms), we further demonstrate that a SWEDA pixel can detect a weak localized signal buried in a high background, while conventional postdetection background subtraction cannot (improved SNR=2.2 versus SNR=0.26).", "doi": "10.1364/OL.35.002636", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2010-08-01", "series_number": "15", "volume": "35", "issue": "15", "pages": "2636-2638" }, { "id": "authors:h5rj5-g0378", "collection": "authors", "collection_id": "h5rj5-g0378", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100806-140136350", "type": "article", "title": "Focus grid generation by in-line holography", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We describe a simple way to generate a wide-area high-resolution focus grid by in-line holography and study the factors that impacts its quality. In our holographic recording setup, the reference beam was the direct transmission of the incoming collimated laser beam through a mask coating with thin metal film, and the sample beam was the transmission of the laser through small apertures fabricated on the mask. The interference of the two beams was then recorded by a holographic plate positioned behind the mask. Compared with other recording schemes, the in-line holography scheme has many distinct advantages and is more suitable for generating a wide-area focus grid. We explored the dependence of diffraction quality, including reconstructed focus spot intensity and spot size, on different parameters for recording, such as optical density of the metal film, size of the apertures, and focal lengths. A wide-area focus grid (170 x 138 spots with area 5.1 mm x 4.1 mm) was recorded using the in-line holography scheme for a demonstration.", "doi": "10.1364/OE.18.014366", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2010-07-05", "series_number": "14", "volume": "18", "issue": "14", "pages": "14366-14374" }, { "id": "authors:3arq8-7hb62", "collection": "authors", "collection_id": "3arq8-7hb62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100712-153457723", "type": "article", "title": "Wide field-of-view microscope based on holographic focus grid illumination", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We have developed a new microscopy design that can achieve wide field-of-view (FOV) imaging and yet possesses resolution that is comparable to a conventional microscope. In our design, the sample is illuminated by a holographically projected light-spot grid. We acquire images by translating the sample across the grid and detecting the transmissions. We have built a prototype system with an FOV of 6mm\u00d75mm and acquisition time of 2.5s. The resolution is fundamentally limited by the spot size\u2014our demonstrated average FWHM spot diameter was 0.74\u03bcm. We demonstrate the prototype by imaging a U.S. Air Force target and a lily anther. This technology is scalable and represents a cost-effective way to implement wide FOV microscopy systems", "doi": "10.1364/OL.35.002188", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2010-07-01", "series_number": "13", "volume": "35", "issue": "13", "pages": "2188-2190" }, { "id": "authors:72gxe-b3m77", "collection": "authors", "collection_id": "72gxe-b3m77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100607-133514272", "type": "article", "title": "Surface-wave-enabled darkfield aperture for background suppression during weak signal detection", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Sensitive optical signal detection can often be confounded by the presence of a significant background, and, as such, predetection background suppression is substantively important for weak signal detection. In this paper, we present a novel optical structure design, termed surface-wave-enabled darkfield aperture (SWEDA), which can be directly incorporated onto optical sensors to accomplish predetection background suppression. This SWEDA structure consists of a central hole and a set of groove pattern that channels incident light to the central hole via surface plasmon wave and surface-scattered wave coupling. We show that the surface wave component can mutually cancel the direct transmission component, resulting in near-zero net transmission under uniform normal incidence illumination. Here, we report the implementation of two SWEDA structures. The first structure, circular-groove-based SWEDA, is able to provide polarization-independent suppression of uniform illumination with a suppression factor of 1230. The second structure, linear-groove-based SWEDA, is able to provide a suppression factor of 5080 for transverse-magnetic wave and can serve as a highly compact (5.5 micrometer length) polarization sensor (the measured transmission ratio of two orthogonal polarizations is 6100). Because the exact destructive interference balance is highly delicate and can be easily disrupted by the nonuniformity of the localized light field or light field deviation from normal incidence, the SWEDA can therefore be used to suppress a bright background and allow for sensitive darkfield sensing and imaging (observed image contrast enhancement of 27 dB for the first SWEDA).", "doi": "10.1073/pnas.0912563107", "pmcid": "PMC2889114", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2010-05-18", "series_number": "20", "volume": "107", "issue": "20", "pages": "9043-9048" }, { "id": "authors:vgv2t-ngn08", "collection": "authors", "collection_id": "vgv2t-ngn08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100611-155019742", "type": "article", "title": "Turbidity suppression from the ballistic to the diffusive regime in biological tissues using optical phase conjugation", "author": [ { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Vellekoop", "given_name": "Ivo M.", "clpid": "Vellekoop-I-M" }, { "family_name": "Senekerimyan", "given_name": "Vahan", "clpid": "Senekerimyan-V" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We describe the amplitude and resolution trends of the signals acquired by turbidity suppression through optical phase conjugation (TSOPC) with samples that span the ballistic and diffusive scattering regimes. In these experiments, the light field scattered through a turbid material is written into a hologram, and a time-reversed copy of the light field is played back through the sample. In this manner, the wavefront originally incident on the sample is reconstructed. We examine a range of scattering samples including chicken breast tissue sections of increasing thickness and polyacrylamide tissue-mimicking phantoms with increasing scattering coefficients. Our results indicate that only a small portion of the scattered wavefront (<0.02%) must be collected to reconstruct a TSOPC signal. Provided the sample is highly scattering, all essential angular information is contained within such small portions of the scattered wavefront due to randomization by scattering. A model is fitted to our results, describing the dependence of the TSOPC signal on other measurable values within the system and shedding light on the efficiency of the phase conjugation process. Our results describe the highest level of scattering that has been phase conjugated in biological tissues to date.", "doi": "10.1117/1.3381188", "pmcid": "PMC2874046", "issn": "1560-2281", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "publication": "Journal of Biomedical Optics", "publication_date": "2010-03", "series_number": "2", "volume": "15", "issue": "2", "pages": "Art. No. 025004" }, { "id": "authors:0dvhx-jmt72", "collection": "authors", "collection_id": "0dvhx-jmt72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110106-091729873", "type": "book_section", "title": "A wide field-of-view microscope based on holographic focus grid", "book_title": "Three-dimensional and multidimensional microscopy : image acquisition and processing XVII", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Conchello", "given_name": "Jose-Angel", "clpid": "Conchello-J-A" }, { "family_name": "Cogswell", "given_name": "Carol J.", "clpid": "Cogswell-C-J" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-T" }, { "family_name": "Brown", "given_name": "Thomas G.", "clpid": "Brown-T-G" } ], "abstract": "We have developed a novel microscope technique that can achieve wide field-of-view (FOV) imaging and yet possess resolution that is comparable to conventional microscope. The principle of wide FOV microscope system breaks the link between resolution and FOV magnitude of traditional microscopes. Furthermore, by eliminating bulky optical elements from its design and utilizing holographic optical elements, the wide FOV microscope system is more cost-effective. In our system, a hologram was made to focus incoming collimated beam into a focus grid. The sample is put in the focal plane and the transmissions of the focuses are detected by an imaging sensor. By scanning the incident angle of the incoming beam, the focus grid will scan across the sample and the time-varying transmission can be detected. We can then reconstruct the transmission image of the sample. The resolution of microscopic image is limited by the size of the focus formed by the hologram. The scanning area of each focus spot is determined by the separation of the focus spots and can be made small for fast imaging speed. We have fabricated a prototype system with a 2.4-mm FOV and 1-\u03bcm resolution. The prototype system was used to image onion skin cells for a demonstration. The preliminary experiments prove the feasibility of the wide FOV microscope technique, and the possibility of a wider FOV system with better resolution.", "doi": "10.1117/12.842303", "isbn": "978-0-8194-7966-2", "publisher": "Society of Photo-optical Instrumentation Engineers", "place_of_publication": "Bellingham, WA", "publication_date": "2010-02-24" }, { "id": "authors:creg9-s5854", "collection": "authors", "collection_id": "creg9-s5854", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100216-140439313", "type": "article", "title": "Implementation of a color-capable optofluidic microscope on a RGB CMOS color sensor chip substrate", "author": [ { "family_name": "Pang", "given_name": "Shuo", "clpid": "Pang-Shuo" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "DeModena", "given_name": "John", "clpid": "DeModena-J" }, { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of a color-capable on-chip lensless microscope system, termed color optofluidic microscope (color OFM), and demonstrate imaging of double stained Caenorhabditis elegans with lacZ gene expression at a light intensity about 10 mW/cm^2.", "doi": "10.1039/b919004j", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2010-02-21", "series_number": "4", "volume": "10", "issue": "4", "pages": "411-414" }, { "id": "authors:f5k9b-h7t50", "collection": "authors", "collection_id": "f5k9b-h7t50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161129-071637596", "type": "book_section", "title": "Simulating the optical phase conjugation phenomenon of light multiply scattered through a macroscopic random medium", "book_title": "Biomedical Applications of Light Scattering IV", "author": [ { "family_name": "Tseng", "given_name": "Snow H.", "clpid": "Tseng-Snow-H" }, { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Wax", "given_name": "Adam P.", "clpid": "Wax-A-P" }, { "family_name": "Backman", "given_name": "Vadim", "clpid": "Backman-V" } ], "abstract": "The light scattering effects of turbid media causing opacity may be undone via Optical Phase Conjugation (OPC). Here we rigorously simulate light scattering through a macroscopic random using the pseudospectral time-domain (PSTD) technique. The OPC phenomenon of multiply scattered light can be quantitatively analyzed which is not feasible otherwise. Specifically, factors affecting the electromagnetic energy propagation and refocusing phenomenon is analyzed. The reported simulation study allows accurate characterization of the optical properties of the OPC phenomenon for practical biomedical applications.", "doi": "10.1117/12.839994", "isbn": "978-0-8194-7969-3", "publisher": "Society of Photo-Optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2010-02-17", "pages": "Art. No. 757302" }, { "id": "authors:jgcdq-c0y94", "collection": "authors", "collection_id": "jgcdq-c0y94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100308-152241045", "type": "article", "title": "Implementation of a digital optical phase conjugation system and its application to study the robustness of turbidity suppression by phase conjugation", "author": [ { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In this work, we report a novel high capacity (number of degrees of freedom) open loop adaptive optics method, termed digital optical phase conjugation (DOPC), which provides a robust optoelectronic optical phase conjugation (OPC) solution. We showed that our prototype can phase conjugate light fields with ~3.9 x 10^(\u22123) degree accuracy over a range of ~3 degrees and can phase conjugate an input field through a relatively thick turbid medium (\u03bc_sl ~13). Furthermore, we employed this system to show that the reversing of random scattering in turbid media by phase conjugation is surprisingly robust and accommodating of phase errors. An OPC wavefront with significant spatial phase errors (error uniformly distributed from \u2013 \u03c0/2 to \u03c0/2) can nevertheless allow OPC reconstruction through a scattering medium with ~40% of the efficiency achieved with phase error free OPC.", "doi": "10.1364/OE.18.003444", "pmcid": "PMC3378352", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2010-02-15", "series_number": "4", "volume": "18", "issue": "4", "pages": "3444-3455" }, { "id": "authors:za6eg-a8137", "collection": "authors", "collection_id": "za6eg-a8137", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100128-092221019", "type": "article", "title": "An in vivo study of turbidity suppression by optical phase conjugation (TSOPC) on rabbit ear", "author": [ { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present a holography-based in vivo optical phase conjugation experiment performed on a living rabbit ear. The motion of live tissues caused the phase conjugate signal to decay with a consistent decay time of less than two seconds. We monitor the signal decay time variation after the ear is excised to postulate different mechanisms that cause the signal decay. The experimental findings address the minimum speed limit of a broad range of optical time reversal experiments for in vivo applications on tissues.", "doi": "10.1364/OE.18.000025", "pmcid": "PMC3369536", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2010-01-04", "series_number": "1", "volume": "18", "issue": "1", "pages": "25-30" }, { "id": "authors:yjpxa-j9b08", "collection": "authors", "collection_id": "yjpxa-j9b08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101208-115854150", "type": "book_section", "title": "Turning Tissues Transparent by Optical Phase Conjugation", "book_title": "2010 IEEE Photonics Society Winter Topicals Meeting Series (WTM)", "author": [ { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We recently implemented a digital optical phase conjugation mirror by combining a spatial light modulator and a digital holography system. This system provides us with additional flexibility in modifying the scattered wavefront for TSOPC transmission experiments. These results are discussed in detail in this presentation.", "doi": "10.1109/PHOTWTM.2010.5421941", "isbn": "978-1-4244-5240-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-01", "pages": "78-79" }, { "id": "authors:yvf97-dhp58", "collection": "authors", "collection_id": "yvf97-dhp58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101004-084011087", "type": "article", "title": "Sub-pixel resolving optofluidic microscope for on-chip cell imaging", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Lee", "given_name": "Seung Ah", "clpid": "Lee-Seung-Ah" }, { "family_name": "Yang", "given_name": "Samuel", "clpid": "Yang-Samuel" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of a fully on-chip, lensless, sub-pixel resolving optofluidic microscope (SROFM). The device utilizes microfluidic flow to deliver specimens directly across a complementary metal oxide semiconductor (CMOS) sensor to generate a sequence of low-resolution (LR) projection images, where resolution is limited by the sensor's pixel size. This image sequence is then processed with a pixel super-resolution algorithm to reconstruct a single high resolution (HR) image, where features beyond the Nyquist rate of the LR images are resolved. We demonstrate the device's capabilities by imaging microspheres, protist Euglena gracilis, and Entamoeba invadens cysts with sub-cellular resolution and establish that our prototype has a resolution limit of 0.75 microns. Furthermore, we also apply the same pixel super-resolution algorithm to reconstruct HR videos in which the dynamic interaction between the fluid and the sample, including the in-plane and out-of-plane rotation of the sample within the flow, can be monitored in high resolution. We believe that the powerful combination of both the pixel super-resolution and optofluidic microscopy techniques within our SROFM is a significant step forwards toward a simple, cost-effective, high throughput and highly compact imaging solution for biomedical and bioscience needs.", "doi": "10.1039/c0lc00213e", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2010", "series_number": "10 (22", "volume": "2010", "issue": "10 (22", "pages": "3125-3129" }, { "id": "authors:qb3x3-bn866", "collection": "authors", "collection_id": "qb3x3-bn866", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100113-153922944", "type": "article", "title": "Characterization of acceptance angles of small circular apertures", "author": [ { "family_name": "Wang", "given_name": "Ying Min", "clpid": "Wang-Ying-Min" }, { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We characterize the acceptance angles of small circular apertures for light collection by simulations and experimental measurements. By examining the full width half maximum acceptance angle as a function of the aperture size, we show that the acceptance angle of a circular aperture reaches a minimum of 67 deg before rebounding around the transition between single mode and multimode transmission (approximately 400 nm). This behavior can be explained by the change of mode-coupling efficiency\nduring the transition from single mode to multimode propagation regime. This work in understanding of the behavior of light transmission through subwavelength apertures will guide the design of better aperture based\nimaging devices where apertures are used as light collection units.", "doi": "10.1364/OE.17.023903", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2009-12-21", "series_number": "26", "volume": "17", "issue": "26", "pages": "23903-23913" }, { "id": "authors:tkyfh-y4r19", "collection": "authors", "collection_id": "tkyfh-y4r19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091123-162311427", "type": "article", "title": "Manual-scanning optical coherence tomography probe based on position tracking", "author": [ { "family_name": "Ren", "given_name": "Jian", "clpid": "Ren-Jian" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "A method based on position tracking to reconstruct images for a manual-scanning optical coherence tomography (OCT) probe is proposed and implemented. The method employs several feature points on a hand-held probe and a camera to track the device's pose. The continuous device poses tracking, and the collected OCT depth scans can then be combined to render OCT images. The tracking accuracy of the system was characterized to be about 6 \u03bcm along two axes and 19 \u03bcm along the third. A phantom target was used to validate the method. In addition, we report OCT images of a 54-stage Xenopus laevis tadpole acquired by manual scanning.", "doi": "10.1364/OL.34.003400", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2009-11-01", "series_number": "21", "volume": "34", "issue": "21", "pages": "3400-3402" }, { "id": "authors:0geyh-cs743", "collection": "authors", "collection_id": "0geyh-cs743", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091029-142950975", "type": "article", "title": "The application of on-chip optofluidic microscopy for imaging Giardia lamblia trophozoites and cysts", "author": [ { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The optofluidic microscope (OFM) is a lensless, low-cost and highly compact on-chip device that can enable high-resolution microscopy imaging. The OFM performs imaging by flowing/scanning the target objects across a slanted hole array; by measuring the time-varying light transmission changes through the holes, we can then render images of the target objects at a resolution that is comparable to the holes' size. This paper reports the adaptation of the OFM for imaging Giardia lamblia trophozoites and cysts, a disease-causing parasite species that is commonly found in poor-quality water sources. We also describe our study of the impact of pressure-based flow and DC electrokinetic-based flow in controlling the flow motion of Giardia cysts\u2014rotation-free translation of the parasite is important for good OFM image acquisition. Finally, we report the successful microscopy imaging of both Giardia trophozoites and cysts with an OFM that has a focal plane resolution of 0.8 microns.", "doi": "10.1007/s10544-009-9312-x", "pmcid": "PMC2888668", "issn": "1387-2176", "publisher": "Springer", "publication": "Biomedical Microdevices", "publication_date": "2009-10", "series_number": "5", "volume": "11", "issue": "5", "pages": "951-958" }, { "id": "authors:bjqxr-7ea90", "collection": "authors", "collection_id": "bjqxr-7ea90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091021-074610309", "type": "article", "title": "Observation of polarization-gate based reconstruction quality improvement during the process of turbidity suppression by optical phase conjugation", "author": [ { "family_name": "Cui", "given_name": "Meng", "clpid": "Cui-Meng" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present experiments that study the impact of polarization selection on the phenomenon of turbidity suppression by optical phase conjugation. Counter to intuition, we discovered that the preferential utilization of multiply scattered light field components over their sparsely scattered counterparts via appropriate polarization selection can lead to better image reconstruction quality. This effect was observed with tissue phantoms and biological tissue sections. The physical origin of this effect and its dependence on scatterer properties are discussed.", "doi": "10.1063/1.3236836", "pmcid": "PMC2766401", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2009-09-21", "series_number": "12", "volume": "95", "issue": "12", "pages": "Art. No. 123702" }, { "id": "authors:6sddx-9sh75", "collection": "authors", "collection_id": "6sddx-9sh75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090821-163239224", "type": "article", "title": "A phase conjugate mirror inspired approach for building cloaking structures with left-handed materials", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In this paper, we propose and examine a new cloaking method, which was inspired by the close correspondence between a phase conjugate mirror and the interface between a pair of matched right-handed material (RHM) and left-handed material (LHM) media. Using this method, we show that a symmetric conducting shell embedded in the interface junction of an isotropic RHM layer and an isotropic negative index or LHM layer can serve as a limited cloaking structure. The proposed structure presents an anomalously small scattering cross-section to an incident propagating electromagnetic (EM) field. The interior of the shell can be used to shield small objects from interrogation. We report the results of 2D finite-element-method (FEM) simulations that were performed to verify the principle, and discuss the limitations of the proposed structure.", "doi": "10.1088/1367-2630/11/3/033010", "pmcid": "PMC2814323", "issn": "1367-2630", "publisher": "IOP", "publication": "New Journal of Physics", "publication_date": "2009-03-04", "series_number": "3", "volume": "11", "issue": "3", "pages": "Art. No. 033010" }, { "id": "authors:x435x-13733", "collection": "authors", "collection_id": "x435x-13733", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WUJoe08", "type": "article", "title": "The application of Fresnel zone plate based projection in optofluidic microscopy", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Optofluidic microscopy (OFM) is a novel technique for low-cost, high-resolution on-chip microscopy imaging. In this paper we report the use of the Fresnel zone plate (FZP) based projection in OFM as a cost-effective and compact means for projecting the transmission through an OFM's aperture array onto a sensor grid. We demonstrate this approach by employing a FZP (diameter = 255 \u00b5m, focal length = 800 \u00b5m) that has been patterned onto a glass slide to project the transmission from an array of apertures (diameter = 1 \u00b5m, separation = 10 \u00b5m) onto a CMOS sensor. We are able to resolve the contributions from 44 apertures on the sensor under the illumination from a HeNe laser (wavelength = 633 nm). The imaging quality of the FZP determines the effective field-of-view (related to the number of resolvable transmissions from apertures) but not the image resolution of such an OFM system -- a key distinction from conventional microscope systems. We demonstrate the capability of the integrated system by flowing the protist Euglena gracilis across the aperture array microfluidically and performing OFM imaging of the samples.", "doi": "10.1364/OE.16.015595", "pmcid": "PMC2688452", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2008-09-29", "series_number": "20", "volume": "16", "issue": "20", "pages": "15595-15602" }, { "id": "authors:b5vm8-vz998", "collection": "authors", "collection_id": "b5vm8-vz998", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CUIapl08", "type": "article", "title": "Quantitative differential interference contrast microscopy based on structured-aperture interference", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Lew", "given_name": "Matthew", "clpid": "Lew-M" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a quantitative differential interference contrast (DIC) microscope based on a structured-aperture (SA) wavefront sensor. Unlike a conventional DIC microscope, the SA-DIC microscope can separate the amplitude and the phase gradient information of the image wavefront, and form quantitative intensity and DIC images of the sample with good resolution; our prototype achieved resolution ~2 \u00b5m. Furthermore, due to the nonpolarization nature of the microscope, we were able to image birefringent samples without artifacts.", "doi": "10.1063/1.2977870", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2008-09-01", "series_number": "9", "volume": "93", "issue": "9", "pages": "Art. No. 091113" }, { "id": "authors:f640y-5p079", "collection": "authors", "collection_id": "f640y-5p079", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CUIpnas08", "type": "article", "title": "Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Zhong", "given_name": "Weiwei", "clpid": "Zhong-Weiwei" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (\u22480.9 \u03bcm for the first and \u22480.8 \u03bcm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.", "doi": "10.1073/pnas.0804612105", "pmcid": "PMC2488383", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2008-08-05", "series_number": "31", "volume": "105", "issue": "31", "pages": "10670-10675" }, { "id": "authors:pddhj-b8h08", "collection": "authors", "collection_id": "pddhj-b8h08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCDoe08", "type": "article", "title": "Fundamental sensitivity limit imposed by dark 1/f noise in the low optical signal detection regime", "author": [ { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Ren", "given_name": "Jian", "clpid": "Ren-Jian" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The impact of dark 1/f noise on fundamental signal sensitivity in direct low optical signal detection is an understudied issue. In this theoretical manuscript, we study the limitations of an idealized detector with a combination of white noise and 1/f noise, operating in detector dark noise limited mode. In contrast to white noise limited detection schemes, for which there is no fundamental minimum signal sensitivity limit, we find that the 1/f noise characteristics, including the noise exponent factor and the relative amplitudes of white and 1/f noise, set a fundamental limit on the minimum signal that such a detector can detect.", "doi": "10.1364/OE.16.006822", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2008-05-12", "series_number": "10", "volume": "16", "issue": "10", "pages": "6822-6832" }, { "id": "authors:vgczw-xd208", "collection": "authors", "collection_id": "vgczw-xd208", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HANjbo08", "type": "article", "title": "Handheld forward-imaging needle endoscope for ophthalmic optical coherence tomography inspection", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Humayun", "given_name": "Mark", "orcid": "0000-0002-5830-5208", "clpid": "Humayun-M-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the narrowest to-date (21 gauge, 820-\u00b5m-diam) handheld forward-imaging optical coherence tomography (OCT) needle endoscope and demonstrate its feasibility for ophthalmic OCT inspection. The probe design is based on paired-angle-rotation scanning (PARS), which enables a linear B-scan pattern in front of the probe tip by using two counterrotating angle polished gradient-index (GRIN) lenses. Despite its small size, the probe can provide a numerical apertune (NA) of 0.22 and an experimental sensitivity of 92 dB at 0.5 frames. The feasibility of retinal imaging is tested on enucleated ex vivo porcine eyes, where structural features including remnant vitreous humor, retina, and choroid can be clearly distinguished. Due to its imaging quality comparable to a commercial OCT system and compatibility with the current ophthalmic surgery standard, the probe can potentially serve as a better alternative to traditional visual inspection by white light illumination during vitreoretinal surgery (e.g., vitrectomy).", "doi": "10.1117/1.2904664", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2008-03", "series_number": "2", "volume": "13", "issue": "2", "pages": "Art. No. 020505" }, { "id": "authors:rwbb9-ynm72", "collection": "authors", "collection_id": "rwbb9-ynm72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-110458635", "type": "book_section", "title": "Optofluidic microscope: a complete on-chip imaging device", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues VI", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-D-L" }, { "family_name": "Nicolau", "given_name": "Dan V,", "clpid": "Nicolau-D-V" }, { "family_name": "Leif", "given_name": "Robert C.", "clpid": "Leif-R-C" } ], "abstract": "This paper reports a complete on-chip high resolution lensless imaging device based on the optofluidic microscopy method, which can form a vital optical microscopy component in a wide range of lab-on-a-chip systems. This imaging device does not use any lens elements and yet is capable of resolution comparable to that of a conventional microscope with a 20\u00d7 objective. We demonstrate the use of the device for Caenorhabditis elegans and microsphere imaging at a resolution of ~ 1 \u03bcm with an imaging time of ~2 sec. The fabrication of this on-chip imaging device is fully compatible with existing semiconductor and microfluidic technologies, so the device can be massively fabricated and integrated into microsystems to form compact and low-cost total analysis systems for biological and colloidal studies.", "doi": "10.1117/12.764957", "isbn": "9780819470348", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2008-02-29", "pages": "Art. No. 68590Y" }, { "id": "authors:93qvp-0re47", "collection": "authors", "collection_id": "93qvp-0re47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-142556625", "type": "book_section", "title": "Two-dimensional differential interference contrast microscopy based on four-hole variation of Young's interference", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues VI", "author": [ { "family_name": "Lew", "given_name": "Matthew", "clpid": "Lew-M" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-D-L" }, { "family_name": "Nicolau", "given_name": "Dan V.", "clpid": "Nicolau-D-V" }, { "family_name": "Leif", "given_name": "Robert C.", "clpid": "Leif-R-C" } ], "abstract": "We demonstrate a novel method of two-dimensional differential interference contrast (DIC) microscopy. Our method is cheaper, more compact, and more robust compared to conventional DIC microscopes; since it uses a simple variation of Young's double-slit geometry, no expensive or complex optical components are needed. In addition, our method quantitatively measures differential phase, unlike conventional DIC, which makes our device useful for optical metrology and cell biology applications. The device consists of four circular holes arranged in a \"plus\" pattern, milled into a metal layer 80 \u03bcm above a complimentary metal-oxide semiconductor (CMOS) image sensor. Light incident upon the four-hole aperture is transmitted through the holes and creates an interference pattern on the CMOS sensor. This pattern shifts as a function of the spatial phase gradient of the incident light. By capturing the amplitude and location of the zero-order fringe of the interference pattern, the amplitude and differential phase of the incident light can be measured simultaneously. In this article, we model the response of the device using both geometric optics and Huygens principle. We then verify these models by experimentally measuring the responsivity of our device. A short analysis on the algorithm used to calculate the fringe location follows. We then show a beam profiling application by measuring the amplitude and spatial phase gradient of a Gaussian laser beam and an optical vortex. Finally, we show a DIC microscope application; we image a phase mask of the letters \"CIT\".", "doi": "10.1117/12.760118", "isbn": "9780819470348", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2008-02-29", "pages": "Art. No. 685916" }, { "id": "authors:aw324-2aj08", "collection": "authors", "collection_id": "aw324-2aj08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-104437388", "type": "book_section", "title": "Observing dynamics of transparent samples by harmonically matched grating-based full-field quadrature phase interferometer", "book_title": "Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XV", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Conchello", "given_name": "Jose-Angel", "clpid": "Conchello-J-A" }, { "family_name": "Cogswell", "given_name": "Carol J.", "clpid": "Cogswell-C-J" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-T" }, { "family_name": "Brown", "given_name": "Thomas G.", "clpid": "Brown-T-G" } ], "abstract": "Our group has reported the use of harmonically matched diffraction grating for full-field quantitative phase imaging. In this paper, we show the improvement of this technique and the application in observing dynamics of transparent samples. By using the grating as a beam splitter/combiner in an interferometer, we are able to obtain non-trivial phase difference between the output ports of the grating. We have built a Mach-Zehnder interferometer using the holographic grating with 600 and 1200 lines/mm spacing. Two CCD cameras at the output ports of the grating-based Mach-Zehnder interferometer are used to record the full-field quadrature interferograms, which are subsequently processed to reconstruct the phase image. Since the two quadrature interferograms are acquired at the same time, the imaging speed of the system is limited only by the frame rate of the CCD cameras. We have demonstrated the capability of our system by observing dynamics of transparent samples.", "doi": "10.1117/12.759210", "isbn": "9780819470362", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2008-02-20", "pages": "Art. No. 686102" }, { "id": "authors:5zdtv-r8396", "collection": "authors", "collection_id": "5zdtv-r8396", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161128-131905468", "type": "article", "title": "Optical phase conjugation for turbidity suppression in biological samples", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Elastic optical scattering, the dominant light-interaction process in biological tissues, prevents tissues from being transparent. Although scattering may appear stochastic, it is in fact deterministic in nature. We show that, despite experimental imperfections, optical phase conjugation (\u03bb = 532 nm) can force a transmitted light field to retrace its trajectory through a biological target and recover the original light field. For a 0.69-mm-thick chicken breast tissue section, we can enhance point-source light return by a factor of ~5 x 10^3 and achieve a light transmission enhancement factor of 3.8 within a collection angle of 29\u00b0. Additionally, we find that the reconstruction's quality, measured by the width of the reconstructed point source, is independent of tissue thickness (up to a thickness of 0.69 mm). This phenomenon may be used to enhance light transmission through tissue, enable measurement of small tissue movements, and form the basis of new tissue imaging techniques.", "doi": "10.1038/nphoton.2007.297", "pmcid": "PMC2688902", "issn": "1749-4885", "publisher": "Nature Publishing Group", "publication": "Nature Photonics", "publication_date": "2008-02", "series_number": "2", "volume": "2", "issue": "2", "pages": "110-115" }, { "id": "authors:vxwqj-47p77", "collection": "authors", "collection_id": "vxwqj-47p77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WUJoe07.pdf", "type": "article", "title": "Harmonically matched grating-based full-field quantitative high-resolution phase microscope for observing dynamics of transparent biological samples", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We have developed a full-field high resolution quantitative phase imaging technique for observing dynamics of transparent biological samples. By using a harmonically matched diffraction grating pair (600 and 1200\nlines/mm), we were able to obtain non-trivial phase difference (other than 0\u00b0 or 180\u00b0) between the output ports of the gratings. Improving upon our previous design, our current system mitigates astigmatism artifacts and is\ncapable of high resolution imaging. This system also employs an improved phase extraction algorithm. The system has a lateral resolution of 1.6 \u03bcm and a phase sensitivity of 62 mrad. We employed the system to acquire high resolution phase images of onion skin cells and a phase movie of amoeba\nproteus in motion.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-12-24", "series_number": "26", "volume": "15", "issue": "26", "pages": "18141-18155" }, { "id": "authors:t1t9x-jjj47", "collection": "authors", "collection_id": "t1t9x-jjj47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HENoe07", "type": "article", "title": "An optical tweezer actuated, nanoaperture-grid based optofluidic microscope implementation method", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Hsiao", "given_name": "Edward", "clpid": "Hsiao-Edward" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a novel grid based Optofluidic Microscope (OFM) method where a closely spaced 2D grid of nanoapertures (diameter = 100 nm, separation = 2.5 \u03bcm) provided patterned illumination. We achieved a one-to-one mapping of the light transmissions through the nanoapertures onto a high-speed CCD camera. By optically tweezing a targeted sample across the grid in a controlled fashion and recording the time varying light reception from the nanoapertures, we were able to generate high-resolution images of the sample. The achievable resolution limit of the prototype was ~ 110 nm (Sparrow's criterion) under optimal conditions. We demonstrated the technique by imaging polystyrene beads and pollen spores.", "doi": "10.1364/OE.15.016367", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-12-10", "series_number": "25", "volume": "15", "issue": "25", "pages": "16367-16375" }, { "id": "authors:bpnj9-k1c17", "collection": "authors", "collection_id": "bpnj9-k1c17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TSEoe07", "type": "article", "title": "2-D PSTD simulation of optical phase conjugation for turbidity suppression", "author": [ { "family_name": "Tseng", "given_name": "Snow H.", "clpid": "Tseng-Snow-H" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Turbidity Suppression via Optical Phase Conjugation (TS-OPC)\nis an optical phenomenon that uses the back propagation nature of optical phase conjugate light field to undo the effect of tissue scattering. We use the computationally efficient and accurate pseudospectral time-domain (PSTD) simulation method to study this phenomenon; a key adaptation is the volumetric inversion of the optical wavefront E-field as a means for simulating a phase conjugate mirror. We simulate a number of scenarios and demonstrate that TS-OPC deteriorates with increased scattering in the medium, or increased mismatch between the random medium and the phase\nconjugate wave during reconstruction.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-11-26", "series_number": "24", "volume": "15", "issue": "24", "pages": "16005-16016" }, { "id": "authors:r00kw-m8v08", "collection": "authors", "collection_id": "r00kw-m8v08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ZHEoe07", "type": "article", "title": "Electromagnetic equivalent model for phase conjugate mirror based on the utilization of left-handed material", "author": [ { "family_name": "Zheng", "given_name": "Guoan", "clpid": "Zheng-Guoan" }, { "family_name": "Ran", "given_name": "Lixin", "clpid": "Ran-Lixin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "An electromagnetic equivalent model for the phase conjugate mirror (PCM) is proposed in this paper. The model is based on the unique property of the isotropic left-handed material (LHM) - the ability of LHM to reverse the phase factors of propagative waves. We show that a PCM interface can be substituted with a LHM-RHM (right-handed material) interface and associated image sources and objects in the LHM. This equivalent model is fully equivalent in the treatment of propagative wave components. However, we note that the presence of evanescent wave components can lead to undesirably surface resonance at the LHM-RHM interface. This artefact can be kept well bounded by introducing a small refractive index mismatch between the LHM and RHM. We demonstrate the usefulness of this model by modelling several representative scenarios of light patterns interacting with a PCM. The simulations were performed by applying the equivalent model to a commercial finite element method (FEM) software. This equivalent model also points to the intriguing possibility of realizing some unique LHM based systems in the optical domain by substituting a PCM in place of a LHM-RHM interface.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-10-17", "series_number": "21", "volume": "15", "issue": "21", "pages": "13877-13885" }, { "id": "authors:j6cp2-qpz62", "collection": "authors", "collection_id": "j6cp2-qpz62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEWol07", "type": "article", "title": "Interference of a four-hole aperture for on-chip quantitative two-dimensional differential phase imaging", "author": [ { "family_name": "Lew", "given_name": "Matthew", "clpid": "Lew-M" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present a novel on-chip method for quantitative two-dimensional differential phase imaging. This technique uses four circular holes (600 nm diameter, 1.2 \u03bcm spacing) arranged in a 'plus' pattern that are fabricated in a layer of metal above a complementary metal-oxide semiconductor (CMOS) imaging sensor. The interference pattern of the aperture shifts position with respect to the differential phase of the incident light. By imaging the interference pattern with the CMOS sensor, this method measures amplitude and differential phase (1\u00b0/\u03bcm sensitivity for signal-to-noise ratio \u226516 dB) of the incident light field simultaneously. An application to optical beam profiling is presented; we show the amplitude and differential phase profiles of a Gaussian laser beam and an optical vortex.", "issn": "0146-9592", "publisher": "Optics Letters", "publication": "Optics Letters", "publication_date": "2007-10-15", "series_number": "20", "volume": "32", "issue": "20", "pages": "2963-2965" }, { "id": "authors:a8kfb-zgg64", "collection": "authors", "collection_id": "a8kfb-zgg64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FINoe07", "type": "article", "title": "Mobility and transverse flow visualization using phase variance contrast with spectral domain optical coherence tomography", "author": [ { "family_name": "Fingler", "given_name": "Jeff", "clpid": "Fingler-J" }, { "family_name": "Schwartz", "given_name": "Dan", "clpid": "Schwartz-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" } ], "abstract": "Phase variance-based motion contrast is demonstrated using two phase analysis methods in a spectral domain optical coherence tomography system. Mobility contrast is demonstrated for an intensity matched Intralipid solution placed without flow within agarose wells. Vasculature oriented transversely to the imaging direction has been imaged for 3-4 dpf in vivo zebrafish using the phase variance contrast methods. 2D phase variance contrast images are demonstrated with imaging times only 25% higher than a Doppler flow image with comparable statistics. En face images created by integrating depth regions of 3D zebrafish intensity and phase variance contrast data demonstrate vasculature consistent with expected images.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-10-01", "series_number": "20", "volume": "15", "issue": "20", "pages": "12636-12653" }, { "id": "authors:yxd7s-eq087", "collection": "authors", "collection_id": "yxd7s-eq087", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCDoe07b", "type": "article", "title": "SNR enhancement through phase dependent signal reconstruction algorithms for phase separated interferometric signals", "author": [ { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report several signal reconstruction algorithms for processing phase separated homodyne interferometric signals. Methods that take advantage of the phase of the signal are experimentally shown to achieve a signal-to-noise ratio (SNR) improvement of up to 5 dB over commonly used algorithms. To begin, we present a derivation of the SNR resulting from five image reconstruction algorithms in the context of a 3x3 fiber-coupler based homodyne optical coherence tomography (OCT) system, and clearly show the improvement in SNR associated with phase-based algorithms. Finally, we experimentally verify this improvement and demonstrate the enhancement in contrast and improved image quality afforded by these algorithms through homodyne OCT imaging of a Xenopus laevis tadpole. These algorithms can be generally applied in signal extraction processing where multiple phase separated measurements are available.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-08-06", "series_number": "16", "volume": "15", "issue": "16", "pages": "10103-10122" }, { "id": "authors:49c9f-72k34", "collection": "authors", "collection_id": "49c9f-72k34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WUJapl07a.997", "type": "article", "title": "Full field phase imaging using a harmonically matched diffraction grating pair based homodyne quadrature interferometer", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In this letter, the authors present a novel quadrature interferometry method based on the use of a harmonically matched shallow grating pair. Unlike a simple beam splitter or single shallow grating, the grating pair can confer a nontrivial interference phase shift (other than 0\u00b0 or 180\u00b0) between the output ports of the interferometer. Using the grating pair as the beam splitter/combiner, the authors implement a homodyne quadrature full field phase interferometer and demonstrate the system's capability to acquire phase and amplitude images.", "doi": "10.1063/1.2722685", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2007-04-09", "series_number": "15", "volume": "90", "issue": "15", "pages": "Art. No. 151123" }, { "id": "authors:9ks91-w6t59", "collection": "authors", "collection_id": "9ks91-w6t59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCDoe07a", "type": "article", "title": "A generalized noise variance analysis model and its application to the characterization of 1/f noise", "author": [ { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We present a novel generalized model for the analysis of noise with a known spectral density. This model is particularly appropriate for the analysis of noise with a 1/f^a distribution in a homodyne interferometer. The noise model reveals that, for \u03b1>1, 1/f^a noise significantly impacts the homodyne signal-to-noise ratio (SNR) for integration times that near a characteristic time, beyond which the SNR will no longer significantly improve with increasing integration time. We experimentally verify our theoretical findings with a set of experiments employing a quadrature homodyne optical coherence tomography (OCT) system, finding good agreement. The characteristic integration time is measured to be approximately 2 ms for our system. Additionally, we find that the 1/f noise characteristics, including the exponent, \u03b1, as well as the characteristic integration time, are system and photodetector dependent.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2007-04-02", "series_number": "7", "volume": "15", "issue": "7", "pages": "3833-3848" }, { "id": "authors:mxb6t-ted56", "collection": "authors", "collection_id": "mxb6t-ted56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-105032476", "type": "book_section", "title": "Toward forward-looking OCT needle tip vision of the spinal neuroforamen: animal studies", "book_title": "Photonic Therapeutics and Diagnostics III", "author": [ { "family_name": "Raphael", "given_name": "David T.", "clpid": "Raphael-D-T" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Tresser", "given_name": "Nancy", "clpid": "Tresser-N" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Zhang", "given_name": "Yaoping", "clpid": "Zhang-Yaoping" }, { "family_name": "Feldchtein", "given_name": "Felix", "clpid": "Feldchtein-F" }, { "family_name": "Rever", "given_name": "Linda", "clpid": "Rever-L" } ], "contributor": [ { "family_name": "Hirschberg", "given_name": "Henry", "clpid": "Hirschberg-H" }, { "family_name": "Madsen", "given_name": "Steen J.", "clpid": "Madsen-S-J" }, { "family_name": "Wong", "given_name": "Brian Jet-Fei", "clpid": "Wong-Brian-Jet-Fei" }, { "family_name": "Ilgner", "given_name": "Justus F. R.", "clpid": "Ilgner-J-F-R" }, { "family_name": "Malek", "given_name": "Reza S.", "clpid": "Malek-R-S" }, { "family_name": "Gregory", "given_name": "Kenton W.", "clpid": "Gregory-K-W" }, { "family_name": "Tearney", "given_name": "Guillermo J.", "clpid": "Tearney-G-J" }, { "family_name": "Kollias", "given_name": "Nikiforos", "clpid": "Kollias-N" }, { "family_name": "Choi", "given_name": "Bernard", "clpid": "Choi-Bernard" }, { "family_name": "Zeng", "given_name": "Haishan", "clpid": "Zeng-Haishan" } ], "abstract": "Neurologic complications have been reported with spinal transforaminal injections. Causes include intraneural injection, plus embolization occlusion of the radicular artery with subsequent spinal cord infarction. 1 Optical coherence tomography (OCT) is a non-invasive imaging modality, which is used to image tissue microstructure with very high resolution (less than 20 microns) in real-time. With a view toward needle tip OCT visualization of the spinal neuroforamen, we conducted animal studies to explore OCT imaging of paraspinal neurovascular structures. With institutional animal care committee approval, we performed ex-vivo and in situ OCT studies in a euthanized dog, pig, and rabbit. Image data was gathered on spinal nerve roots, dura, and brachial plexus. Two systems were used: frequency domain OCT imaging system developed at California Institute of Technology, and time domain Imalux NIRIS system with a 2.7 mm diameter probe. In a euthanized pig, excised dura was punctured with a 17-gauge Tuohy needle. FDOCT dural images of the puncture showed a subsurface cone-shaped defect. In a rabbit in situ study, puncture of the dura with a 26-gauge needle is imaged as a discontinuity. FDOCT imaging of both small artery and large arteries will be presented, along with H&E and OCT images of the brachial plexus.", "doi": "10.1117/12.703188", "isbn": "0819465372", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-03-23", "pages": "Art. No. 642429" }, { "id": "authors:pfasm-1gt96", "collection": "authors", "collection_id": "pfasm-1gt96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-110055154", "type": "book_section", "title": "Harmonically-related gratings-based quadrature phase interferometers", "book_title": "Practical Holography XXI: Materials and Applications", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Lessard", "given_name": "Roger A.", "clpid": "Lessard-R-A" }, { "family_name": "Bjelkhagen", "given_name": "Hans I.", "clpid": "Bjelkhagen-H-I" } ], "abstract": "We report a new method for obtaining non-trivial phase difference between the output ports of an interferometer through the use of shallow diffraction gratings. We show that as opposed to a single shallow diffraction grating-based interferometer (which provides only trivial phase shifts, i.e., 0\u00b0 or 180\u00b0), a pair of harmonically-related shallow diffraction gratings can be used to design interferometers with non-trivial phase shifts between different output ports. More importantly, the phase shifts can be adjusted by simply shearing one grating with respect to the other. This approach does not change the path length relationships of the different interference beams within the interferometer, which is an advantage for metrology and low coherence interferometry applications.", "doi": "10.1117/12.701585", "isbn": "9780819466013", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-20", "pages": "Art. No. 64880J" }, { "id": "authors:b8m8q-4vp06", "collection": "authors", "collection_id": "b8m8q-4vp06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-110718056", "type": "book_section", "title": "A high-resolution optofluidic microscope with optical tweezer actuation", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues V", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Hsiao", "given_name": "Edward", "clpid": "Hsiao-Edward" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-D-L" }, { "family_name": "Leif", "given_name": "Robert C.", "clpid": "Leif-R-C" }, { "family_name": "Nicolau", "given_name": "Dan V.", "clpid": "Nicolau-D-V" } ], "abstract": "In this paper, we will report our recent development of a new type of OptoFluidic Microscope (OFM) that is capable of delivering resolution beyond the diffraction limit of light. Accurate control of the sample translation is accomplished by adopting an optical tweezer scanner into the system. During the image acquisition, a two-dimensional nanoaperture array defined on a thin aluminum film acts as an array of ultra-fine illumination sources. The imaging system is tested and demonstrated by using polystyrene beads and green algae (Chlamydomonas). Properties of the system are reported and discussed.", "doi": "10.1117/12.701728", "isbn": "9780819465542", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-19", "pages": "Art. No. 644113" }, { "id": "authors:exjvd-ye151", "collection": "authors", "collection_id": "exjvd-ye151", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-111252346", "type": "book_section", "title": "On-chip differential interference contrast (DIC) phase imager and beam profiler based on Young's interference", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues V", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Lew", "given_name": "Matthew", "clpid": "Lew-M" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-D-L" }, { "family_name": "Leif", "given_name": "Robert C.", "clpid": "Leif-R-C" }, { "family_name": "Nicolau", "given_name": "Dan V.", "clpid": "Nicolau-D-V" } ], "abstract": "In this article, we will present a novel differential interference contrast (DIC) phase imaging device based on Young's interference. It is mainly based on either two or four nano apertures defined in an optically opaque aluminum film on a CMOS imaging sensor chip. It provides linear and disentangled differential phase and intensity images simultaneously. Furthermore, it's simple, free of bulky optical elements and compatible to the planar micro fabrication process. All of these features make it a promising device for the on-chip high resolution DIC phase imaging and beam profiling. The fabrication and operation of the device is explained in details. The performance is evaluated theoretically and is verified experimentally by examining the phase and intensity profile of a Gaussian beam and an optical vortex. The 2D quantitive differential phase distribution of an optical vortex has been recorded directly by our device with 1\u03bcm resolution.", "doi": "10.1117/12.699920", "isbn": "9780819465542", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-19", "pages": "Art. no. 64411F" }, { "id": "authors:ynjfk-azn64", "collection": "authors", "collection_id": "ynjfk-azn64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-111909823", "type": "book_section", "title": "Quantitative phase imaging using grating-based quadrature phase interferometer", "book_title": "Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Conchello", "given_name": "Jose-Angel", "clpid": "Conchello-J-A" }, { "family_name": "Cogswell", "given_name": "Carol J.", "clpid": "Cogswell-C-J" }, { "family_name": "Wilson", "given_name": "Tony", "clpid": "Wilson-T" } ], "abstract": "In this paper, we report the use of holographic gratings, which act as the free-space equivalent of the 3x3 fiber-optic coupler, to perform full field phase imaging. By recording two harmonically-related gratings in the same holographic plate, we are able to obtain nontrivial phase shift between different output ports of the gratings-based Mach-Zehnder interferometer. The phase difference can be adjusted by changing the relative phase of the recording beams when recording the hologram. We have built a Mach-Zehnder interferometer using harmonically-related holographic gratings with 600 and 1200 lines/mm spacing. Two CCD cameras at the output ports of the gratings-based Mach-Zehnder interferometer are used to record the full-field quadrature interferograms, which are subsequently processed to reconstruct the phase image. The imaging system has ~12X magnification with ~420\u03bcmx315\u03bcm field-of-view. To demonstrate the capability of our system, we have successfully performed phase imaging of a pure phase object and a paramecium caudatum.", "doi": "10.1117/12.701694", "isbn": "9780819465566", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-14", "pages": "Art. No. 64430J" }, { "id": "authors:b98ev-gb183", "collection": "authors", "collection_id": "b98ev-gb183", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-112420158", "type": "book_section", "title": "Imaging vasculature independent of direction of flow using spectral domain optical coherence tomography", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine XI", "author": [ { "family_name": "Fingler", "given_name": "J.", "clpid": "Fingler-J" }, { "family_name": "Williams", "given_name": "J.", "clpid": "Williams-J" }, { "family_name": "Yang", "given_name": "C.", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Fraser", "given_name": "S. E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" } ], "contributor": [ { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" } ], "abstract": "A variation to the analysis of phase data achieved with spectral domain optical coherence tomography (SDOCT) is presented. By using the variance of the phase changes observed in the OCT images, scatterer motion has been imaged which is not readily observable with conventional Doppler OCT techniques. Dynamic motion contrast has been demonstrated for imaging Brownian motion of a sample system as well as imaging vasculature of in vivo 3dpf zebrafish.", "doi": "10.1117/12.697231", "isbn": "9780819465429", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-07", "pages": "Art. No. 64290P" }, { "id": "authors:psdhm-zmm56", "collection": "authors", "collection_id": "psdhm-zmm56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-112901034", "type": "book_section", "title": "Endoscopic optical coherence tomography of the retina at 1310 nm using paired-angle rotating scanning", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine XI", "author": [ { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Humayun", "given_name": "Mark", "orcid": "0000-0002-5830-5208", "clpid": "Humayun-M-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" } ], "abstract": "Vitrectomy (removal of the vitreous humor) is an ophthalmic surgery required as a precursor to several posterior chamber procedures. Vitrectomy is commonly performed using an endoscopic vitreous cutter and fiber based light delivery for observation through a surgical microscope. Cross-sectional visualization of the retina and remnant vitreous layers during surgery using an external optical coherence tomography (OCT) scanner is impractical due to deformation in the shape of the eye and the cornea. We present a forward imaging probe with 820 &mgr;m outer diameter (21 gauge needle) for cross-sectional endoscopic OCT imaging during ophthalmic surgeries. The Paired-Angle-Rotating Scanner (PARS) OCT probe is based on angle polished gradient index (GRIN) lenses which are rotated about the optical axis. The scan pattern is determined by the angle between the GRIN lenses and the relative angular velocity. Endoscopic placement of the PARS-OCT probe tip near the retinal surface permits use of a longer wavelength light, in particular 1310 nm, which would otherwise suffer significant attenuation traversing the vitreous humor. The prototype endoscopic PARS-OCT probe is coupled to a commercially available 1310 nm swept laser source, and uses commercial software for data acquisition, processing, and display of retinal images in real time at an A-scan rate of 16 kHz. We present an analysis of aberrations due to off axis use of GRIN lenses and measure the scan pattern of the PARS probe. Images acquired on an ex vivo porcine retina are presented, motivating development of the endoscopic PARS-OCT probe for clinical evaluation.", "doi": "10.1117/12.701226", "isbn": "9780819465429", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2007-02-07", "pages": "Art. No. 642911" }, { "id": "authors:tx2an-83n23", "collection": "authors", "collection_id": "tx2an-83n23", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100827-134405754", "type": "book_section", "title": "The optofluidic microscope - A high resolution microscope-on-a-chip system", "book_title": "Pacific Rim Conference on Lasers and Electro-Optics", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Lee", "given_name": "Lap Man", "clpid": "Lee-Lap-Man" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "In this article, a complete on-chip high resolution OFM device is presented. The OFM method abandons the conventional microscope design and, instead, shares some similarities with direct shadow imaging method where the target object is directly placed on top of a CCD or CMOS imaging sensor chip. In direct shadow imaging, the image resolution is no better than the sensor pixel size. As the typical sensor pixel size is around 10 microns, direct shadow imaging systems are unable to provide images that are comparable in resolution to those of conventional microscopes.", "doi": "10.1109/CLEOPR.2007.4391165", "isbn": "978-1-4244-1173-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007", "pages": "162-163" }, { "id": "authors:ycfzc-7vn74", "collection": "authors", "collection_id": "ycfzc-7vn74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CUIol06", "type": "article", "title": "Slanted hole array beam profiler (SHArP)\u2014a high-resolution portable beam profiler based on a linear aperture array", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Scherer", "given_name": "Axel", "orcid": "0000-0002-2160-9064", "clpid": "Scherer-A" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate a novel high-resolution portable beam profiler based on a slanted linear array of small apertures, termed a slanted hole array beam profiler (SHArP). The apertures are directly fabricated on a metal-coated CMOS imaging sensor. With a single linear scan, the aperture array can establish a virtual grid of sampling points for beam profiling. With our prototype, we demonstrate beam profiling of Gaussian beams over an area of 66.5 \u03bcm\u00d766.5 \u03bcm with a resolution of 0.8 \u03bcm (compare with the CMOS pixel size of 10 \u03bcm). The resolution can be improved into the range of submicrometers by fabricating smaller apertures. The good correspondence between the measured and calculated beam profiles proves the fidelity of our new beam profiling scheme.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2006-11-01", "series_number": "21", "volume": "31", "issue": "21", "pages": "3161-3163" }, { "id": "authors:fpgnc-q9690", "collection": "authors", "collection_id": "fpgnc-q9690", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161007-100317237", "type": "article", "title": "Methods and application areas of endoscopic optical coherence tomography", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We review the current state of research in endoscopic optical coherence tomography (OCT). We first survey the range of available endoscopic optical imaging techniques. We then discuss the various OCT-based endoscopic methods that have thus far been developed. We compare the different endoscopic OCT methods in terms of their scan performance. Next, we examine the application range of endoscopic OCT methods. In particular, we look at the reported utility of the methods in digestive, intravascular, respiratory, urinary and reproductive systems. We highlight two additional applications\u2014biopsy procedures and neurosurgery\u2014where sufficiently compact OCT-based endoscopes can have significant clinical impacts.", "doi": "10.1117/1.2400214", "issn": "1560-2281", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "publication": "Journal of Biomedical Optics", "publication_date": "2006-11", "series_number": "6", "volume": "11", "issue": "6", "pages": "Art. No. 063001" }, { "id": "authors:9q5h1-tg975", "collection": "authors", "collection_id": "9q5h1-tg975", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HENoe06", "type": "article", "title": "Characterization of light collection through a subwavelength aperture from a point source", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Knapp", "given_name": "David W.", "clpid": "Knapp-D-W" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We experimentally measure and theoretically model the light transmission characteristics of subwavelength apertures. The characterization consists of translating a point source at varying vertical height and lateral displacement from the aperture and measuring the resulting transmission. We define the variation of the transmission with lateral source displacement as the collection mode point spread function (CPSF). This transmission geometry is particularly relevant to subwavelength aperture based imaging devices and enables determination of their resolution. This study shows that the achieved resolutions degrade as a function of sample height and that the behavior of sensor devices based on the use of apertures for detection is different from those devices where the apertures are used as light sources. In addition, we find that the measured CPSF is dependent on the collection numerical aperture (NA). Finally, we establish that resolution beyond the diffraction limit for a nominal optical wavelength of 650 nm and nominal medium refractive index of 1.5 is achievable with subwavelength aperture based devices when the aperture size is smaller than 225 nm.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2006-10-30", "series_number": "22", "volume": "14", "issue": "22", "pages": "10410-10425" }, { "id": "authors:r8heh-n5r16", "collection": "authors", "collection_id": "r8heh-n5r16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-113829146", "type": "book_section", "title": "A compact optofluidic microscope", "book_title": "Optofluidics", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Baugh", "given_name": "Larry R.", "clpid": "Baugh-L-R" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Fainman", "given_name": "Yeshaiahu", "clpid": "Fainman-Y" } ], "abstract": "We demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is free of bulk optics and is based on a nanohole array defined in a non-transmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope will be explained in details and its performance is examined by using a popular animal model, Caenorhabditis elegans (C. elegans). Images from a large population of nematode worms are efficiently acquired within a short time frame. The quality of the OFM images of C. elegans and the morphological characteristics revealed therein are evaluated. Two groups of early-stage C. elegans larvae, wild-type and dpy-24 are successfully separated even though their morphological difference at the larval stage is subtle. The experimental results support our claim that the methodology described therein can be effectively used to develop a powerful tool for fulfilling high-resolution, high-throughput imaging task in microfluidics-based systems.", "doi": "10.1117/12.678940", "isbn": "0819464082", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-09-13", "pages": "Art. no. 632908" }, { "id": "authors:n2y21-q1752", "collection": "authors", "collection_id": "n2y21-q1752", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YAQoe06", "type": "article", "title": "Harmonically-related diffraction gratings-based interferometer for quadrature phase measurements", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate the use of shallow diffraction gratings for quadrature phase interferometry. A single shallow diffraction grating-based Michelson interferometer yields only trivial (0\u00b0 or 180\u00b0) phase shift between different output ports. In comparison, a combination of two parallel shallow diffraction gratings can be useful to achieve desired phase shifts (e.g., 90\u00b0 for quadrature phase interferometry). We show that the phase at different output ports of a grating-pair based interferometer can be adjusted by shearing the two gratings with respect to each other. Two harmonically-related diffraction gratings are used to demonstrate phase shift control at the output ports of a modified Michelson interferometer. Our experimental data is in good agreement with theory.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2006-09-04", "series_number": "18", "volume": "14", "issue": "18", "pages": "8127-8137" }, { "id": "authors:t8nzv-52091", "collection": "authors", "collection_id": "t8nzv-52091", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161005-135059869", "type": "article", "title": "Molecular contrast optical coherence tomography: a pump-probe scheme using indocyanine green as a contrast agent", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "McDowell", "given_name": "Emily J.", "clpid": "McDowell-E-J" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Fingler", "given_name": "Jeff", "clpid": "Fingler-J" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "The use of indocyanine green (ICG), a U.S. Food and Drug Administration approved dye, in a pump-probe scheme for molecular contrast optical coherence tomography (MCOCT) is proposed and demonstrated for the first time. In the proposed pump-probe scheme, an optical coherence tomography (OCT) scan of the sample containing ICG is first acquired. High fluence illumination (\u223c190kJ/cm^2) is then used to permanently photobleach the ICG molecules\u2014resulting in a permanent alteration of the overall absorption of the ICG. A second OCT scan is next acquired. The difference of the two OCT scans is used to determine the depth resolved distribution of ICG within a sample. To characterize the extent of photobleaching in different ICG solutions, we determine the cumulative probability of photobleaching, \u03d5_(B,cum), defined as the ratio of the total photobleached ICG molecules to the total photons absorbed by the ground state molecules. An empirical study of ICG photobleaching dynamics shows that \u03d5_(B,cum) decreases with fluence as well as with increasing dye concentration. The quantity \u03d5_(B,cum) is useful for estimating the extent of photobleaching in an ICG sample (MCOCT contrast) for a given fluence of the pump illumination. The paper also demonstrates ICG-based MCOCT imaging in tissue phantoms as well as within stage 54 Xenopus laevis.", "doi": "10.1117/1.2360525", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2006-09", "series_number": "5", "volume": "11", "issue": "5", "pages": "Art. No. 054017" }, { "id": "authors:7jfg1-wh868", "collection": "authors", "collection_id": "7jfg1-wh868", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150325-110150114", "type": "article", "title": "Developing optofluidic technology through the fusion of microfluidics and optics", "author": [ { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Quake", "given_name": "Stephen R.", "clpid": "Quake-S-R" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We describe devices in which optics and fluidics are used synergistically to synthesize novel functionalities. Fluidic replacement or modification leads to reconfigurable optical systems, whereas the implementation of optics through the microfluidic toolkit gives highly compact and integrated devices. We categorize optofluidics according to three broad categories of interactions: fluid\u2013solid interfaces, purely fluidic interfaces and colloidal suspensions. We describe examples of optofluidic devices in each category.", "doi": "10.1038/nature05060", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2006-07-27", "series_number": "7101", "volume": "442", "issue": "7101", "pages": "381-386" }, { "id": "authors:8ayrv-6d492", "collection": "authors", "collection_id": "8ayrv-6d492", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YAQol06", "type": "article", "title": "Homodyne en face optical coherence tomography", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Fingler", "given_name": "Jeff", "clpid": "Fingler-J" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We demonstrate, for what we believe to be the first time, the use of a 3\u00d73 fiber-optic coupler to realize a homodyne optical coherence tomography (OCT) system for en face imaging of highly scattering tissues and turbid media. The homodyne OCT setup exploits the inherent phase shifts between different output ports of a 3\u00d73 fiber-optic coupler to extract amplitude information of a sample. Our homodyne en face OCT system features a measured resolution of 14 \u03bcm axially and 9.4 \u03bcm laterally with a 90 dB signal-to-noise ratio at 10 \u03bcs integration time. En face OCT imaging of a stage 52 Xenopus laevis was successfully demonstrated at a depth of 600 \u03bcm within the sample.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2006-06-15", "series_number": "12", "volume": "31", "issue": "12", "pages": "1815-1817" }, { "id": "authors:e2sch-84989", "collection": "authors", "collection_id": "e2sch-84989", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WUJol06", "type": "article", "title": "Paired-angle-rotation scanning optical coherence tomography forward-imaging probe", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Conry", "given_name": "Michael", "clpid": "Conry-M" }, { "family_name": "Gu", "given_name": "Chunhui", "clpid": "Gu-Chunhui" }, { "family_name": "Wang", "given_name": "Fei", "clpid": "Wang-Fei" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report a novel forward-imaging optical coherence tomography (OCT), needle-probe paired-angle-rotation scanning OCT (PARS-OCT) probe. The probe uses two rotating angled gradient-index lenses to scan the output OCT probe beam over a wide angular arc (\u223c19\u00b0 half-angle) of the region forward of the probe. Among other advantages, this probe design is readily amenable to miniaturization and is capable of a variety of scan modes, including volumetric scans. To demonstrate the advantages of the probe design, we have constructed a prototype probe with an outer diameter of 1.65 mm and employed it to acquire four OCT images, with a 45\u00b0 angle between adjacent images, of the gill structure of a Xenopus laevis tadpole. The system sensitivity was measured to be 93 dB by using the prototype probe with an illumination power of 450 \u03bcW on the sample. Moreover, the axial and the lateral resolutions of the probe are 9.3 and 10.3-12.5 \u03bcm, respectively.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2006-05-01", "series_number": "9", "volume": "31", "issue": "9", "pages": "1265-1267" }, { "id": "authors:yj1p3-zbp15", "collection": "authors", "collection_id": "yj1p3-zbp15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170516-162925628", "type": "book_section", "title": "Nano-Aperture Array Based Optical Imaging System on a Microfluidic Chip", "book_title": "Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference and Photonic Applications Systems Technologies", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Reynolds", "given_name": "Kevin W.", "clpid": "Reynolds-K-W" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "We report the implementation of a novel nano-aperture array based imaging technique in a microfluidic network, termed \"Optofluidic Microscopy (OFM)\". The OFM prototype features high resolution, compact volume and capable of high-throughput sample imaging.", "isbn": "1-55752-813-6", "publisher": "Optical Society of America", "place_of_publication": "Washington, DC", "publication_date": "2006-05", "pages": "paper CMH1" }, { "id": "authors:vhq23-03g10", "collection": "authors", "collection_id": "vhq23-03g10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-114404185", "type": "book_section", "title": "Portable optical microscope-on-a-chip", "book_title": "Nanobiophotonics and Biomedical Applications III", "author": [ { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Cartwright", "given_name": "Alexander N.", "clpid": "Cartwright-A-N" }, { "family_name": "Nicolau", "given_name": "Dan V.", "clpid": "Nicolau-D-V" } ], "abstract": "In this paper, we present a novel high resolution optical imaging device on chip. It is based on a line of nano holes defined in an optically opaque aluminum film on a CMOS imaging sensor chip. Because it's free of bulky optical elements and compatible to the planar micro fabrication process, it is very promising to become an important component for the on-chip high resolution imaging in the future. The fabrication and operation of this novel on-chip microscope is explained in details. The performance is evaluated theoretically and is verified experimentally by examining the profile of a laser spot formed by a 10X objective lens.", "doi": "10.1117/12.640328", "isbn": "0819461377", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-02-28", "pages": "Art. No. 609509" }, { "id": "authors:zf851-2a983", "collection": "authors", "collection_id": "zf851-2a983", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-160347524", "type": "book_section", "title": "Optofluidic microscope and its applications in biology", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Reynolds", "given_name": "Kevin W.", "clpid": "Reynolds-K-W" }, { "family_name": "Cui", "given_name": "Xiquan", "clpid": "Cui-Xiquan" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Farkas", "given_name": "Daniel L.", "clpid": "Farkas-D-L" }, { "family_name": "Nicolau", "given_name": "Dan V.", "clpid": "Nicolau-D-V" }, { "family_name": "Leif", "given_name": "Robert C.", "clpid": "Leif-R-C" } ], "abstract": "In this article, we will demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is potentially free of bulk optics and is based on a nanohole array defined in a nontransmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope will be explained in details and its performance is examined by using a popular animal model, Caenorhabditis elegans (C. elegans). Images from a large population of nematode worms are efficiently acquired within a short time frame. The quality of the OFM images of C. elegans and the morphological characteristics revealed therein are evaluated. Two groups of early-stage C elegans larvae, wild-type and dpy-24 are successfully separated even though their morphological difference at the larval stage is subtle. The experimental results support our claim that the methodology described therein can be effectively used to develop a powerful tool for fulfilling high-resolution, high-throughput imaging task in microfluidics-based systems.", "doi": "10.1117/12.640325", "isbn": "081946130X", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-02-21", "pages": "Art. No. 608816" }, { "id": "authors:d0b7y-qtk76", "collection": "authors", "collection_id": "d0b7y-qtk76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-161051003", "type": "book_section", "title": "Transverse priority phase sensitive optical coherence tomography", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine X", "author": [ { "family_name": "Fingler", "given_name": "Jeff", "clpid": "Fingler-J" }, { "family_name": "Williams", "given_name": "Jon", "orcid": "0000-0001-5058-695X", "clpid": "Williams-J-P" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Haskell", "given_name": "Richard", "clpid": "Haskell-R-C" }, { "family_name": "Fraser", "given_name": "Scott", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "A variation on the standard time domain optical coherence tomography (TDOCT) system is presented. Using an inexpensive piezoelectric stack to modulate the reference mirror position, the amplitude and phase of the sample reflection is determined without scanning. With the primary scan in the transverse direction, en face and B-scan OCT images can be readily produced with phase information. This project plans to use the dynamic phase information to add an extra level of contrast to the images, based on the motion of the scatterers.", "doi": "10.1117/12.648997", "isbn": "0819461210", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-02-20", "pages": "Art. No. 607922" }, { "id": "authors:n0v6d-tjv85", "collection": "authors", "collection_id": "n0v6d-tjv85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-161601674", "type": "book_section", "title": "Forward-cone-imaging OCT needle probe", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine X", "author": [ { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Conry", "given_name": "Michael", "clpid": "Conry-M" }, { "family_name": "Gu", "given_name": "Chunhui", "clpid": "Gu-Chunhui" }, { "family_name": "Wang", "given_name": "Fei", "clpid": "Wang-Fei" }, { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "We propose a novel forward-imaging OCT needle probe. The probe is based on the use of two angled GRIN lenses that can freely rotate with respect to each other. The probe is capable of scanning a forward cone volume ahead of the probe tip. Different scanning modes, such as the conventional OCT B-scan mode, spiral mode and starburst B-scan mode, can be obtained by adjusting the angular scan velocities of the two GRIN lenses. We develop a prototype probe and demonstrate its capability to acquire OCT images. In this paper we give the characteristics of the prototype probe and display images of different part of tadpole acquired by the probe. The longitudinal resolution, lateral resolution and the signal-to-noise ratio of the system are 10 \u03bcm, 10 \u03bcm and 93 dB, respectively.", "doi": "10.1117/12.646554", "isbn": "0819461210", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-02-20", "pages": "Art. No. 60791J" }, { "id": "authors:hh80e-0a469", "collection": "authors", "collection_id": "hh80e-0a469", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-162002796", "type": "book_section", "title": "Pump-probe optical coherence tomography using indocyanine green as a contrast agent", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine X", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "McDowell", "given_name": "Emily", "clpid": "McDowell-E-J" }, { "family_name": "Wu", "given_name": "Jigang", "clpid": "Wu-Jigang" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "Use of indocyanine green (ICG), an FDA-approved dye, in a pump-probe scheme for optical coherence tomography (OCT) is reported. Aqueous solutions of ICG are not stable, i.e., the dye degrades over time especially in the presence of light. Addition of protein such as bovine serum albumin (BSA) stabilizes the ICG; however, when exposed to high intensity illumination, the dye still degrades. Moreover, the photodegradation is permanent and occurs swiftly if the illumination band corresponds to the ICG absorption peak. The permanence of the photobleached state illustrates that ICG photobleaching phenomenon has great potential to achieve contrast in OCT. ICG solutions with 50 micromolar concentration were prepared in water, 1% BSA, and 0.8% agarose to study the dynamics of the dye for different illumination intensity levels. In addition, different molar concentrations of ICG in water were studied for fixed illumination intensity. In each case, probability of photobleaching, defined as the ratio of the total photobleached ICG molecules to the total photons absorbed by the ground-state molecules, is evaluated to characterize the photobleaching phenomenon in ICG. We also demonstrate ICG-based pump-probe MCOCT imaging by mapping the distribution of ICG in a stage 54 Xenopus laevis.", "doi": "10.1117/12.646509", "isbn": "0819461210", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2006-02-20", "pages": "Art. No. 607904" }, { "id": "authors:pvfgm-bqt09", "collection": "authors", "collection_id": "pvfgm-bqt09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-162340521", "type": "book_section", "title": "A new imaging method: optofluidic microscopy", "book_title": "Nanostructure Integration Techniques for Manufacturable Devices, Circuits, and Systems: Interfaces, Interconnects, and Nanosystems", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "contributor": [ { "family_name": "Freund", "given_name": "Minoru M.", "clpid": "Freund-M-M" }, { "family_name": "Islam", "given_name": "M. Salim", "clpid": "Islam-M-S" }, { "family_name": "Dutta", "given_name": "Achyut K.", "clpid": "Dutta-A-K" } ], "abstract": "In this work, we present a novel optical imaging device that can be directly integrated into a microfluidic network, and can therefore enable on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is free of bulk optics and is based on a nanohole array defined in a non-transmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope is explained in details and its performance is examined with Caenorhabditis elegans (C. elegans) of various genotypes. Images from a large population of worms have been efficiently acquired within a short time frame. The quality of the OFM images of C elegans and the morphological characteristics revealed by the images are evaluated. The experimental results support our claim that the methodology described therein promises to create a powerful tool for fulfilling high- resolution, high-throughput imaging task of the microscopic biological samples.", "doi": "10.1117/12.632157", "isbn": "0819460273", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2005-11-12", "pages": "Art. No. 60030F" }, { "id": "authors:s9fp7-h5071", "collection": "authors", "collection_id": "s9fp7-h5071", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:APPoe05", "type": "article", "title": "Theoretical comparison of the sensitivity of molecular contrast optical coherence tomography techniques", "author": [ { "family_name": "Applegate", "given_name": "Brian E.", "clpid": "Applegate-B-E" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "Molecular contrast optical coherence tomography (MCOCT) is an extension of OCT in which contrast resulting from the interaction of light with a contrast agent, leads to the enhanced visualization of a specific morphology or biochemical process in a target specimen. In order to improve the sensitivity and specificity of MCOCT, several spectroscopic techniques have recently been introduced which depend upon coherent detection of scattered light which has been modified by interaction with the molecules of interest in a sample. These techniques include harmonic generation, coherent anti-Stokes Raman scattering, linear absorption, and several different forms of pump-probe spectroscopy. We have developed a theoretical framework to facilitate the comparison of the sensitivity of different MCOCT techniques. This framework is based upon the observation that since the noise floor is defined by the reference field power in a shot-noise limited OCT system, the relevant comparison among the techniques is isolated to the available molecular contrast signal power and the algorithm used to extract the signal. We have derived theoretical expressions for the signal power and signal-to-noise ratio for the MCOCT techniques described in the literature based on molecular spectroscopy, as well as several new techniques introduced here.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2005-10-03", "series_number": "20", "volume": "13", "issue": "20", "pages": "8146-8163" }, { "id": "authors:q5cby-vc792", "collection": "authors", "collection_id": "q5cby-vc792", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180709-105849547", "type": "book_section", "title": "Optofluidics", "book_title": "Optical Information Systems III", "author": [ { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Li", "given_name": "Zhenyu", "clpid": "Li-Zhenyu" }, { "family_name": "Rockwood", "given_name": "Troy", "clpid": "Rockwood-T" }, { "family_name": "Emery", "given_name": "Teresa", "clpid": "Emery-T-H" }, { "family_name": "Zhang", "given_name": "Zhaoyu", "clpid": "Zhang-Zhaoyu" }, { "family_name": "Scherer", "given_name": "Axel", "orcid": "0000-0002-2160-9064", "clpid": "Scherer-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" } ], "contributor": [ { "family_name": "Javidi", "given_name": "Bahram", "clpid": "Javidi-B" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" } ], "abstract": "\"Optofluidics\" is the marriage of optics, optoelectronics and nanophotonics with fluidics. Such integration represents a new approach for dynamic manipulation of optical properties at length scales both greater than and smaller than the wavelength of light with applications ranging from reconfigurable photonic circuits to fluidically adaptable optics to high sensitivity bio-detection currently under development. The capabilities in terms of fluidic control, mixing, miniaturization and optical property tuning afforded by micro-, nano- and electro-fluidics combined with soft lithography based fabrication provides an ideal platform upon which to build such devices. In this paper we provide a general overview of some of the important issues related to the fabrication, integration and operation of optofluidic devices and present three comprehensive application examples: nanofluidically tunable photonic crystals, optofluidic microscopy and DFB dye lasers.", "doi": "10.1117/12.623629", "isbn": "9780819459138", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2005-09-10", "pages": "Art. No. 59080S" }, { "id": "authors:q8kfw-gvb84", "collection": "authors", "collection_id": "q8kfw-gvb84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHOol05c", "type": "article", "title": "Spectral-domain phase microscopy", "author": [ { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Ellerbee", "given_name": "Audrey K.", "clpid": "Ellerbee-A-K" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Creazzo", "given_name": "Tony L.", "clpid": "Creazzo-T-L" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "Broadband interferometry is an attractive technique for the detection of cellular motions because it provides depth-resolved phase information via coherence gating. We present a phase-sensitive technique called spectral-domain phase microscopy (SDPM). SDPM is a functional extension of spectral-domain optical coherence tomography that allows for the detection of nanometer-scale motions in living cells. The sensitivity of the technique is demonstrated, and its calibration is verified. A shot-noise limit to the displacement sensitivity of this technique is derived. Measurement of cellular dynamics was performed on spontaneously beating cardiomyocytes isolated from chick embryos.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2005-05-15", "series_number": "10", "volume": "30", "issue": "10", "pages": "1162-1164" }, { "id": "authors:ncc8c-9mx12", "collection": "authors", "collection_id": "ncc8c-9mx12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110818-093816350", "type": "book_section", "title": "Optofluidic microscopy", "book_title": "2005 Conference on Lasers & Electro-Optics (CLEO)", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "This research aims to integrate optical microscopy with microfluidic systems and create a device which is potentially capable of achieving sub wavelength resolution. This paper reports on our initial results of this optofluidic microscope (OFM).", "doi": "10.1109/CLEO.2005.202400", "isbn": "1-55752-795-4", "publisher": "Optical Society of America", "place_of_publication": "Washington, D.C.", "publication_date": "2005-05", "pages": "2154-2156" }, { "id": "authors:83fwb-c9n90", "collection": "authors", "collection_id": "83fwb-c9n90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110829-093722171", "type": "book_section", "title": "Pump-probe scheme for optical coherence tomography using indocyanine green mixed with albumin or human plasma", "book_title": "2005 Conference on Lasers & Electro-Optics (CLEO)", "author": [ { "family_name": "Yaqoob", "given_name": "Zahid", "clpid": "Yaqoob-Z" }, { "family_name": "Fingler", "given_name": "Jeffrey P.", "clpid": "Fingler-J" }, { "family_name": "Lintner", "given_name": "St\u00e9phane", "clpid": "Lintner-S" }, { "family_name": "Applegate", "given_name": "Brian E.", "clpid": "Applegate-B-E" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Use of indocyanine green (ICG) in a pump-probe scheme for OCT is proposed. The study illustrates that ICG in protein solution shows unusual pump-probe imaging potential, indicating its usefulness as a contrast agent for OCT.", "doi": "10.1109/CLEO.2005.202366", "isbn": "1-55752-795-4", "publisher": "Optical Society of America", "place_of_publication": "Washington, D.C.", "publication_date": "2005-05", "pages": "2055-2057" }, { "id": "authors:2edat-rhr17", "collection": "authors", "collection_id": "2edat-rhr17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-164319113", "type": "book_section", "title": "Molecular contrast optical coherence tomography: SNR comparison of techniques and introduction of ground state recovery pump-probe OCT", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine IX", "author": [ { "family_name": "Applegate", "given_name": "Brian E.", "clpid": "Applegate-B-E" }, { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "Molecular contrast OCT (MCOCT) is an extension of OCT in which specific molecular species are imaged based on their spectroscopic characteristics. In order to improve the sensitivity and specificity of MCOCT, several techniques have recently been introduced which depend upon coherent detection of inelastically scattered light from molecules of interest in a sample. These techniques include harmonic generation, coherent anti-Stokes Raman scattering, and several different forms of pump-probe spectroscopy. We have developed a theoretical framework to facilitate the comparison of different inelastic scattering-based contrast mechanisms for molecular contrast OCT. This framework is based upon the observation that since the noise floor is defined by the reference arm power in a shot-noise limited heterodyne detection system, the relevant comparison among the techniques is isolated to the available molecular-specific signal power. We have derived the value of the molecular contrast signal power for second harmonic generation OCT (SHOCT) and three different pump-probe OCT (PPOCT) techniques. Motivated by this analysis, we have constructed a preliminary ground state recovery pump-probe OCT system, and demonstrated its performance using rhodamine 6G as the MCOCT contrast agent.", "doi": "10.1117/12.592866", "isbn": "0819456640", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2005-04-13", "pages": "182-186" }, { "id": "authors:r4ffy-w4797", "collection": "authors", "collection_id": "r4ffy-w4797", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:AHNao05", "type": "article", "title": "Harmonic phase-dispersion microscope with a Mach-Zehnder interferometer", "author": [ { "family_name": "Ahn", "given_name": "Andrew", "clpid": "Ahn-Andrew" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Popescu", "given_name": "Gabriel", "clpid": "Popescu-G" }, { "family_name": "Fang-Yen", "given_name": "Christopher", "clpid": "Fang-Yen-Christopher" }, { "family_name": "Badizadegan", "given_name": "Kamran", "clpid": "Badizadegan-K" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "Harmonic phase-dispersion microscopy (PDM) is a new imaging technique in which contrast is provided by differences in refractive index at two harmonically related wavelengths. We report a new configuration of the harmonic phase-dispersion microscope in a Mach-Zehnder geometry as an instrument for imaging biological samples. Several improvements on the earlier design are demonstrated, including a single-pass configuration and acousto-optic modulators for generating the heterodyne signals without mechanical arm scanning. We demonstrate quantitative phase-dispersion images of test structures and biological samples.", "issn": "0003-6935", "publisher": "Optical Society of America", "publication": "Applied Optics", "publication_date": "2005-03-01", "series_number": "7", "volume": "44", "issue": "7", "pages": "1188-1190" }, { "id": "authors:zxcv4-aqf96", "collection": "authors", "collection_id": "zxcv4-aqf96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANpp05", "type": "article", "title": "Molecular Contrast Optical Coherence Tomography: A Review", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "This article reviews the current state of research on the use of molecular contrast agents in optical coherence tomography (OCT) imaging techniques. After a brief discussion of the basic principle of OCT and the importance of incorporating molecular contrast agent usage into this imaging modality, we shall present an overview of the different molecular contrast OCT (MCOCT) methods that have been developed thus far. We will then discuss several important practical issues that define the possible range of contrast agent choice, the design criteria for engineered molecular contrast agent and the implementability of a given MCOCT method for clinical or biological applications. We will conclude by outlining a few areas of pursuit that deserve a greater degree of research and development.", "issn": "0031-8655", "publisher": "Elsevier", "publication": "Photochemistry and Photobiology", "publication_date": "2005-03", "series_number": "2", "volume": "81", "issue": "2", "pages": "215-237" }, { "id": "authors:590v0-7q297", "collection": "authors", "collection_id": "590v0-7q297", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SARoe05", "type": "article", "title": "Instantaneous complex conjugate resolved spectral domain and swept-source OCT using 3x3 fiber couplers", "author": [ { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We report that the complex conjugate artifact in Fourier domain optical coherence tomography approaches (including spectral domain and swept source OCT) may be resolved by the use of novel interferometer designs based on 3x3 and higher order fiber couplers. Interferometers built from NxN (N>2) truly fused fiber couplers provide simultaneous access to non-complementary phase components of the complex interferometric signal. These phase components may be converted to quadrature components by trigonometric manipulation, then inverse Fourier transformed to obtain A-scans and images with resolved complex conjugate artifact. We demonstrate instantaneous complex conjugate resolved Fourier domain OCT using 3x3 couplers in both spectral domain and swept source implementations. Complex conjugate artifact suppression by factors of ~20dB and ~25dB are demonstrated for spectral domain and swept source implementations, respectively.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2005-02-07", "series_number": "3", "volume": "13", "issue": "3", "pages": "957-967" }, { "id": "authors:d7zf4-xgv53", "collection": "authors", "collection_id": "d7zf4-xgv53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YAZoe05", "type": "article", "title": "Frequency estimation precision in Doppler optical coherence tomography using the Cramer-Rao lower bound", "author": [ { "family_name": "Yazdanfar", "given_name": "Siavash", "clpid": "Yazdanfar-S" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "Doppler optical coherence tomography (DOCT) is a technique for simultaneous cross-sectional imaging of tissue structure and blood flow. We derive the fundamental uncertainty limits on frequency estimation precision in DOCT using the Cramer-Rao lower bound in the case of additive (e.g., thermal, shot) noise. Experimental results from a mirror and a scattering phantom are used to verify the theoretical limits. Our results demonstrate that the stochastic nature of frequency noise influences the precision of flow imaging, and that the noise model must be selected judiciously in order to estimate the frequency precision.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2005-01-24", "series_number": "2", "volume": "13", "issue": "2", "pages": "410-416" }, { "id": "authors:yt796-m0037", "collection": "authors", "collection_id": "yt796-m0037", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110812-143350079", "type": "book_section", "title": "Optofluidic microscopy", "book_title": "2005 Proceedings of the 3rd International Conference on Microchannels and Minichannels", "author": [ { "family_name": "Heng", "given_name": "Xin", "clpid": "Heng-Xin" }, { "family_name": "Erickson", "given_name": "David", "clpid": "Erickson-D" }, { "family_name": "Psaltis", "given_name": "Demetri", "clpid": "Psaltis-D" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Recent advances in the development of lab-on-a-chip devices have been rapid and broad ranging. In general however these devices, while containing micro- or even nano-scale components, rely heavily on macroscale infrastructure (e.g. microscopes, chip readers and power sources) to perform much of the actual product detection and subsequent analysis. As such to enable the next generation of portable lab-on-chip devices, techniques for simply and cheaply integrating on-chip analysis functionalities will be required. In this work we present our work directed towards the development of a new concept in rapid on-chip imaging which we refer to as \"optofluidic microscopy (OFM)\". Here we present an overview of the imaging theory, fabrication procedure and operational details of the initial prototype. Preliminary experimental results of this on-chip optical imager are also reported. A significant advantage of the technique is that through proper spatial scaling, sub-wavelength resolution can be achieved without bulk optics.", "doi": "10.1115/ICMM2005-75206", "isbn": "0-7918-4185-5", "publisher": "American Society of Mechanical Engineers", "place_of_publication": "New York", "publication_date": "2005", "pages": "569-574" }, { "id": "authors:y6awc-byb77", "collection": "authors", "collection_id": "y6awc-byb77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:APPol04", "type": "article", "title": "Polarization-resolved second-harmonic-generation optical coherence tomography in collagen", "author": [ { "family_name": "Applegate", "given_name": "Brian E.", "clpid": "Applegate-B-E" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Rollins", "given_name": "Andrew M.", "clpid": "Rollins-A-M" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We describe a novel imaging technique, second-harmonic-generation optical coherence tomography (SHOCT). This technique combines the spatial resolution and depth penetration of optical coherence tomography (OCT) with the molecular sensitivity of second-harmonic-generation spectroscopy. As a consequence of the coherent detection required for OCT, polarization-resolved images arise naturally. We demonstrate this new technique on a skin sample from the belly of Icelandic salmon, acquiring polarization-resolved SHOCT and OCT images simultaneously.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2004-10-01", "series_number": "19", "volume": "29", "issue": "19", "pages": "2252-2254" }, { "id": "authors:cehbe-bnz48", "collection": "authors", "collection_id": "cehbe-bnz48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol04", "type": "article", "title": "Spectral triangulation molecular contrast optical coherence tomography with indocyanine green as the contrast agent", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "McGuckin", "given_name": "Laura E. L.", "clpid": "McGuckin-L-E-L" }, { "family_name": "Simon", "given_name": "John D.", "clpid": "Simon-J-D" }, { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Applegate", "given_name": "Brian E.", "clpid": "Applegate-B-E" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We report a new molecular contrast optical coherence tomography (MCOCT) implementation that profiles the contrast agent distribution in a sample by measuring the agent's spectral differential absorption. The method, spectra triangulation MCOCT, can effectively suppress contributions from spectrally dependent scatterings from the sample without a priori knowledge of the scattering properties. We demonstrate molecular imaging with this new MCOCT modality by mapping the distribution of indocyanine green, a FDA-approved infrared red dye, within a stage 54 Xenopus laevis.", "pmcid": "PMC1283115", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2004-09-01", "series_number": "17", "volume": "29", "issue": "17", "pages": "2016-2018" }, { "id": "authors:mkh36-dtm19", "collection": "authors", "collection_id": "mkh36-dtm19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-163516918", "type": "book_section", "title": "Protein-based molecular contrast optical coherence tomography", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine VIII", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Lamb", "given_name": "Laura E.", "clpid": "Lamb-L-E" }, { "family_name": "Simon", "given_name": "John D.", "clpid": "Simon-J-D" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "We describe a novel technique for contrast enhancement in optical coherence tomography (OCT) which uses optically switchable protein based chromophores. Photosensitive proteins, such as bacteriorhodopsin and phytochrome, are promising OCT molecular contrast agents by reason of their remarkably low transition activation intensities compatible with in vivo imaging, and their potential for use as genetically expressible markers for molecular imaging. This study details the use of a novel optical switch suppression scheme which uses the absorption change between the two state groups of phytochrome to extract concentration and distribution information of the contrast agent within a target sample.", "doi": "10.1117/12.531353", "isbn": "0819452246", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2004-07-01", "pages": "85-90" }, { "id": "authors:3p8wz-y8x21", "collection": "authors", "collection_id": "3p8wz-y8x21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-162933494", "type": "book_section", "title": "Instantaneous complex spectral domain OCT using 3x3 fiber couplers", "book_title": "Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine VIII", "author": [ { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-J-G" } ], "abstract": "We report that the complex conjugate ambiguity in spectral domain OCT approaches (including swept source OCT and Fourier-domain OCT) may be removed by the use of novel interferometer designs based on NxN couplers. An interferometer based on a 3x3 truly fused fiber coupler with equal splitting ratios provides simultaneous access to components of the complex interferometric signal separated by 120o. These phase components may be converted to quadrature components by use of a simple trigonometric operation, and then inverse Fourier transformed to obtain A-scans and images free of complex conjugate artifact. We demonstrate instantaneous complex spectral-domain OCT using a novel Fourier-domain OCT system employing photodiode arrays, and will also report on a similar system design for instantaneous complex swept-source OCT.", "doi": "10.1117/12.531422", "isbn": "0819452246", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2004-07-01", "pages": "241-247" }, { "id": "authors:86f7p-qcq47", "collection": "authors", "collection_id": "86f7p-qcq47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol04b", "type": "article", "title": "Protein-based molecular contrast optical coherence tomography with phytochrome as the contrast agent", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Lamb", "given_name": "Laura E.", "clpid": "Lamb-L-E" }, { "family_name": "Simon", "given_name": "John D.", "clpid": "Simon-J-D" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We report the use of phytochrome A (phyA), a plant protein that can reversibly switch between two states with different absorption maxima (at 660 and 730 nm), as a contrast agent for molecular contrast optical coherence tomography (MCOCT). Our MCOCT scheme builds up a difference image revealing the distribution of phyA within a target sample from pairs of consecutive OCT A-scans acquired at a probe wavelength of 750 nm, both with and without additional illumination of the target sample with 660-nm light. We demonstrate molecular imaging with this new MCOCT modality in a target sample containing a mixture of 0.2% Intralipid and 83 \u00b5M of phyA.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2004-06-15", "series_number": "12", "volume": "29", "issue": "12", "pages": "1396-1398" }, { "id": "authors:hkhwb-pr280", "collection": "authors", "collection_id": "hkhwb-pr280", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol04a", "type": "article", "title": "Amplification of optical delay by use of matched linearly chirped fiber Bragg gratings", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Yazdanfar", "given_name": "Siavash", "clpid": "Yazdanfar-S" }, { "family_name": "Izatt", "given_name": "Joseph", "clpid": "Izatt-J-A" } ], "abstract": "We describe the use of a matched linearly chirped fiber Bragg grating (FBG) pair as a key element in an adjustable optical delay line. This delay line has the unique property that the achievable optical group delay is orders of magnitude greater (factor of 10^2 in our experiment) than the actual physical displacement. We demonstrate operation of such an optical delay line over a delay range of 3.5 mm using a pair of matched 1300-nm chirped FBGs with a bandwidth of 20 nm each.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2004-04-01", "series_number": "7", "volume": "29", "issue": "7", "pages": "685-687" }, { "id": "authors:x3jh3-6w651", "collection": "authors", "collection_id": "x3jh3-6w651", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHOol03", "type": "article", "title": "Instantaneous quadrature low-coherence interferometry with 3x3 fiber-optic couplers", "author": [ { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We describe fiber-based quadrature low-coherence interferometers that exploit the inherent phase shifts of 3 x 3 and higher-order fiber-optic couplers. We present a framework based on conservation of energy to account for the interferometric shifts in 3 x 3 interferometers, and we demonstrate that the resulting interferometers provide the entire complex interferometric signal instantaneously in homodyne and heterodyne systems. In heterodyne detection we demonstrate the capability for extraction of the magnitude and sign of Doppler shifts from the complex data. In homodyne detection we show the detection of subwavelength sample motion. N x N (N> 2) low-coherence interferometer topologies will be useful in Doppler optical coherence tomography (OCT), optical coherence microscopy, Fourier-domain OCT, optical frequency domain reflectometry, and phase-referenced interferometry.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2003-11-15", "series_number": "22", "volume": "28", "issue": "22", "pages": "2162-2164" }, { "id": "authors:d8xb9-vs019", "collection": "authors", "collection_id": "d8xb9-vs019", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180719-110832273", "type": "book_section", "title": "Molecular contrast in optical coherence tomography using a pump-probe technique and a optical switch suppression technique", "book_title": "Optical Coherence Tomography and Coherence Techniques", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Rao", "given_name": "K. Divakar", "clpid": "Rao-K-D" }, { "family_name": "Choma", "given_name": "Michael", "clpid": "Choma-M-A" }, { "family_name": "Yazdanfar", "given_name": "Siavash", "clpid": "Yazdanfar-S" }, { "family_name": "Rollins", "given_name": "Andrew M.", "clpid": "Rollins-A-M" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "contributor": [ { "family_name": "Drexler", "given_name": "Wolfgang", "clpid": "Drexler-W" } ], "abstract": "We describe two novel techniques for contrast enhancement in optical coherence tomography (OCT) which enables molecular specific imaging. The first, a pump-probe technique, is employed in which a pulsed pump laser is tuned to ground-state absorption in a molecule of interest. The location of the target molecule population is derived from the resulting transient absorption of OCT sample arm light acting as probe light. Preliminary results exhibiting contrast enhancement in cross-sectional OCT images using methylene blue dye are presented. The second method is an optical switch suppression technique based on the use of a transmembrane protein called bacteriorhodopsin. Initial experiments indicate that biochemical optical switches, such as bacteriorhodopsin, are excellent contrast agent candidates for molecular contrast OCT.", "doi": "10.1117/12.501007", "isbn": "0819467715", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2003-10-02", "pages": "95-100" }, { "id": "authors:afpz1-87a65", "collection": "authors", "collection_id": "afpz1-87a65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180716-165052547", "type": "book_section", "title": "Fast-scanning dispersion-adjustable reference delay for OCT using fiber Bragg gratings", "book_title": "Optical Coherence Tomography and Coherence Techniques", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Yazdanfar", "given_name": "Siavash", "clpid": "Yazdanfar-S" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "contributor": [ { "family_name": "Drexler", "given_name": "Wolfgang", "clpid": "Drexler-W" } ], "abstract": "We report on the use of two matched linearly chirped fiber Bragg grating (FBG) in the reference arm of a Michelson interferometer as a means to achieve variable optical delay. We demonstrate that the properties of a linearly chirped FBG can be exploited to achieve millimeters of optical delay with physical stretches of the FBG on the order of tens of microns; this allows for optical delay line configurations that are easily driven by piezo-electric actuators.", "doi": "10.1117/12.500987", "isbn": "0819450103", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2003-10-02", "pages": "53-59" }, { "id": "authors:yx529-g3n22", "collection": "authors", "collection_id": "yx529-g3n22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHOoe03", "type": "article", "title": "Sensitivity advantage of swept source and Fourier domain optical coherence tomography", "author": [ { "family_name": "Choma", "given_name": "Michael A.", "clpid": "Choma-M-A" }, { "family_name": "Sarunic", "given_name": "Marinko V.", "clpid": "Sarunic-M-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We present theoretical and experimental results which demonstrate the superior sensitivity of swept source (SS) and Fourier domain (FD) optical coherence tomography (OCT) techniques over the conventional time domain (TD) approach. We show that SS- and FD-OCT have equivalent expressions for system signal-to-noise ratio which result in a typical sensitivity advantage of 20-30dB over TD-OCT. Experimental verification is provided using two novel spectral discrimination (SD) OCT systems: a differential fiber-based 800nm FD-OCT system which employs deep-well photodiode arrays, and a differential 1300nm SS-OCT system based on a swept laser with an 87nm tuning range.", "issn": "1094-4087", "publisher": "Optical Society of America", "publication": "Optics Express", "publication_date": "2003-09-08", "series_number": "18", "volume": "11", "issue": "18", "pages": "2183-2189" }, { "id": "authors:d0nr2-2eb83", "collection": "authors", "collection_id": "d0nr2-2eb83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAXol03", "type": "article", "title": "Fourier-domain low-coherence interferometry for light-scattering spectroscopy", "author": [ { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" } ], "abstract": "We present a novel method for obtaining depth-resolved spectra for determining scatterer size through elastic- scattering properties. Depth resolution is achieved with a white-light source in a Michelson interferometer with the mixed signal and reference fields dispersed by a spectrograph. The spectrum is Fourier transformed to yield the axial spatial cross correlation between the signal and reference fields with near 1 m m depth resolution. Spectral information is obtained by windowing to yield the scattering amplitude as a function of wave number. The technique is demonstrated by determination of the size of polystyrene microspheres in a subsurface layer with subwavelength accuracy. Application of the technique to probing the size of cell nuclei in living epithelial tissues is discussed.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2003-07-15", "series_number": "14", "volume": "28", "issue": "14", "pages": "1230-1232" }, { "id": "authors:q8p4n-4er68", "collection": "authors", "collection_id": "q8p4n-4er68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180719-111608529", "type": "book_section", "title": "New implementation of second harmonic generation microscopy for three-dimensional resolution", "book_title": "Multiphoton Microscopy in the Biomedical Sciences III", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Mertz", "given_name": "Jerome", "clpid": "Mertz-J" } ], "contributor": [ { "family_name": "Periasamy", "given_name": "Ammasi", "clpid": "Periasamy-A" }, { "family_name": "So", "given_name": "Peter T. C.", "clpid": "So-Peter-T-C" } ], "abstract": "We present a fast scanning transmission-mode confocal scanning laser microscope system based on the use of a second harmonic generation (SHG) crystal for signal detection. The quadratic intensity dependence of SHG is exploited to preferentially reveal unscattered signal light and reject out-of-focus scattered background. The SHG crystal plays the role of a virtual pinhole that remains self-aligned without a need for de-scanning. We demonstrate that this new microscope method produces images with higher contrast and less speckle than transmission scanning microscopy with linear detection.", "doi": "10.1117/12.478032", "isbn": "0819447633", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2003-07-10", "pages": "52-59" }, { "id": "authors:ycb4a-v4x51", "collection": "authors", "collection_id": "ycb4a-v4x51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180719-112222225", "type": "book_section", "title": "The Study of Cell Dynamics with a Novel Phase Referenced Low Coherence Interferometer with sub-wavelength and sub-hertz Sensitivity", "book_title": "Coherence Domain Optical Methods in Biomedical Science and Clinical Applications VI", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Badizadegan", "given_name": "Kamran", "clpid": "Badizadegan-K" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-James-G" } ], "abstract": "We report the use of a highly sensitive phase based motion measurement technique to study the correlation of cellular metabolic rate with cellular motions. The technique is based on a modified Michelson interferometer with a composite laser beam of 1550 nm low coherence light and 775 nm CW light. In this system, motional artifacts from vibrations in the interferometer are completely eliminated. We demonstrate that the system is sensitive to motions as small as 3.6 nm and velocities as small as 1 nm/s. Using the system, we show that the cellular motions are strongly dependent on the ambient temperature. We observe that the dependency does not conform to Brownian motion predictions but instead appears to correlate with the optical ambient temperature that the cells have evolved to operate in.", "doi": "10.1117/12.470484", "isbn": "0819447560", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2002-06-14", "pages": "202-209" }, { "id": "authors:wqpam-0ga54", "collection": "authors", "collection_id": "wqpam-0ga54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAXjosaa02", "type": "article", "title": "Determination of particle size by using the angular distribution of backscattered light as measured with low-coherence interferometry", "author": [ { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Backman", "given_name": "Vadim", "clpid": "Backman-V" }, { "family_name": "Kalashnikov", "given_name": "Maxim", "clpid": "Kalashnikov-M" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We employ a novel interferometer to measure the angular distribution of light backscattered by a turbid medium. Through comparison of the measured data with the predictions of Mie theory, we are able to determine the size of the scatterers comprising the medium with subwavelength precision. As the technique is based on low-coherence interferometry, we are able to examine the evolution of the angular distribution of scattered light as it propagates into the medium. The effects of multiple scattering as a function of penetration depth in the medium are analyzed. We also present various considerations for extending this technique to determining structural information in biological tissues, such as the effects of a distribution of particle sizes and the need to average out speckle contributions.", "issn": "1084-7529", "publisher": "Optical Society of America", "publication": "Journal of the Optical Society of America A", "publication_date": "2002-04", "series_number": "4", "volume": "19", "issue": "4", "pages": "737-744" }, { "id": "authors:mzsxg-yxg92", "collection": "authors", "collection_id": "mzsxg-yxg92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol02b", "type": "article", "title": "2pi ambiguity-free optical distance measurement with subnanometer precision with a novel phase-crossing low-coherence interferometer", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We report a highly accurate phase-based technique for measuring arbitrarily long optical distance with subnanometer precision. The method employs a Michelson interferometer with a pair of harmonically related light sources, one cw and the other low coherence. By slightly detuning (~2 nm) the center wavelength of the low-coherence source between scans of the target sample, we can use the phase relationship between the heterodyne signals of the cw and the low-coherence light to measure the separation between reflecting interfaces with subnanometer precision. As this technique is completely free of 2pi ambiguity, an issue that plagues most phase-based techniques, it can be used to measure arbitrarily long optical distances without loss of precision. We demonstrate one application of this technique, the high-precision determination of the differential refractive index.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2002-01-15", "series_number": "2", "volume": "27", "issue": "2", "pages": "77-79" }, { "id": "authors:wmzwy-78091", "collection": "authors", "collection_id": "wmzwy-78091", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAXao01", "type": "article", "title": "Path-Length-Resolved Dynamic Light Scattering: Modeling the Transition From Single to Diffusive Scattering", "author": [ { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "Dynamic light-scattering spectroscopy is used to study Brownian motion within highly scattering samples. The fluctuations of the light field that is backscattered by a suspension of polystyrene microspheres are measured as power spectra by use of low-coherence interferometry to obtain path-length resolution. The data are modeled as the sum of contributions to the detected light weighted by a Poisson probability for the number of events that each component has experienced. By analyzing the broadening of the power spectra as a function of the path length for various sizes of particles, we determine the contribution of multiple scattering to the detected signal as a function of scattering anisotropy.", "issn": "0003-6935", "publisher": "Optical Society of America", "publication": "Applied Optics", "publication_date": "2001-08-20", "series_number": "24", "volume": "40", "issue": "24", "pages": "4222-4227" }, { "id": "authors:n9768-2p740", "collection": "authors", "collection_id": "n9768-2p740", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol01c", "type": "article", "title": "Phase-referenced interferometer with subwavelength and subhertz sensitivity applied to the study of cell membrane dynamics", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Hahn", "given_name": "Mariah S.", "clpid": "Hahn-M-S" }, { "family_name": "Badizadegan", "given_name": "Kamran", "clpid": "Badizadegan-K" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We report a highly sensitive means of measuring cellular dynamics with a novel interferometer that can measure motional phase changes. The system is based on a modified Michelson interferometer with a composite laser beam of 1550-nm low-coherence light and 775-nm CW light. The sample is prepared on a coverslip that is highly reflective at 775nm. By referencing the heterodyne phase of the 1550-nm light reflected from the sample to that of the 775-nm light reflected from the coverslip, small motions in the sample are detected, and motional artifacts from vibrations in the interferometer are completely eliminated. We demonstrate that the system is sensitive to motions as small as 3.6nm and velocities as small as 1nm/s. Using the instrument, we study transient volume changes of a few (approximately three) cells in a monolayer immersed in weakly hypotonic and hypertonic solutions.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2001-08-15", "series_number": "16", "volume": "26", "issue": "16", "pages": "1271-1273" }, { "id": "authors:2mgsy-ggm15", "collection": "authors", "collection_id": "2mgsy-ggm15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-101918940", "type": "book_section", "title": "Interferometric phase-based dual-wavelength tomography", "book_title": "Coherence Domain Optical Methods in Biomedical Science and Clinical Applications V", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" }, { "family_name": "Izatt", "given_name": "Joseph A.", "clpid": "Izatt-J-A" }, { "family_name": "Fujimoto", "given_name": "James G.", "clpid": "Fujimoto-James-G" } ], "abstract": "We describe our phase-sensitive interferometry technique implemented as phase dispersion microscopy (PDM)/optical tomography (PDOT). The technique is based on measuring the phase difference between fundamental and second harmonic low coherence light in a novel interferometer. We attain high sensitivity to subtle refractive index differences due to dispersion with a differential optical path sensitivity of 5 nm. Using PDM, we show that ballistic light in a turbid medium undergoes a phase velocity change that is dependent on scatterer size. We demonstrate that the microscopy technique performs better than a conventional phase contrast microscope in imaging dispersive and weakly scattering samples. The tomographic implementation of the technique (PDOT) can complement Optical Coherence Tomography (OCT) by providing phase information about the scanned object.", "doi": "10.1117/12.427872", "isbn": "0819439290", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2001-05-23", "pages": "63-70" }, { "id": "authors:a15rf-r9059", "collection": "authors", "collection_id": "a15rf-r9059", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-144715081", "type": "book_section", "title": "Angular light scattering studies using low-coherence interferometry", "book_title": "Coherence Domain Optical Methods in Biomedical Science and Clinical Applications V", "author": [ { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "contributor": [ { "family_name": "Tuchin", "given_name": "Valery V.", "clpid": "Tuchin-V-V" } ], "abstract": "A modified Michelson interferometer is used to measure path- length resolved angular distributions of light backscattered by turbid media. The path length resolution is obtained by exploiting the coherence properties of a broadband source. The angular distribution is mapped out using a simple optical system to scan the angle at which the reference field intersects the detector plane. Angular scattering distributions can be compared to Mie theory to determine the size and refractive index of spherical scatterers. Initial studies utilizing this system demonstrate the potential of low coherence interferometry for obtaining structural information using angular distributions.", "doi": "10.1117/12.427903", "isbn": "0819439290", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_publication": "Bellingham, WA", "publication_date": "2001-05-23", "pages": "32-42" }, { "id": "authors:ays67-5t974", "collection": "authors", "collection_id": "ays67-5t974", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol01b", "type": "article", "title": "Phase-dispersion optical tomography", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We report on phase-dispersion optical tomography, a new imaging technique based on phase measurements using low-coherence interferometry. The technique simultaneously probes the target with fundamental and second-harmonic light and interferometrically measures the relative phase shift of the backscattered light fields. This phase change can arise either from reflection at an interface within a sample or from bulk refraction. We show that this highly sensitive 5 phase technique can complement optical coherence tomography, which measures electric field amplitude, by revealing otherwise undetectable dispersive variations in the sample.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2001-05-15", "series_number": "10", "volume": "26", "issue": "10", "pages": "686-688" }, { "id": "authors:c597j-e3186", "collection": "authors", "collection_id": "c597j-e3186", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAXol01", "type": "article", "title": "Measurement of angular distributions by use of low-coherence interferometry for light-scattering spectroscopy", "author": [ { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We present a novel interferometer for measuring angular distributions of backscattered light. The new system exploits a low-coherence source in a modified Michelson interferometer to provide depth resolution, as in optical coherence tomography, but includes an imaging system that permits the angle of the reference field to be varied in the detector plane by simple translation of an optical element. We employ this system to examine the angular distribution of light scattered by polystyrene microspheres. The measured data indicate that size information can be recovered from angular-scattering distributions and that the coherence length of the source influences the applicability of Mie theory.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2001-03-15", "series_number": "6", "volume": "26", "issue": "6", "pages": "322-324" }, { "id": "authors:5ezk5-rny78", "collection": "authors", "collection_id": "5ezk5-rny78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol00", "type": "article", "title": "Interferometric phase-dispersion microscopy", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Georgakoudi", "given_name": "Irene", "clpid": "Georgakaoudi-I" }, { "family_name": "Hanlon", "given_name": "Eugene B.", "clpid": "Hanlon-E-B" }, { "family_name": "Badizadegan", "given_name": "Kamran", "clpid": "Badizadegan-K" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We describe a new scanning microscopy technique, phase-dispersion microscopy (PDM). The technique is based on measuring the phase difference between the fundamental and the second-harmonic light in a novel interferometer. PDM is highly sensitive to subtle refractive-index differences that are due to dispersion (differential optical path sensitivity, 5 nm). We apply PDM to measure minute amounts of DNA in solution and to study biological tissue sections. We demonstrate that PDM performs better than conventional phase-contrast microscopy in imaging dispersive and weakly scattering samples.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2000-10-15", "series_number": "20", "volume": "25", "issue": "20", "pages": "1526-1528" }, { "id": "authors:rx4ap-q9h36", "collection": "authors", "collection_id": "rx4ap-q9h36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANol01a", "type": "article", "title": "Measurement of the anomalous phase velocity of ballistic light in a random medium by use of a novel interferometer", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "Ballistic light, i.e., radiation that propagates undeflected through a turbid medium, undergoes a small change in phase velocity and exhibits unusual dispersion because of its wave nature. We use a novel highly sensitive differential phase optical interferometer to study these previously unmeasurable phenomena. We find that ballistic propagation can be classified into three regimes based on the wavelength-to-size ratio. In the regime in which the scatterer size is comparable with the wavelength, there is an anomalous phase-velocity increase as a result of adding scatterers of higher refractive index. We also observe an anomaly in the relative phase velocity, where red light is slowed more than blue light even though the added scatterers are made of material with normal dispersion.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "2000-09-11", "series_number": "4", "volume": "26", "issue": "4", "pages": "235-237" }, { "id": "authors:4pa0g-fc632", "collection": "authors", "collection_id": "4pa0g-fc632", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-143825869", "type": "article", "title": "Feasibility of field-based light scattering spectroscopy", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Perelman", "given_name": "Lev T.", "clpid": "Perelman-L-T" }, { "family_name": "Wax", "given_name": "Adam", "clpid": "Wax-A" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "Light scattering spectroscopy (LSS) is a new technique capable of accurately measuring the features of nuclei and other cellular organelles in situ. We present the considerations required to implement and interpret field-based detection in LSS, where the scattered electric field is detected interferometrically, and demonstrate that the technique is experimentally feasible. A theoretical formalism for modeling field-based LSS signals based on Mie scattering is presented. Phase-front uniformity is shown to play an important and novel role. Results of heterodyne experiments with polystyrene microspheres that localize LSS signals to a region about 30 mm in axial extent are reported. In addition, differences between field-based LSS and the earlier intensity-based LSS are discussed.", "doi": "10.1117/1.429980", "issn": "1083-3668", "publisher": "Society of Photo-Optical Instrumentation Engineers", "publication": "Journal of Biomedical Optics", "publication_date": "2000-04", "series_number": "2", "volume": "5", "issue": "2", "pages": "138-143" }, { "id": "authors:x8bxs-s1z22", "collection": "authors", "collection_id": "x8bxs-s1z22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANjosaa99", "type": "article", "title": "Spatial coherence of forward-scattered light in a turbid medium", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "An", "given_name": "Kyungwon", "clpid": "An-Kyungwon" }, { "family_name": "Perelman", "given_name": "Lev T.", "clpid": "Perelman-L-T" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We study spatially coherent forward-scattered light propagating in a turbid medium of moderate optical depth (0-9 mean free paths). Coherent detection was achieved by using a tilted heterodyne geometry, which desensitizes coherent detection of the attenuated incident light. We show that the degree of spatial coherence is significantly higher for light scattered only once in comparison with that for multiply scattered light and that it approaches a small constant value for large numbers of scattering events.", "issn": "1084-7529", "publisher": "Optical Society of America", "publication": "Journal of the Optical Society of America A", "publication_date": "1999-04", "series_number": "4", "volume": "16", "issue": "4", "pages": "866-871" }, { "id": "authors:qxn60-hp219", "collection": "authors", "collection_id": "qxn60-hp219", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YANpra97", "type": "article", "title": "Quantum trajectory analysis of a thresholdlike transition in the microlaser", "author": [ { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "An", "given_name": "Kyungwon", "clpid": "An-Kyungwon" } ], "abstract": "In a recent microlaser experiment [K. An et al., Phys. Rev. Lett. 73, 3375 (1994)], a thresholdlike transition of intracavity mean photon number as a function of intracavity mean atom number has been observed. In this paper the behavior is explored with quantum trajectory simulations. It is shown that the transition is caused by enhanced atom-cavity Rabi interaction due to the increase of the intracavity photon number as the intracavity atom number is increased. The transition is further accentuated by the position-dependent variation of the coupling constant in the Fabry-P\u00e9rot cavity. In addition, it is demonstrated that multiatom collective effects are negligible in the microlaser under consideration, in which atoms are injected into the cavity at random times and the product of the coupling constant and atom-cavity interaction time is much less than \u03c0. In this case the analytic theory of the one-atom micromaser [P. Filipowicz et al., Phys. Rev. A 34, 3077 (1986)] can be extrapolated into the multiatom region, assuming uniform atom-cavity coupling throughout the cavity and monovelocity atomic injection. Finally, simulations are performed which account for spatial variation of coupling constant, velocity distribution of injected atoms, and spontaneous atomic decay in the actual experiment. The results are in good agreement with experiment.", "doi": "10.1103/PhysRevA.55.4492", "issn": "1050-2947", "publisher": "American Physical Society", "publication": "Physical Review A", "publication_date": "1997-06", "series_number": "6", "volume": "55", "issue": "6", "pages": "4492-4500" }, { "id": "authors:kwd4j-b7842", "collection": "authors", "collection_id": "kwd4j-b7842", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ANKol95", "type": "article", "title": "Cavity ring-down technique and its application to the measurement of ultraslow velocities", "author": [ { "family_name": "An", "given_name": "Kyungwon", "clpid": "An-Kyungwon" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Dasari", "given_name": "Ramachandra R.", "clpid": "Dasari-R-R" }, { "family_name": "Feld", "given_name": "Michael S.", "clpid": "Feld-M-S" } ], "abstract": "We have developed a new ring-down technique that does not require a shutter to turn a probe laser on and off. With a rapid cavity scan we can measure a simple exponential cavity decay from which a cavity finesse can be found. When the cavity is scanned slowly, the cavity decay exhibits an amplitude modulation, and an analytic expression is derived for this modulation. With this new technique we measured the ultraslow relative velocity of the mirrors (of the order of micrometers per second) as well as the linewidth (~100 kHz) of the probe laser.", "issn": "0146-9592", "publisher": "Optical Society of America", "publication": "Optics Letters", "publication_date": "1995-05-01", "series_number": "9", "volume": "20", "issue": "9", "pages": "1068-1070" } ]