[ { "id": "https://authors.library.caltech.edu/records/cdttg-nr455", "eprint_id": 103528, "eprint_status": "archive", "datestamp": "2023-08-19 20:47:48", "lastmod": "2023-12-22 23:20:51", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Guerrero-Pe\u00f1a-F-A", "name": { "family": "Guerrero Pe\u00f1a", "given": "Fidel A." } }, { "id": "Marrero-Fernandez-P-D", "name": { "family": "Marrero Fernandez", "given": "Pedro D." } }, { "id": "Tarr-P-T", "name": { "family": "Tarr", "given": "Paul T." } }, { "id": "Ren-Tsang-Ing", "name": { "family": "Ren", "given": "Tsang Ing" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" } ] }, "title": "J Regularization Improves Imbalanced Multiclass Segmentation", "ispublished": "unpub", "full_text_status": "public", "keywords": "Loss modeling, deep learning, instance segmentation, multiclass segmentation, cell segmentation, data imbalance", "note": "\u00a9 2020 IEEE. \n\nWe thank financial support from the Brazilian funding agencies FACEPE, CAPES and CNPq (FAG, PF, TIR), from the Beckman Institute at Caltech to the Center for Advanced Methods in Biological Image Analysis (AC, FAG), from the Howard Hughes Medical Institute (PTT, EMM), and thank the IBM Matching Grants Program for computer donation (AC).\n\n
Submitted - 1910.09783.pdf
", "abstract": "We propose a new loss formulation to further advance the multiclass segmentation of cluttered cells under weakly supervised conditions. When adding a Youden's J statistic regularization term to the cross entropy loss we improve the separation of touching and immediate cells, obtaining sharp segmentation boundaries with high adequacy. This regularization intrinsically supports class imbalance thus eliminating the necessity of explicitly using weights to balance training. Simulations demonstrate this capability and show how the regularization leads to correct results by helping advancing the optimization when cross entropy stagnates. We build upon our previous work on multiclass segmentation by adding yet another training class representing gaps between adjacent cells. This addition helps the classifier identify narrow gaps as background and no longer as touching regions. We present results of our methods for 2D and 3D images, from bright field images to confocal stacks containing different types of cells, and we show that they accurately segment individual cells after training with a limited number of images, some of which are poorly annotated.", "date": "2020-04", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "948-952", "id_number": "CaltechAUTHORS:20200528-143929426", "isbn": "9781538693308", "book_title": "2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200528-143929426", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Funda\u00e7\u00e3o do Amparo a Ci\u00eancia e Tecnologia (FACEPE)" }, { "agency": "Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)" }, { "agency": "Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico (CNPq)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1109/isbi45749.2020.9098550", "primary_object": { "basename": "1910.09783.pdf", "url": "https://authors.library.caltech.edu/records/cdttg-nr455/files/1910.09783.pdf" }, "resource_type": "book_section", "pub_year": "2020", "author_list": "Guerrero Pe\u00f1a, Fidel A.; Marrero Fernandez, Pedro D.; et el." }, { "id": "https://authors.library.caltech.edu/records/a4pm4-yd120", "eprint_id": 97236, "eprint_status": "archive", "datestamp": "2023-08-19 15:15:06", "lastmod": "2023-10-20 22:05:45", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Eschweiler-D", "name": { "family": "Eschweiler", "given": "Dennis" } }, { "id": "Spina-T-V", "name": { "family": "Spina", "given": "Thiago V." } }, { "id": "Choudhury-Rohan-C", "name": { "family": "Choudhury", "given": "Rohan C." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot" }, "orcid": "0000-0003-4798-5153" }, { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" }, { "id": "Stegmaier-J", "name": { "family": "Stegmaier", "given": "Johannes" }, "orcid": "0000-0003-4072-3759" } ] }, "title": "CNN-Based Preprocessing to Optimize Watershed-Based Cell Segmentation in 3D Confocal Microscopy Images", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Watershed, CNN, Multi-Instance, Cell Segmentation, Developmental Biology, 3D Image Analysis", "note": "\u00a9 2019 IEEE.", "abstract": "The quantitative analysis of cellular membranes helps understanding developmental processes at the cellular level. Particularly 3D microscopic image data offers valuable insights into cell dynamics, but error-free automatic segmentation remains challenging due to the huge amount of data generated and strong variations in image intensities. In this paper, we propose a new 3D segmentation approach that combines the discriminative power of convolutional neural networks (CNNs) for preprocessing and investigates the performance of three watershed-based postprocessing strategies (WS), which are well suited to segment object shapes, even when supplied with vague seed and boundary constraints. To leverage the full potential of the watershed algorithm, the multi-instance segmentation problem is initially interpreted as three-class semantic segmentation problem, which in turn is well-suited for the application of CNNs. Using manually annotated 3D confocal microscopy images of Arabidopsis thaliana, we show the superior performance of the proposed method compared to the state of the art.", "date": "2019-04", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "223-227", "id_number": "CaltechAUTHORS:20190718-132802709", "isbn": "978-1-5386-3640-4", "book_title": "2019 IEEE 16th International Symposium on Biomedical Imaging", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190718-132802709", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1109/ISBI.2019.8759242", "resource_type": "book_section", "pub_year": "2019", "author_list": "Eschweiler, Dennis; Spina, Thiago V.; et el." }, { "id": "https://authors.library.caltech.edu/records/tmbpn-8xb32", "eprint_id": 86734, "eprint_status": "archive", "datestamp": "2023-08-19 08:36:02", "lastmod": "2023-10-18 19:56:51", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stegmaier-J", "name": { "family": "Stegmaier", "given": "Johannes" }, "orcid": "0000-0003-4072-3759" }, { "id": "Spina-T-V", "name": { "family": "Spina", "given": "Thiago V." } }, { "id": "Falc\u00e3o-A-X", "name": { "family": "Falc\u00e3o", "given": "Alexandre X." } }, { "id": "Bartschat-A", "name": { "family": "Bartschat", "given": "Andreas" } }, { "id": "Mikut-R", "name": { "family": "Mikut", "given": "Ralf" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot" }, "orcid": "0000-0003-4798-5153" }, { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" } ] }, "title": "Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Cell Segmentation, Convolutional Neural Networks, Developmental Biology, Arabidopsis, Meristem", "note": "\u00a9 2018 IEEE. \n\nWe are grateful for funding by the Helmholtz Association in the program BioInterfaces in Technology and Medicine (RM), the German Research Foundation DFG in the project MI1315/4-1 (JS, RM), the Center for Advanced Methods in Biological Image Analysis, Beckman Institute at Caltech (JS, TS, EM, AC), the Howard Hughes Medical Institute (EM), the Gordon and Betty Moore Foundation (EM and AC), the S\u00e3o Paulo Research Foundation in projects 2016/11853-2, 2015/09446-7, and 2014/12236-1 (TS, AF), and the Serrapilheira Institute in the project Serra-1708-16161 (TS). The Titan Xp used for this research was donated by the NVIDIA Corporation.", "abstract": "Automated segmentation approaches are crucial to quantitatively analyze large-scale 3D microscopy images. Particularly in deep tissue regions, automatic methods still fail to provide error-free segmentations. To improve the segmentation quality throughout imaged samples, we present a new supervoxel-based 3D segmentation approach that outperforms current methods and reduces the manual correction effort. The algorithm consists of gentle preprocessing and a conservative super-voxel generation method followed by supervoxel agglomeration based on local signal properties and a postprocessing step to fix under-segmentation errors using a Convolutional Neural Network. We validate the functionality of the algorithm on manually labeled 3D confocal images of the plant Arabidopsis thaliana and compare the results to a state-of-the-art meristem segmentation algorithm.", "date": "2018-04", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "382-386", "id_number": "CaltechAUTHORS:20180601-083044304", "isbn": "978-1-5386-3636-7", "book_title": "2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180601-083044304", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "MI1315/4-1" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2016/11853-2" }, { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2015/09446-7" }, { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2014/12236-1" }, { "agency": "Serrapilheira Institute", "grant_number": "Serra-1708-16161" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1109/ISBI.2018.8363598", "resource_type": "book_section", "pub_year": "2018", "author_list": "Stegmaier, Johannes; Spina, Thiago V.; et el." }, { "id": "https://authors.library.caltech.edu/records/03fef-h1j67", "eprint_id": 92562, "eprint_status": "archive", "datestamp": "2023-08-19 08:38:05", "lastmod": "2023-10-20 15:51:27", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Spina-T-V", "name": { "family": "Spina", "given": "Thiago V." } }, { "id": "Stegmaier-J", "name": { "family": "Stegmaier", "given": "Johannes" }, "orcid": "0000-0003-4072-3759" }, { "id": "Falc\u00e3o-A-X", "name": { "family": "Falc\u00e3o", "given": "Alexandre X." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot" }, "orcid": "0000-0003-4798-5153" }, { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" } ] }, "title": "SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "3D Image Segmentation, Shoot Apical Meristem, Web-based Tool, Collaborative Segmentation, Confocal Microscopy", "note": "\u00a9 2018 IEEE. \n\nWe are grateful for funding by the S\u00e3o Paulo Research Foundation in projects 2016/11853-2, 2015/09446-7, and 2014/12236-1 (TS, AF), CNPq (AF), the Center for Advanced Methods in Biological Image Analsysis, Beckman Institute at Caltech (TS, JS, EM, AC), the German Research Foundation DFG in the project MI1315/4-1 (JS), the Howard Hughes Medical Institute (EM) and the Gordon and Betty Moore Foundation through grant GBMF3406 (EM, AC), and the Serrapilheira Institute in the project Serra-1708-16161 (TS).", "abstract": "The quantitative analysis of 3D confocal microscopy images of the shoot apical meristem helps understanding the growth process of some plants. Cell segmentation in these images is crucial for computational plant analysis and many automated methods have been proposed. However, variations in signal intensity across the image mitigate the effectiveness of those approaches with no easy way for user correction. We propose a web-based collaborative 3D image segmentation application, SEGMENT3D, to leverage automatic segmentation results. The image is divided into 3D tiles that can be either segmented interactively from scratch or corrected from a pre-existing segmentation. Individual segmentation results per tile are then automatically merged via consensus analysis and then stitched to complete the segmentation for the entire image stack. SEGMENT3D is a comprehensive application that can be applied to other 3D imaging modalities and general objects. It also provides an easy way to create supervised data to advance segmentation using machine learning models.", "date": "2018-04", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "391-395", "id_number": "CaltechAUTHORS:20190201-111653966", "isbn": "9781538636367", "book_title": "2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190201-111653966", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2016/11853-2" }, { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2015/09446-7" }, { "agency": "Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Sao Paulo (FAPESP)", "grant_number": "2014/12236-1" }, { "agency": "Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico (CNPq)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "MI1315/4-1" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF3406" }, { "agency": "Serrapilheira Institute", "grant_number": "Serra-1708-16161" } ] }, "doi": "10.1109/isbi.2018.8363600", "resource_type": "book_section", "pub_year": "2018", "author_list": "Spina, Thiago V.; Stegmaier, Johannes; et el." }, { "id": "https://authors.library.caltech.edu/records/nhnjq-69c26", "eprint_id": 62978, "eprint_status": "archive", "datestamp": "2023-08-22 17:05:34", "lastmod": "2024-01-13 16:29:39", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tobin-C", "name": { "family": "Tobin", "given": "Cory" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Real-Time Lineage Analysis to Study Cell Division Orientation in the Arabidopsis Shoot Meristem", "ispublished": "unpub", "full_text_status": "public", "keywords": "Live imaging; Image processing; Cell division; Segmentation; Arabidopsis", "note": "\u00a9 2015 Springer Science+Business Media New York.", "abstract": "Cells in the Arabidopsis shoot apical meristem are small and divide frequently throughout the life-time of the organism making them good candidates for studying the mechanisms of cell division in plants. But tracking these cell divisions requires multiple images to be taken of the same specimen over time which means the specimen must stay alive throughout the process. This chapter provides details on how to prepare plants for live imaging, keep them alive and growing through multiple time points, and how to process the data to extract cell boundary coordinates from three-dimensional images.", "date": "2016", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York, NY", "pagerange": "147-167", "id_number": "CaltechAUTHORS:20151216-110613825", "isbn": "978-1-4939-3141-5", "book_title": "Plant Cell Division: Methods and Protocols", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151216-110613825", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Caillaud-M-C", "name": { "family": "Caillaud", "given": "Marie-C\u00e9cile" } } ] }, "doi": "10.1007/978-1-4939-3142-2_12", "resource_type": "book_section", "pub_year": "2016", "author_list": "Tobin, Cory and Meyerowitz, Elliot M." }, { "id": "https://authors.library.caltech.edu/records/xsb8c-zzb43", "eprint_id": 72700, "eprint_status": "archive", "datestamp": "2023-08-22 11:04:38", "lastmod": "2024-01-13 20:22:05", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wellmer-F", "name": { "family": "Wellmer", "given": "Frank" } }, { "id": "Bowman-J-L", "name": { "family": "Bowman", "given": "John L." } }, { "id": "Davies-B", "name": { "family": "Davies", "given": "Brendan" } }, { "id": "Ferr\u00e1ndiz-C", "name": { "family": "Ferr\u00e1ndiz", "given": "Cristina" } }, { "id": "Fletcher-J-C", "name": { "family": "Fletcher", "given": "Jennifer C." } }, { "id": "Franks-R-G", "name": { "family": "Franks", "given": "Robert G." } }, { "id": "Graciet-E", "name": { "family": "Graciet", "given": "Emmanuelle" } }, { "id": "Gregis-V", "name": { "family": "Gregis", "given": "Veronica" } }, { "id": "Ito-Toshiro", "name": { "family": "Ito", "given": "Toshiro" }, "orcid": "0000-0002-8206-2787" }, { "id": "Jack-T-P", "name": { "family": "Jack", "given": "Thomas P." } }, { "id": "Jiao-Yuling", "name": { "family": "Jiao", "given": "Yuling" }, "orcid": "0000-0002-1189-1676" }, { "id": "Kater-M-M", "name": { "family": "Kater", "given": "Martin M." } }, { "id": "Ma-Hong", "name": { "family": "Ma", "given": "Hong" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Prunet-N", "name": { "family": "Prunet", "given": "Nathana\u00ebl" }, "orcid": "0000-0002-8939-5920" }, { "id": "Riechmann-J-L", "name": { "family": "Riechmann", "given": "Jos\u00e9 Luis" } } ] }, "title": "Flower Development: Open Questions and Future Directions", "ispublished": "unpub", "full_text_status": "public", "keywords": "Flower development; Floral meristems; ABC model; Floral evolution", "note": "\u00a9 2014 Springer Science+Business Media, New York.", "abstract": "Almost three decades of genetic and molecular analyses have resulted in detailed insights into many of the processes that take place during flower development and in the identification of a large number of key regulatory genes that control these processes. Despite this impressive progress, many questions about how flower development is controlled in different angiosperm species remain unanswered. In this chapter, we discuss some of these open questions and the experimental strategies with which they could be addressed. Specifically, we focus on the areas of floral meristem development and patterning, floral organ specification and differentiation, as well as on the molecular mechanisms underlying the evolutionary changes that have led to the astounding variations in flower size and architecture among extant and extinct angiosperms.", "date": "2013-12-02", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York, NY", "pagerange": "103-124", "id_number": "CaltechAUTHORS:20161209-154022495", "isbn": "978-1-4614-9407-2", "book_title": "Flower Development", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161209-154022495", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Riechmann-J-L", "name": { "family": "Riechmann", "given": "Jos\u00e9 Luis" } }, { "id": "Wellmer-F", "name": { "family": "Wellmer", "given": "Frank" } } ] }, "doi": "10.1007/978-1-4614-9408-9_5", "resource_type": "book_section", "pub_year": "2013", "author_list": "Wellmer, Frank; Bowman, John L.; et el." }, { "id": "https://authors.library.caltech.edu/records/fffth-ynt66", "eprint_id": 36364, "eprint_status": "archive", "datestamp": "2023-08-19 13:56:48", "lastmod": "2024-01-13 05:58:19", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sugimoto-Kaoru", "name": { "family": "Sugimoto", "given": "Kaoru" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Regeneration in Arabidopsis Tissue Culture", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Arabidopsis thaliana , Plant regeneration , Tissue culture , Plant hormone , Callus formation , Shoot induction , Root induction", "note": "\u00a9 2013 Springer Science+Business Media. \n\nWe thank Kazuhito Akama, Toshiro Ito, and Tatsuo Kakimoto for valuable information about tissue culture media formulations, Cory Tobin and Paul Tarr for information and technical suggestions about FM dye staining, and Carolyn Ohno for information about seeds sterilization. This work was supported by the US National Science Foundation (Grant IOS-0846192 to E.M.M.) and the Japan Society for the Promotion of Science (to K.S.).", "abstract": "An entire Arabidopsis plant can be regenerated from a small piece of tissue by two sequential hormonal treatments in tissue culture. Currently this in vitro regeneration system is a good system to study the mechanism by which plants show regenerative plasticity. Also, it is useful to test the hormone sensitivity of plants and to propagate sterile lines in Arabidopsis. Here we describe a standard protocol for regenerating Arabidopsis plants in tissue culture, and for preparing and observing samples using confocal microscopy to study cells during regeneration.", "date": "2013", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York", "pagerange": "265-275", "id_number": "CaltechAUTHORS:20130114-151324440", "isbn": "9781627032209", "book_title": "Plant Organogenesis: Methods and Protocols", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130114-151324440", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "IOS-0846192" }, { "agency": "Japan Society for the Promotion of Science (JSPS)" } ] }, "contributors": { "items": [ { "id": "De-Smet-I", "name": { "family": "De Smet", "given": "Ive" } } ] }, "doi": "10.1007/978-1-62703-221-6_18", "resource_type": "book_section", "pub_year": "2013", "author_list": "Sugimoto, Kaoru and Meyerowitz, Elliot M." }, { "id": "https://authors.library.caltech.edu/records/vd4sw-2hh42", "eprint_id": 30091, "eprint_status": "archive", "datestamp": "2023-08-22 05:25:53", "lastmod": "2024-01-13 05:52:00", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre" }, "orcid": "0000-0002-2541-6024" }, { "id": "Tarr-P-T", "name": { "family": "Tarr", "given": "Paul T." } }, { "id": "Roeder-A-H", "name": { "family": "Roeder", "given": "Adrienne H. K." } }, { "id": "Altinok-A", "name": { "family": "Altinok", "given": "Alphan" } }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "Eric" } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Contrast; Denoising; Enhancement; Imaging; Meristem; Segmentation", "note": "\u00a9 2012 Elsevier Inc. \n\nAvailable online 5 April 2012. \n\nWe acknowledge funding support from the Gordon and Betty Moore Foundation Cell Center (http://www.cellcenter.caltech.edu/) (AC and AHKR), the Department of Energy Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences grant DE-FG02-88ER13873 (EMM), National Science Foundation grant IOS-0846192 (EMM), and NIH NRSA Postdoctoral Fellowship F32-GM090534 (PTT). Work of EM was partially supported by NIH R01 GM086883, and NSF's Frontiers in Biological Research (FIBR) program Award No. EF-0330786.", "abstract": "Quantitative studies in plant developmental biology require monitoring and measuring the changes in cells and tissues as growth gives rise to intricate patterns. The success of these studies has been amplified by the combined strengths of two complementary techniques, namely live imaging and computational image analysis. Live imaging records time-lapse images showing the spatial-temporal progress of tissue growth with cells dividing and changing shape under controlled laboratory experiments. Image processing and analysis make sense of these data by providing computational ways to extract and interpret quantitative developmental information present in the acquired images. Manual labeling and qualitative interpretation of images are limited as they don't scale well to large data sets and cannot provide field measurements to feed into mathematical and computational models of growth and patterning. Computational analysis, when it can be made sufficiently accurate, is more efficient, complete, repeatable, and less biased. \n\nIn this chapter, we present some guidelines for the acquisition and processing of images of sepals and the shoot apical meristem of Arabidopsis thaliana to serve as a basis for modeling. We discuss fluorescent markers and imaging using confocal laser scanning microscopy as well as present protocols for doing time-lapse live imaging and static imaging of living tissue. Image segmentation and tracking are discussed. Algorithms are presented and demonstrated together with low-level image processing methods that have proven to be essential in the detection of cell contours. We illustrate the application of these procedures in investigations aiming to unravel the mechanical and biochemical signaling mechanisms responsible for the coordinated growth and patterning in plants.", "date": "2012-04-05", "date_type": "published", "publisher": "Academic Press", "pagerange": "285-323", "id_number": "CaltechAUTHORS:20120416-081534198", "isbn": "9780123884039", "book_title": "Computational Methods in Cell Biology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120416-081534198", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-88ER13873" }, { "agency": "NSF", "grant_number": "IOS-0846192" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32-GM090534" }, { "agency": "NIH", "grant_number": "R01 GM086883" }, { "agency": "NSF", "grant_number": "EF-0330786" } ] }, "contributors": { "items": [ { "id": "Asthagiri-A-R", "name": { "family": "Asthagiri", "given": "Anand R." } }, { "id": "Arkin-A", "name": { "family": "Arkin", "given": "Adam" } } ] }, "doi": "10.1016/B978-0-12-388403-9.00012-6", "resource_type": "book_section", "pub_year": "2012", "author_list": "Cunha, Alexandre; Tarr, Paul T.; et el." }, { "id": "https://authors.library.caltech.edu/records/47178-nrb27", "eprint_id": 23581, "eprint_status": "archive", "datestamp": "2023-08-19 03:41:23", "lastmod": "2024-01-13 05:16:02", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cunha-A", "name": { "family": "Cunha", "given": "Alexandre L." }, "orcid": "0000-0002-2541-6024" }, { "id": "Roeder-A-H-K", "name": { "family": "Roeder", "given": "Adrienne H. K." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Segmenting the sepal and shoot apical meristem of Arabidopsis thaliana", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2010 IEEE. \n\nIssue Date: Aug. 31 2010-Sept. 4 2010. Date of Current Version: 11 November 2010. \n\nThis research was supported by a grant to the California Institute of Technology from the Gordon and Betty Moore Foundation, by Department of Energy Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences grant DE-FG02-88ER13873, and by National Science Foundation grant IOS-0846192. We thank Marcus Heisler from EMBL Heidelberg for providing confocal images of shoot apical meristems and members of the Computable Plant and Computational Morphodynamics projects at Caltech and UCI for valuable discussions and feedback.\n\nPublished - Cunha2010p13784Conf_Proc_IEEE_Eng_Med_Biol_Soc.pdf
", "abstract": "We present methods for segmenting the sepal and shoot apical meristem of the Arabidopsis thaliana plant. We propose a mathematical morphology pipeline and a modified numerical scheme for the active contours without edges algorithm to extract the geometry and topology of plant cells imaged using confocal laser scanning microscopy. We demonstrate our methods in typical images used in the studies of cell endoreduplication and hormone transport and show that in practice they produce highly accurate results requiring little human intervention to cope with image aberrations.", "date": "2010-09", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "5338-5342", "id_number": "CaltechAUTHORS:20110506-134229918", "isbn": "978-1-4244-4123-5", "book_title": "2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110506-134229918", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-88ER13873" }, { "agency": "NSF", "grant_number": "IOS-0846192" } ] }, "doi": "10.1109/IEMBS.2010.5626342", "primary_object": { "basename": "Cunha2010p13784Conf_Proc_IEEE_Eng_Med_Biol_Soc.pdf", "url": "https://authors.library.caltech.edu/records/47178-nrb27/files/Cunha2010p13784Conf_Proc_IEEE_Eng_Med_Biol_Soc.pdf" }, "resource_type": "book_section", "pub_year": "2010", "author_list": "Cunha, Alexandre L.; Roeder, Adrienne H. K.; et el." }, { "id": "https://authors.library.caltech.edu/records/x3q7v-pkc05", "eprint_id": 72627, "eprint_status": "archive", "datestamp": "2023-08-22 04:50:07", "lastmod": "2023-10-23 22:47:20", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gor-V", "name": { "family": "Gor", "given": "V." } }, { "id": "Shapiro-B-E", "name": { "family": "Shapiro", "given": "B. E." } }, { "id": "J\u00f6nsson-H", "name": { "family": "J\u00f6nsson", "given": "H." }, "orcid": "0000-0003-2340-588X" }, { "id": "Heisler-M-G", "name": { "family": "Heisler", "given": "M." }, "orcid": "0000-0001-5644-8398" }, { "id": "Reddy-G-V", "name": { "family": "Reddy", "given": "G. V." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "E. M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "E." } } ] }, "title": "A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Arabidopsis; Cellerator; correspondence; Delaunay triangulation; meristem; SAM; SBML; softassign; Voronoi diagram", "note": "\u00a9 2006 Springer Science+Business Media, Inc. \n\nThis work was supported by the United States National Science Foundation (NSF) under Frontiers in Integrative Biological Research (FIBR) grant No. EF-0330786. HJ was supported, in part, by the Knut and Alice Wallenberg Foundation through Swegene. Portions of the research described in this paper were performed at the California Institute of Technology.", "abstract": "We present the software architecture of the Computable Plant Project, a multidisciplinary computationally based approach to the study of plant development. Arabidopsis thaliana is used as a model organism, and shoot apical meristem (SAM) development as a model process. SAMs are the plant tissues where regulated cell division and differentiation lead to plant parts such as flowers and leaves. We are using green fluorescent proteins to mark specific cell types and acquire time series of three-dimensional images via laser scanning confocal microscopy. To support this, we have developed an interoperable architecture for experiment design that involves automated code generation, computational modeling, and image analysis. Automated image analysis, model fitting, and code generation allow us to explore alternative hypothesis in silico and guide in vivo experimental design. These predictions are tested using standard techniques, such as inducible mutants and altered hormone gradients. The present paper focuses on the automated code generation architecture.", "date": "2006", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York, NY", "pagerange": "345-354", "id_number": "CaltechAUTHORS:20161207-110017153", "isbn": "978-0-387-29450-6", "book_title": "Bioinformatics of Genome Regulation and Structure II", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161207-110017153", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "EF-0330786" }, { "agency": "Knut and Alice Wallenberg Foundation" } ] }, "contributors": { "items": [ { "id": "Kolchanov-N", "name": { "family": "Kolchanov", "given": "Nikolay" } }, { "id": "Hofestaedt-R", "name": { "family": "Hofestaedt", "given": "Ralf" } }, { "id": "Milanesi-L", "name": { "family": "Milanesi", "given": "Luciano" } } ] }, "doi": "10.1007/0-387-29455-4_33", "resource_type": "book_section", "pub_year": "2006", "author_list": "Gor, V.; Shapiro, B. E.; et el." }, { "id": "https://authors.library.caltech.edu/records/skc9p-xef67", "eprint_id": 72632, "eprint_status": "archive", "datestamp": "2023-08-22 04:50:15", "lastmod": "2023-10-23 22:47:32", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Omelyanchuk-N", "name": { "family": "Omelyanchuk", "given": "N." } }, { "id": "Mironova-V", "name": { "family": "Mironova", "given": "V." } }, { "id": "Poplavsky-A", "name": { "family": "Poplavsky", "given": "A." } }, { "id": "Podkoldny-N", "name": { "family": "Podkoldny", "given": "N." } }, { "id": "Kolchanov-N", "name": { "family": "Kolchanov", "given": "N." } }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "E." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "E." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "AGNS\u2014A Database on Expression of Arabidopsis Genes", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Arabidopsis; gene expression; phenotype; database \u2013 mutant; transgenic plants", "note": "\u00a9 2006 Springer Science+Business Media, Inc. \n\nThe work was supported in part by the Russian Foundation for Basic Research (grants Nos. 03-04-48506, 05-07-98012 and 03-04-48469), Presidium of the Russian Academy of Sciences (grant No. 10.4), Siberian Branch of the Russian Academy of Sciences (Integration project No. 119), and the US National Science Foundation (FIBR EF-0330786 Development Modeling and Bioinformatics).", "abstract": "AGNS (Arabidopsis GeneNet supplementary database) is an Internet-available resource that provides access to description of the functions of the known Arabidopsis genes at various levels\u2014the levels of mRNA, protein, cell, tissue, and ultimately at the levels of organs and the organism in both wild type and mutant backgrounds. AGNS annotates published papers on gene expression and function and by this way integrates, systematizes, and classifies this heterogeneous, disparate, and scattered information. AGNS consists of three databases\u2014the Expression Database (ED), the Phenotype Database (PD), and the Reference Database (RD)\u2014and two controlled vocabularies. ED describes gene expression in wild type, mutants, and transgenic plants; PD contains information on phenotypic abnormalities in mutant and transgenic plants; and RD includes references to the papers and description of plant growth conditions with an indication of the ecotypes used as control in the experiments. Detailed controlled vocabularies on growth stages and morphology were developed around the annotated data. AGNS makes possible the search for genes expressed in particular organs, at particular stages, for genes whose expression is altered in particular mutants, for alleles causing particular phenotypic abnormalities, and for pleiotropic effect of particular mutations. Navigation table and search tools are used to browse the informational content of the database and controlled vocabularies.", "date": "2006", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York, NY", "pagerange": "433-442", "id_number": "CaltechAUTHORS:20161207-130209103", "isbn": "978-0-387-29450-6", "book_title": "Bioinformatics of Genome Regulation and Structure II", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161207-130209103", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Russian Foundation for Basic Research", "grant_number": "03-04-48506" }, { "agency": "Russian Foundation for Basic Research", "grant_number": "05-07-98012" }, { "agency": "Russian Foundation for Basic Research", "grant_number": "03-04-48469" }, { "agency": "Presidium of the Russian Academy of Sciences", "grant_number": "10.4" }, { "agency": "Russian Academy of Sciences", "grant_number": "119" }, { "agency": "NSF", "grant_number": "EF-0330786" } ] }, "contributors": { "items": [ { "id": "Kolchanov-N", "name": { "family": "Kolchanov", "given": "Nikolay" } }, { "id": "Hofestaedt-R", "name": { "family": "Hofestaedt", "given": "Ralf" } }, { "id": "Milanesi-L", "name": { "family": "Milanesi", "given": "Luciano" } } ] }, "doi": "10.1007/0-387-29455-4_41", "resource_type": "book_section", "pub_year": "2006", "author_list": "Omelyanchuk, N.; Mironova, V.; et el." }, { "id": "https://authors.library.caltech.edu/records/b879s-17453", "eprint_id": 72559, "eprint_status": "archive", "datestamp": "2023-08-22 01:20:46", "lastmod": "2023-10-23 22:43:30", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "J\u00f6nsson-H", "name": { "family": "J\u00f6nsson", "given": "H." }, "orcid": "0000-0003-2340-588X" }, { "id": "Shapiro-B-E", "name": { "family": "Shapiro", "given": "B. E." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "E. M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "E." } } ] }, "title": "Modeling Plant Development with Gene Regulation Networks Including Signaling and Cell Division", "ispublished": "unpub", "full_text_status": "public", "keywords": "arabidopsis; shoot apical meristem (SAM); Cellerator; computer modeling", "note": "\u00a9 2004 Springer Science+Business Media New York.", "abstract": "The shoot apical meristem of Arabidopsis thaliana is an example of a developmental system which can be modeled at genetic and mechanical levels provided that suitable mathematical and computational tools are available to represent intercellular signaling, cell cycling, mechanical stresses, and a changing topology of neighborhood relationships between compartments. In this paper, we present a simplified dynamical 2-dimensional model of a growing plant. Cells in the shoot grow and proliferate, while the number of stem cells at the apex stays constant due to differentiation into tissue cells. Cell types are defined by protein concentrations within the cells, and the dynamics of the differentiation follows from a gene regulation network, which includes intercellular signals.", "date": "2004", "date_type": "published", "publisher": "Springer", "place_of_pub": "Boston", "pagerange": "311-318", "id_number": "CaltechAUTHORS:20161205-125349225", "isbn": "978-1-4757-4613-6", "book_title": "Bioinformatics of Genome Regulation and Structure", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161205-125349225", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Kolchanov-N", "name": { "family": "Kolchanov", "given": "Nikolay" } }, { "id": "Hofestaedt-R", "name": { "family": "Hofestaedt", "given": "Ralf" } } ] }, "doi": "10.1007/978-1-4419-7152-4_33", "resource_type": "book_section", "pub_year": "2004", "author_list": "J\u00f6nsson, H.; Shapiro, B. E.; et el." }, { "id": "https://authors.library.caltech.edu/records/tcv13-v7169", "eprint_id": 72558, "eprint_status": "archive", "datestamp": "2023-08-19 10:37:45", "lastmod": "2023-10-23 22:43:27", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "J\u00f6nsson-H", "name": { "family": "J\u00f6nsson", "given": "Henrik" }, "orcid": "0000-0003-2340-588X" }, { "id": "Shapiro-B-E", "name": { "family": "Shapiro", "given": "Bruce E." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Mjolsness-E-D", "name": { "family": "Mjolsness", "given": "Eric" } } ] }, "title": "Signalling in multicellular models of plant development", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2003 Elsevier Ltd.", "abstract": "The shoot apical meristem (SAM) is the source of the complete part of a plant above ground. Arabidopsis thaliana has become a model system for dicot plants (Meinke et al., 1998; The-Arabidopsis-Genome-Initiative, 2000), and it has a SAM of about 10^3 cells. It retains this size and its almost half-spherical shape throughout the post-embryonic life of the plant. The SAM can be divided into cytologically defined zones where the central zone is at the very apex, the peripheral zone is on the sides, and the rib meristem is in the central parts of the meristem (Steeves and Sussex, 1989; Meyerowitz, 1997).", "date": "2003", "date_type": "published", "publisher": "Elsevier", "place_of_pub": "Amsterdam", "pagerange": "156-161", "id_number": "CaltechAUTHORS:20161205-124921688", "isbn": "9780080497587", "book_title": "On Growth, Form and Computers", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161205-124921688", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Kumar-Sanjeev", "name": { "family": "Kumar", "given": "Sanjeev" } }, { "id": "Bentley-P-J", "name": { "family": "Bentley", "given": "Peter J." } } ] }, "doi": "10.1016/B978-012428765-5/50041-4", "resource_type": "book_section", "pub_year": "2003", "author_list": "J\u00f6nsson, Henrik; Shapiro, Bruce E.; et el." }, { "id": "https://authors.library.caltech.edu/records/75rgn-f4s69", "eprint_id": 72533, "eprint_status": "archive", "datestamp": "2023-08-19 08:47:43", "lastmod": "2023-10-23 22:42:13", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vishnevetsky-M", "name": { "family": "Vishnevetsky", "given": "M." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "E. M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Molecular Control of Flower Development", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2002 Springer Science+Business Media Dordrecht.", "abstract": "The last decade has been an exciting period in plant molecular biology in general and in molecular studies of flower development in particular. The isolation of the first floral meristem identity and floral homeotic genes of Arabidopsis in the late 1980s\u2014early '80s opened the way to in-depth studies of molecular aspects of floral development (Bowman et al., 1989; Coen et al., 1990; Sommer et al., 1990; Yanofsky et al., 1990). These investigations have led to insights into inflorescence and flower development in higher eudicotyledonous flowering plants, using mainly the predominant model of Arabidopsis thaliana (thale cress). The abundance of mutants, a relatively small genome, and easy transformation procedures have made this small plant a primary tool of modern plant biology. Among the ornamentals, Antirrhinum majus (snapdragon) and Petunia hybrida (petunia) are the best-characterized plants at the molecular level. As far as is known, flower development in these species follows genetic principles and mechanisms similar to those in Arabidopsis, although some differences exist in the details at the molecular level, and will be discussed later.", "date": "2002", "date_type": "published", "publisher": "Springer", "place_of_pub": "Dordrecht", "pagerange": "239-252", "id_number": "CaltechAUTHORS:20161202-134251036", "isbn": "978-90-481-5975-8", "book_title": "Breeding For Ornamentals: Classical and Molecular Approaches", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161202-134251036", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Vainstein-A", "name": { "family": "Vainstein", "given": "Alexander" } } ] }, "doi": "10.1007/978-94-017-0956-9_12", "resource_type": "book_section", "pub_year": "2002", "author_list": "Vishnevetsky, M. and Meyerowitz, E. M." }, { "id": "https://authors.library.caltech.edu/records/b4sqw-5dh77", "eprint_id": 72852, "eprint_status": "archive", "datestamp": "2023-08-20 05:09:58", "lastmod": "2023-10-23 23:00:58", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Running-M-P", "name": { "family": "Running", "given": "Mark P." } }, { "id": "Clark-S-E", "name": { "family": "Clark", "given": "Steven E." } }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Confocal Microscopy of the Shoot Apex", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 1995 Academic Press. \n\nWe thank C. Chang, S. Jacobsen, Z. Liu, J.-L. Riechmann, H. Sakai, L. Sieberth, and B. Williams for review of the manuscript, and A. Readhead for help with tissue preparation. We especially thank Dr. Jean-Paul Revel for advice and help with using the CLSM instrument, advice and suggestions for sample preparation, and review of the manuscript. This work was supported by U.S. National Science Foundation (NSF) Grant MCB-9204839 to E.M.M. M.P.R. was a Howard Hughes Predoctoral Fellow, and S.E.C. was supported by an NSF Postdoctoral Fellowship in Plant Biology.", "abstract": "This chapter focuses on confocal laser scanning microscopy (CLSM). In CLSM, a sample is treated with a fluorescent dye, and a laser beam is focused on a point in the sample, causing the emission of fluorescent light. The use of CLSM in the study of plant development has many advantages over conventional histological techniques. Because CLSM data are stored digitally, the data can not only be reconstructed in three dimensions, but also animated or displayed as stereo images, to aid in visual interpretation. Once the sample is reconstructed on a computer, virtual sections can be made from any orientation. Specimen preparation for CLSM is also much less labor intensive compared to serial sectioning, and avoids problems such as recovering and mounting individual sections, a time-consuming and error-prone task. The integrity of the sample is preserved in CLSM, allowing rescanning using different parameters. The chapter describes the method of examining plant tissue using CLSM, particularly in studies of the structure, cell number, and cell pattern of shoot apical meristems and floral meristems. The development of this technique is timely because of the recent explosion of interest in developmental mutants that affect apical and floral meristem structure.", "date": "1995", "date_type": "published", "publisher": "Elsevier", "place_of_pub": "New York, NY", "pagerange": "217-229", "id_number": "CaltechAUTHORS:20161215-122419408", "isbn": "978-0-12-564151-7", "book_title": "Methods in Cell Biology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161215-122419408", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MCB-9204839" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF Plant Biology Postdoctoral Fellowship" } ] }, "contributors": { "items": [ { "id": "Galbraith-D-W", "name": { "family": "Galbraith", "given": "David W." } }, { "id": "Bohnert-H-J", "name": { "family": "Bohnert", "given": "Hans J." } }, { "id": "Bourque-D-P", "name": { "family": "Bourque", "given": "Don P." } } ] }, "doi": "10.1016/S0091-679X(08)61456-9", "resource_type": "book_section", "pub_year": "1995", "author_list": "Running, Mark P.; Clark, Steven E.; et el." }, { "id": "https://authors.library.caltech.edu/records/ha1hv-ez433", "eprint_id": 106254, "eprint_status": "archive", "datestamp": "2023-08-22 09:43:24", "lastmod": "2024-01-15 18:13:58", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "The Genetic and Molecular Basis of Flower Development in Arabidopsis", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Flower Development; Floral Organ; Organ Identity; Homeotic Gene; Floral Meristem Identity", "note": "\u00a9 Springer-Verlag Berlin Heidelberg 1994.", "abstract": "My laboratory studies pattern development in flowers, concentrating on two basic patterns that develop in parallel. The first is the pattern of organ number and position. The flowers of the plant we study, the mustard Arabidopsis thaliana, have a total of 16 organs: four organs in the first organ whorl, with a 90-degree angle between adjacent organs, four organs inside and alternate to the first whorl organs, six third-whorl organs with their own characteristic spacing and divergence angles, and two fourth-whorl organs (M\u00fcller, 1961; Smyth et al., 1990). This number and position of floral organs is specific to members of the mustard family and close relatives; other families have quite different patterns of organ number and position. The second pattern, which develops to a large degree independently of the first, is the pattern of organ identity. From the outside to the inside of the flower, one finds the four organ types sepal, petal, stamen, then carpel occurring in this order in successive organ whorls. This radial order of organ identities is not at all family-specific, being almost completely uniform in flowering plants. We would like to understand how the activities of specific genes produce both patterns in developing floral primordia, to understand how these patterns have arisen in the evolution of flowering plants, and to know what differences in the genes that control these patterns give the diversity of flower forms that exists in nature.", "date": "1994", "date_type": "published", "publisher": "Springer Berlin Heidelberg", "place_of_pub": "Berlin, Heidelberg", "pagerange": "1-6", "id_number": "CaltechAUTHORS:20201023-102057819", "isbn": "9783642788543", "book_title": "Plant Molecular Biology : Molecular Genetic Analysis of Plant Development and Metabolism", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201023-102057819", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Coruzzi-G", "name": { "family": "Coruzzi", "given": "Gloria" } }, { "id": "Puigdom\u00e8nech-P", "name": { "family": "Puigdom\u00e8nech", "given": "Pere" } } ] }, "doi": "10.1007/978-3-642-78852-9_1", "resource_type": "book_section", "pub_year": "1994", "author_list": "Meyerowitz, Elliot M." }, { "id": "https://authors.library.caltech.edu/records/bp6xm-grp26", "eprint_id": 72770, "eprint_status": "archive", "datestamp": "2023-08-19 20:08:52", "lastmod": "2024-01-13 20:22:11", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Chang-Caren", "name": { "family": "Chang", "given": "Caren" } } ] }, "title": "Molecular Biology of Plant Growth and Development", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1988 Plenum Press, New York.", "abstract": "Plant development differs from animal development in several fundamental respects. Since plant cells are immobilized in a rigid cell wall, morphogenesis is dependent upon control of cell growth and plane of cell division, rather than cell migration as occurs in animal development. The meristematic cells of plants display a degree of plasticity not found in animal cells; they remain embryonic throughout the life of the plant and produce both adult organs and germ cells. Furthermore, individual differentiated cells from vegetative plant parts are able to dedifferentiate and regenerate into new, fertile plants.", "date": "1988", "date_type": "published", "publisher": "Springer", "place_of_pub": "Boston, MA", "pagerange": "353-366", "id_number": "CaltechAUTHORS:20161213-103629709", "isbn": "978-1-4615-6819-3", "book_title": "The Molecular Biology of Cell Determination and Cell Differentiation", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161213-103629709", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Browder-L-W", "name": { "family": "Browder", "given": "Leon W." } } ] }, "doi": "10.1007/978-1-4615-6817-9_13", "resource_type": "book_section", "pub_year": "1988", "author_list": "Meyerowitz, Elliot M. and Chang, Caren" } ]