[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/682pk-6sh21", "eprint_status": "archive", "datestamp": "2023-12-06 18:51:43", "lastmod": "2024-01-09 22:23:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shao-Shuai", "name": { "family": "Shao", "given": "Shuai" }, "orcid": "0000-0002-0916-1578" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Gjorgjieva-Julijana", "name": { "family": "Gjorgjieva", "given": "Julijana" }, "orcid": "0000-0001-7118-4079" } ] }, "title": "Efficient population coding of sensory stimuli", "ispublished": "pub", "full_text_status": "public", "keywords": "General Physics and Astronomy", "note": "
The efficient coding theory postulates that single cells in a neuronal population should be optimally configured to efficiently encode information about a stimulus subject to biophysical constraints. This poses the question of how multiple neurons that together represent a common stimulus should optimize their activation functions to provide the optimal stimulus encoding. Previous theoretical approaches have solved this problem with binary neurons that have a step activation function, and have assumed that spike generation is noisy and follows a Poisson process. Here we derive a general theory of optimal population coding with neuronal activation functions of any shape, different types of noise and heterogeneous firing rates of the neurons by maximizing the Shannon mutual information between a stimulus and the neuronal spiking output subject to a constraint on the maximal firing rate. We find that the optimal activation functions are discrete in the biological case of non-negligible noise and demonstrate that the information does not depend on how the population is divided into ON and OFF cells described by monotonically increasing vs decreasing activation functions, respectively. However, the population with an equal number of ON and OFF cells has the lowest mean firing rate, and hence encodes the highest information per spike. These results are independent of the shape of the activation functions and the nature of the spiking noise. Finally, we derive a relationship for how these activation functions should be distributed in stimulus space as a function of the neurons' firing rates.
\n\nThis work is supported by the funding from the Max Planck Society (S.S. and J.G.), the Technical University of Munich (J.G.), and NIH Grant No. R01 NS111477 (M.M.). We also would like thank the \"Computation in Neural Circuits\" group for comments on this work, especially our colleagues Claudia Cusseddu and Judith Parkinson-Schwarz for providing feedback on the manuscript.
\n\nThis article is part of the Physical Review Research collection titled Physics of Neuroscience.
", "abstract": "Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Open access publication funded by the Max Planck Society.
", "date": "2023-12", "date_type": "published", "publication": "Physical Review Research", "volume": "5", "number": "4", "publisher": "American Physical Society", "pagerange": "043205", "issn": "2643-1564", "official_url": "https://authors.library.caltech.edu/records/682pk-6sh21", "funders": { "items": [ {}, {}, { "grant_number": "R01 NS111477" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1103/physrevresearch.5.043205", "primary_object": { "basename": "PhysRevResearch.5.043205.pdf", "url": "https://authors.library.caltech.edu/records/682pk-6sh21/files/PhysRevResearch.5.043205.pdf" }, "related_objects": [ { "basename": "supp_mat.pdf", "url": "https://authors.library.caltech.edu/records/682pk-6sh21/files/supp_mat.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Shao, Shuai; Meister, Markus; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5m31y-wfa08", "eprint_id": 122034, "eprint_status": "archive", "datestamp": "2023-08-20 16:47:40", "lastmod": "2023-12-22 23:39:31", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hahn-Joshua", "name": { "family": "Hahn", "given": "Joshua" }, "orcid": "0000-0002-4776-2067" }, { "id": "Monavarfeshani-Aboozar", "name": { "family": "Monavarfeshani", "given": "Aboozar" }, "orcid": "0000-0001-8906-5115" }, { "id": "Qiao-Mu", "name": { "family": "Qiao", "given": "Mu" }, "orcid": "0000-0001-7309-4237" }, { "id": "Kao-Allison", "name": { "family": "Kao", "given": "Allison" } }, { "id": "K\u00f6lsch-Yvonne", "name": { "family": "K\u00f6lsch", "given": "Yvonne" }, "orcid": "0000-0002-9953-7312" }, { "id": "Kumar-Ayush", "name": { "family": "Kumar", "given": "Ayush" } }, { "id": "Kunze-Vincent-P", "name": { "family": "Kunze", "given": "Vincent P." }, "orcid": "0000-0002-7869-9793" }, { "id": "Rasys-Ashley-M", "name": { "family": "Rasys", "given": "Ashley M." }, "orcid": "0000-0002-4589-5456" }, { "id": "Richardson-Rose", "name": { "family": "Richardson", "given": "Rose" }, "orcid": "0000-0001-7164-0337" }, { "id": "Baier-Herwig", "name": { "family": "Baier", "given": "Herwig" }, "orcid": "0000-0002-7268-0469" }, { "id": "Lucas-Robert-J", "name": { "family": "Lucas", "given": "Robert J." }, "orcid": "0000-0002-1088-8029" }, { "id": "Li-Wei", "name": { "family": "Li", "given": "Wei" }, "orcid": "0000-0002-2897-649X" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Trachtenberg-Joshua-T", "name": { "family": "Trachtenberg", "given": "Joshua T." }, "orcid": "0000-0002-5041-774X" }, { "id": "Yan-Wenjun", "name": { "family": "Yan", "given": "Wenjun" }, "orcid": "0000-0003-3568-4265" }, { "id": "Peng-Yi-Rong", "name": { "family": "Peng", "given": "Yi-Rong" }, "orcid": "0000-0002-5689-2779" }, { "id": "Sanes-Joshua-R", "name": { "family": "Sanes", "given": "Joshua R." }, "orcid": "0000-0001-8926-8836" }, { "id": "Shejkhar-Karthik", "name": { "family": "Shekhar", "given": "Karthik" }, "orcid": "0000-0003-4349-6600" } ] }, "title": "Evolution of neuronal cell classes and types in the vertebrate retina", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nThis work was supported by the NIH (K99EY033457, R00EY028625, R21EY028633, U01MH105960 and T32GM007103), the Chan-Zuckerberg Initiative (CZF-2019-002459), the Glaucoma Research Foundation (K.S.), startup funds from the UC Berkeley (K.S.), an award from Research to Prevent Blindness and a Klingenstein-Simons Fellowship Award (Y.R.P.), a Wellcome Trust Investigator Award (210684/Z/18/Z) (R.J.L.), an ARCS Foundation Scholarship and a Society for Developmental Biology Emerging Models grant (A.M.R.), and grants from Children's Glaucoma Foundation and NSF (1827647) to James Lauderdale and Douglas B. Menke. We thank James D. Lauderdale and Douglas B. Menke (University of Georgia) for supervision of A.M.R.; Mallory Laboulaye and Rebecca Schaffer for assistance; Joseph Wekselblatt for tree-shrew tissue.; Guoping Feng for marmoset tissue; Hopi Hoekstra for peromyscus tissue; and Steve Van Hooser for ferret tissue. Icons for species in the figures were obtained from BioRender.com. \n\nCode Availability. scRNA-seq data clustering, integration, and visualization was performed in the R statistical language, and heavily relied on the Seurat package (https://satijalab.org/seurat/). All scripts are available at https://github.com/shekharlab/RetinaEvolution including R markdown notebooks. FLDA analysis was performed in Python, and the code and documentation are available at https://github.com/muqiao0626/FLDA. \n\nThe authors have declared no competing interest.\n\nSubmitted - nihpp-2023.04.07.536039v1.pdf
Supplemental Material - media-1.xlsx
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
", "abstract": "The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and M\u00fcller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.", "date": "2023-06-29", "date_type": "published", "id_number": "CaltechAUTHORS:20230628-257286000.41", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257286000.41", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K99EY033457" }, { "agency": "NIH", "grant_number": "R00EY028625" }, { "agency": "NIH", "grant_number": "R21EY028633" }, { "agency": "NIH", "grant_number": "U01MH105960" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32GM007103" }, { "agency": "Chan Zuckerberg Initiative", "grant_number": "CZF-2019-002459" }, { "agency": "Glaucoma Research Foundation" }, { "agency": "University of California, Berkeley" }, { "agency": "Research to Prevent Blindness" }, { "agency": "Klingenstein-Simons Foundation" }, { "agency": "Wellcome Trust", "grant_number": "210684/Z/18/Z" }, { "agency": "ARCS Foundation" }, { "agency": "Society for Developmental Biology" }, { "agency": "Children's Glaucoma Foundation" }, { "agency": "NSF", "grant_number": "IOS-1827647" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.04.07.536039", "pmcid": "PMC10104162", "primary_object": { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/5m31y-wfa08/files/media-1.xlsx" }, "related_objects": [ { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/5m31y-wfa08/files/media-2.xlsx" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/5m31y-wfa08/files/media-3.xlsx" }, { "basename": "nihpp-2023.04.07.536039v1.pdf", "url": "https://authors.library.caltech.edu/records/5m31y-wfa08/files/nihpp-2023.04.07.536039v1.pdf" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Hahn, Joshua; Monavarfeshani, Aboozar; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0wd1r-y8426", "eprint_id": 121367, "eprint_status": "archive", "datestamp": "2023-08-22 20:42:04", "lastmod": "2023-12-22 23:39:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Ya-tang", "name": { "family": "Li", "given": "Ya-tang" }, "orcid": "0000-0003-2763-1534" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Functional cell types in the mouse superior colliculus", "ispublished": "pub", "full_text_status": "public", "keywords": "General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Medicine; General Neuroscience", "note": "\u00a9 2023, Li and Meister. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nMM was supported by grants from NIH (R01 NS111477) and from the Simons Foundation (543015SPI). Y-t L was supported by a grant from the NEI (K99EY028640) and a Helen Hay Whitney Postdoctoral Fellowship. \n\nData availability. Data and code are available in a Caltech DATA Repository (https://doi.org/10.22002/w3n8w-wgx37) and in a public Github repository (https://github.com/yatangli/Li-CellTypes-2023 copy archived at Li and Meister, 2023). \n\nEthics. All animal procedures were performed according to relevant guidelines and approved by the Caltech IACUC (protocol 1656).\n\nPublished - elife-82367.pdf
", "abstract": "The superior colliculus (SC) represents a major visual processing station in the mammalian brain that receives input from many types of retinal ganglion cells (RGCs). How many parallel channels exist in the SC, and what information does each encode? Here, we recorded from mouse superficial SC neurons under a battery of visual stimuli including those used for classification of RGCs. An unsupervised clustering algorithm identified 24 functional types based on their visual responses. They fall into two groups: one that responds similarly to RGCs and another with more diverse and specialized stimulus selectivity. The second group is dominant at greater depths, consistent with a vertical progression of signal processing in the SC. Cells of the same functional type tend to cluster near each other in anatomical space. Compared to the retina, the visual representation in the SC has lower dimensionality, consistent with a sifting process along the visual pathway.", "date": "2023-04-19", "date_type": "published", "publication": "eLife", "volume": "12", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e82367", "id_number": "CaltechAUTHORS:20230510-345799900.1", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230510-345799900.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS111477" }, { "agency": "Simons Foundation", "grant_number": "543015SPI" }, { "agency": "NIH", "grant_number": "K99EY028640" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.82367", "pmcid": "PMC10121220", "primary_object": { "basename": "elife-82367.pdf", "url": "https://authors.library.caltech.edu/records/0wd1r-y8426/files/elife-82367.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Li, Ya-tang and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pm0hw-3cn95", "eprint_id": 115059, "eprint_status": "archive", "datestamp": "2023-08-22 17:02:16", "lastmod": "2023-12-22 23:39:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Learning, fast and slow", "ispublished": "pub", "full_text_status": "restricted", "keywords": "General Neuroscience", "note": "\u00a9 2022 Elsevier. \n\nAvailable online 23 May 2022, Version of Record 23 May 2022. \n\nThis review comes from a themed issue on Neurobiology of Behavior; Edited by Tiago Branco and Mala Murthy. \n\nMM acknowledges support from NIH (R01 NS111477), the Simons Collaboration on the Global Brain (543015) and the Tianqiao and Chrissy Chen Institute for Neuroscience. Thanks to Ralph Adolphs, Pietro Perona, Ueli Rutishauser, Doris Tsao, and Tony Zador for helpful comments and critiques. \n\nCode and data. Code and data supporting this article can be found at https://github.com/markusmeister/Learning_Fast_And_Slow. \n\nConflict of interest statement: Nothing declared.", "abstract": "Animals can learn efficiently from a single experience and change their future behavior in response. However, in other instances, animals learn very slowly, requiring thousands of experiences. Here, I survey tasks involving fast and slow learning and consider some hypotheses for what differentiates the underlying neural mechanisms. It has been proposed that fast learning relies on neural representations that favor efficient Hebbian modification of synapses. These efficient representations may be encoded in the genome, resulting in a repertoire of fast learning that differs across species. Alternatively, the required neural representations may be acquired from experience through a slow process of unsupervised learning from the environment.", "date": "2022-08", "date_type": "published", "publication": "Current Opinion in Neurobiology", "volume": "75", "publisher": "Elsevier", "pagerange": "Art. No. 102555", "id_number": "CaltechAUTHORS:20220607-425325000", "issn": "0959-4388", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220607-425325000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS111477" }, { "agency": "Simons Foundation", "grant_number": "543015" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.conb.2022.102555", "resource_type": "article", "pub_year": "2022", "author_list": "Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gmn1a-mm051", "eprint_id": 114181, "eprint_status": "archive", "datestamp": "2023-08-20 07:28:34", "lastmod": "2023-12-22 23:39:35", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Ya-tang", "name": { "family": "Li", "given": "Ya-tang" }, "orcid": "0000-0003-2763-1534" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Functional Cell Types in the Mouse Superior Colliculus", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nVersion 1 - April 5, 2022; Version 2 - August 1, 2022. \n\nM.M. was supported by grants from NIH (R01 NS111477) and from the Simons Foundation (543015SPI). Y.-t.L was supported by a grant from the NEI (K99EY028640) and a Helen Hay Whitney Postdoctoral Fellowship. \n\nAuthor contributions: Y.-t.L designed the study, performed all experiments, interpreted results, and wrote the manuscript. M.M. helped design the study, interpret results, and write the manuscript. \n\nThe authors declare no competing interests. \n\nData and code availability: Data and code will be available in a public repository following acceptance of the manuscript.\n\nSubmitted - 2022.04.01.486789v2.full.pdf
", "abstract": "The superior colliculus (SC) represents a major visual processing station in the mammalian brain that receives input from many types of retinal ganglion cells (RGCs). How many parallel channels exist in the SC, and what information does each encode? Here we recorded from mouse superficial SC neurons under a battery of visual stimuli including those used for classification of RGCs. An unsupervised clustering algorithm identified 24 functional types based on their visual responses. They fall into two groups: one that responds similarly to RGCs, and another with more diverse and specialized stimulus selectivity. The second group is dominant at greater depths, consistent with a vertical progression of signal processing in the SC. Cells of the same functional type tend to cluster near each other in anatomical space. Compared to the retina, the visual representation in the SC has lower dimensionality, consistent with a sifting process along the visual pathway.", "date": "2022-04-06", "date_type": "published", "id_number": "CaltechAUTHORS:20220406-729141742", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220406-729141742", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS111477" }, { "agency": "Simons Foundation", "grant_number": "543015SPI" }, { "agency": "National Eye Institute", "grant_number": "K99EY028640" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.04.01.486789", "primary_object": { "basename": "2022.04.01.486789v2.full.pdf", "url": "https://authors.library.caltech.edu/records/gmn1a-mm051/files/2022.04.01.486789v2.full.pdf" }, "resource_type": "monograph", "pub_year": "2022", "author_list": "Li, Ya-tang and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kc0zb-px694", "eprint_id": 112530, "eprint_status": "archive", "datestamp": "2023-08-20 04:20:24", "lastmod": "2023-12-13 17:01:26", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Curved Micro-Electrode Arrays", "ispublished": "unpub", "full_text_status": "public", "note": "Attribution 4.0 International (CC BY 4.0).\n\nThanks to Kyu Hyun Lee, Sotiris Masmanidis, and Harri Kytomaa for feedback and advice. MM is supported in part by grants from the Simons Foundation (543015) and from the NINDS (5R01NS111477).\n\nSubmitted - 2107.13532.pdf
", "abstract": "Multi-electrode arrays serve to record electrical signals of many neurons in the brain simultaneously. For most of the past century, electrodes that penetrate brain tissue have had exactly one shape: a straight needle. Certainly this was a good starting choice at the time, but there is no reason to think that a straight line would be the optimal shape in all Neuroscience applications. Here I argue that, in fact, a wide variety of curved shapes is equally practical: all possible helices. I discuss the manufacture and manipulation of such devices, and illustrate a few use cases where they will likely outperform conventional needles. With some collective action from the research community, curved arrays could be manufactured and distributed at low cost.", "date": "2021-12-20", "date_type": "published", "id_number": "CaltechAUTHORS:20211217-233144809", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211217-233144809", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "543015" }, { "agency": "NIH", "grant_number": "5R01NS111477" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.48550/arXiv.2107.13532", "primary_object": { "basename": "2107.13532.pdf", "url": "https://authors.library.caltech.edu/records/kc0zb-px694/files/2107.13532.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9ddh3-bfe46", "eprint_id": 111089, "eprint_status": "archive", "datestamp": "2023-08-20 05:12:16", "lastmod": "2023-12-13 17:01:23", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Tony", "name": { "family": "Zhang", "given": "Tony" } }, { "id": "Rosenberg-Matthew", "name": { "family": "Rosenberg", "given": "Matthew" } }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Endotaxis: A Universal Algorithm for Mapping, Goal-Learning, and Navigation", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.\n\nThis version posted September 25, 2021.\n\nThis work was supported by the Simons Collaboration on the Global Brain (grant 543015 to MM and 543025 to PP), by NSF award 1564330 to PP, and by a gift from Google to PP.\n\nData and code availability:\nData and code to reproduce the reported results are available at https://github.com/tonyzhang25/Zhang-2021-Endotaxis. Following acceptance of the manuscript they will be archived in a permanent public repository.\n\nAuthor contributions:\nConception of the study TZ, MR, PP, MM; Numerical work TZ, PP; Analytical work MM; Drafting the manuscript MM; Revision and approval TZ, MR, PP, MM.\n\nCompeting interests:\nThe authors declare no competing interests.\n\nColleagues:\nWe thank Kyu Hyun Lee and Ruben Portugues for comments.\n\nSubmitted - 2021.09.24.461751v1.full.pdf
", "abstract": "An animal entering a new environment typically faces three challenges: explore the space for resources, memorize their locations, and navigate towards those targets as needed. Experimental work on exploration, mapping, and navigation has mostly focused on simple environments \u2013 such as an open arena, a pond [1], or a desert [2] \u2013 and much has been learned about neural signals in diverse brain areas under these conditions [3, 4]. However, many natural environments are highly constrained, such as a system of burrows, or of paths through the underbrush. More generally, many cognitive tasks are equally constrained, allowing only a small set of actions at any given stage in the process. Here we propose an algorithm that learns the structure of an arbitrary environment, discovers useful targets during exploration, and navigates back to those targets by the shortest path. It makes use of a behavioral module common to all motile animals, namely the ability to follow an odor to its source [5]. We show how the brain can learn to generate internal \"virtual odors\" that guide the animal to any location of interest. This endotaxis algorithm can be implemented with a simple 3-layer neural circuit using only biologically realistic structures and learning rules. Several neural components of this scheme are found in brains from insects to humans. Nature may have evolved a general mechanism for search and navigation on the ancient backbone of chemotaxis.", "date": "2021-09-29", "date_type": "published", "id_number": "CaltechAUTHORS:20210929-162922601", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-162922601", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "543015" }, { "agency": "Simons Foundation", "grant_number": "543025" }, { "agency": "NSF", "grant_number": "IIS-1564330" }, { "agency": "Google" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.09.24.461751", "primary_object": { "basename": "2021.09.24.461751v1.full.pdf", "url": "https://authors.library.caltech.edu/records/9ddh3-bfe46/files/2021.09.24.461751v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Zhang, Tony; Rosenberg, Matthew; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zwfrv-rbn84", "eprint_id": 100076, "eprint_status": "archive", "datestamp": "2023-08-22 11:08:28", "lastmod": "2023-12-22 23:39:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Kyu-Hyun", "name": { "family": "Lee", "given": "Kyu Hyun" }, "orcid": "0000-0001-6483-9444" }, { "id": "Ni-Yu-Li", "name": { "family": "Ni", "given": "Yu-Li" }, "orcid": "0000-0003-1600-9854" }, { "id": "Colonell-Jennifer", "name": { "family": "Colonell", "given": "Jennifer" } }, { "id": "Karsh-Bill", "name": { "family": "Karsh", "given": "Bill" } }, { "id": "Putzeys-Jan", "name": { "family": "Putzeys", "given": "Jan" }, "orcid": "0000-0001-8834-5852" }, { "id": "Pachitariu-Marius", "name": { "family": "Pachitariu", "given": "Marius" }, "orcid": "0000-0001-7106-814X" }, { "id": "Harris-Timothy-D", "name": { "family": "Harris", "given": "Timothy D." }, "orcid": "0000-0002-6289-4439" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes", "ispublished": "pub", "full_text_status": "public", "keywords": "Extracellular recording; Neural circuits", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 21 December 2020; Accepted 28 July 2021; Published 02 September 2021. \n\nThis work was supported by a grant to M.M. from NINDS (5R01NS111477) and an award to M.M. from the Tianqiao and Chrissy Chen Institute for Neuroscience. Y.L.N. was supported by the Taipei Veterans General Hospital \u2013 National Yang-Ming University Physician Scientists Cultivation Program, No. 103-Y-A-003. \n\nData availability: All data relevant to the reported results are available in a public repository: https://github.com/markusmeister/Electrode-Pooling-Data-and-Code. An archived version is available from CaltechDATA: https://doi.org/10.22002/D1.2032. \n\nCode availability: All code used to obtain the reported results are available in a public repository: https://github.com/markusmeister/Electrode-Pooling-Data-and-Code. An archived version is available from CaltechDATA: https://doi.org/10.22002/D1.2032. \n\nThese authors contributed equally: Kyu Hyun Lee, Yu-Li Ni. \n\nAuthor Contributions: K.H.L., Y.L.N., and M.M. conceived of the study. K.H.L. and Y.L.N. did experiments and simulations. K.H.L., Y.L.N., and M.M. analyzed the resulting data. J.C., B.K., J.P., M.P., and T.D.H. wrote software for acquisition and analysis, and advised on the use of Neuropixels. K.H.L., Y.L.N., and M.M. drafted the article. All authors edited the manuscript. \n\nThe authors declare no competing interests. \n\nPeer review information: Nature Communications thanks Srinjoy Mitra and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-021-25443-4.pdf
Submitted - 851691v2.full.pdf
Supplemental Material - 41467_2021_25443_MOESM1_ESM.pdf
Supplemental Material - 41467_2021_25443_MOESM2_ESM.pdf
", "abstract": "State-of-the-art silicon probes for electrical recording from neurons have thousands of recording sites. However, due to volume limitations there are typically many fewer wires carrying signals off the probe, which restricts the number of channels that can be recorded simultaneously. To overcome this fundamental constraint, we propose a method called electrode pooling that uses a single wire to serve many recording sites through a set of controllable switches. Here we present the framework behind this method and an experimental strategy to support it. We then demonstrate its feasibility by implementing electrode pooling on the Neuropixels 1.0 electrode array and characterizing its effect on signal and noise. Finally we use simulations to explore the conditions under which electrode pooling saves wires without compromising the content of the recordings. We make recommendations on the design of future devices to take advantage of this strategy.", "date": "2021-09-02", "date_type": "published", "publication": "Nature Communications", "volume": "12", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 5245", "id_number": "CaltechAUTHORS:20191126-145230904", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191126-145230904", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5R01NS111477" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "Taipei Veterans General Hospital / National Yang-Ming University", "grant_number": "103-Y-A-003" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-021-25443-4", "primary_object": { "basename": "41467_2021_25443_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/zwfrv-rbn84/files/41467_2021_25443_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41467_2021_25443_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/zwfrv-rbn84/files/41467_2021_25443_MOESM2_ESM.pdf" }, { "basename": "851691v2.full.pdf", "url": "https://authors.library.caltech.edu/records/zwfrv-rbn84/files/851691v2.full.pdf" }, { "basename": "s41467-021-25443-4.pdf", "url": "https://authors.library.caltech.edu/records/zwfrv-rbn84/files/s41467-021-25443-4.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Lee, Kyu Hyun; Ni, Yu-Li; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m2n5a-kd302", "eprint_id": 110961, "eprint_status": "archive", "datestamp": "2023-08-20 04:42:17", "lastmod": "2023-12-22 23:20:39", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bagherian-Dawna", "name": { "family": "Bagherian", "given": "Dawna" } }, { "id": "Gornet-James", "name": { "family": "Gornet", "given": "James" } }, { "id": "Bernstein-Jeremy-D", "name": { "family": "Bernstein", "given": "Jeremy" }, "orcid": "0000-0001-9110-7476" }, { "id": "Ni-Yu-Li", "name": { "family": "Ni", "given": "Yu-Li" }, "orcid": "0000-0003-1600-9854" }, { "id": "Yue-Yisong", "name": { "family": "Yue", "given": "Yisong" }, "orcid": "0000-0001-9127-1989" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Fine-Grained System Identification of Nonlinear Neural Circuits", "ispublished": "unpub", "full_text_status": "public", "keywords": "nonlinear system identification, neural networks, neuroscience", "note": "\u00a9 2021 Copyright held by the owner/author(s). This work is licensed under a Creative Commons Attribution International 4.0 License. \n\nThis material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1745301. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. This work was also funded by a cloud computing grant from Amazon Web Services in collaboration with the Information Science and Technology initiative at Caltech. This work was also supported by the Simons Collaboration on the Global Brain (grant 543015 to Markus Meister). Jeremy Bernstein was supported in part by an NVIDIA Fellowship and by NASA TRISH-RFA-BRASH 1901. Yu-Li\nNi was supported by Taipei Veterans General Hospital-National Yang-Ming University Excellent Physician Scientists Cultivation Program, No. 103-Y-A-003. The authors thank James Parkin for providing original illustrations of retinal neurons.\n\nPublished - 3447548.3467402.pdf
Accepted Version - 2106.05400.pdf
", "abstract": "We study the problem of sparse nonlinear model recovery of high dimensional compositional functions. Our study is motivated by emerging opportunities in neuroscience to recover fine-grained models of biological neural circuits using collected measurement data. Guided by available domain knowledge in neuroscience, we explore conditions under which one can recover the underlying biological circuit that generated the training data. Our results suggest insights of both theoretical and practical interests. Most notably, we find that a sign constraint on the weights is a necessary condition for system recovery, which we establish both theoretically with an identifiability guarantee and empirically on simulated biological circuits. We conclude with a case study on retinal ganglion cell circuits using data collected from mouse retina, showcasing the practical potential of this approach.", "date": "2021-08-14", "date_type": "published", "publisher": "Association for Computing Machinery", "place_of_pub": "New York, NY", "pagerange": "14-24", "id_number": "CaltechAUTHORS:20210920-171551019", "isbn": "978-1-4503-8332-5", "book_title": "Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery & Data Mining", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210920-171551019", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Amazon Web Services" }, { "agency": "Simons Foundation", "grant_number": "543015" }, { "agency": "NVIDIA Corporation" }, { "agency": "NASA", "grant_number": "TRISH-RFA-BRASH 1901" }, { "agency": "Taipei Veterans General Hospital / National Yang-Ming University", "grant_number": "103-Y-A-003" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1145/3447548.3467402", "primary_object": { "basename": "2106.05400.pdf", "url": "https://authors.library.caltech.edu/records/m2n5a-kd302/files/2106.05400.pdf" }, "related_objects": [ { "basename": "3447548.3467402.pdf", "url": "https://authors.library.caltech.edu/records/m2n5a-kd302/files/3447548.3467402.pdf" } ], "resource_type": "book_section", "pub_year": "2021", "author_list": "Bagherian, Dawna; Gornet, James; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/85fpv-smk36", "eprint_id": 107545, "eprint_status": "archive", "datestamp": "2023-08-20 04:05:39", "lastmod": "2023-12-22 23:39:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rosenberg-Matthew", "name": { "family": "Rosenberg", "given": "Matthew" } }, { "id": "Zhang-Tony", "name": { "family": "Zhang", "given": "Tony" }, "orcid": "0000-0002-5198-499X" }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Mice in a labyrinth show rapid learning, sudden insight, and efficient exploration", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Rosenberg et al.\nThis article is distributed under\nthe terms of the Creative\nCommons Attribution License,\nwhich permits unrestricted use\nand redistribution provided that\nthe original author and source are\ncredited.\n\nReceived: 31 December 2020;\nAccepted: 30 June 2021;\nPublished: 01 July 2021.\n\nFunding: \nThis work was supported by the Simons Collaboration on the Global Brain (grant 543015 to MM and 543025 to PP), by NSF award 1564330 to PP, and by a gift from Google to PP.\n\nThe funders had no role in study design, data collection and interpretation, or the\ndecision to submit the work for publication.\n\nAuthor contributions:\nMatthew Rosenberg, Tony Zhang, Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - review and editing; Pietro Perona, Conceptualization, Software, Formal analysis, Supervision, Funding acquisition, Validation, Visualization, Methodology, Project administration, Writing - review and editing; Markus Meister, Conceptualization, Software, Formal analysis, Supervision, Funding acquisition, Validation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing.\n\nCompeting interests:\nMarkus Meister: Reviewing editor, eLife. The other authors declare that no competing interests\nexist.\n\nEthics:\nAnimal experimentation: This study was performed in strict accordance with the recommendations\nin the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of\nthe animals were handled according to animal protocol 1656 approved by the institutional animal\ncare and use committee (IACUC) at Caltech.\n\nData Availability:\nThe behavioral data and code that produced the figures are available in a public Github repository cited in the article https://github.com/markusmeister/Rosenberg-2021-Repository (copy archived at https://archive.softwareheritage.org/swh:1:rev:224141473e53d6e8963a77fbe625f570b0903ef1). We also prepared a permanent institutional repository at https://data.caltech.edu/badge/latestdoi/329740227.\n\nPublished - elife-66175-v2.pdf
Submitted - 2021.01.14.426746v1.full.pdf
Supplemental Material - elife-66175-transrepform-v2.pdf
", "abstract": "Animals learn certain complex tasks remarkably fast, sometimes after a single experience. What behavioral algorithms support this efficiency? Many contemporary studies based on two-alternative-forced-choice (2AFC) tasks observe only slow or incomplete learning. As an alternative, we study the unconstrained behavior of mice in a complex labyrinth and measure the dynamics of learning and the behaviors that enable it. A mouse in the labyrinth makes ~2000 navigation decisions per hour. The animal explores the maze, quickly discovers the location of a reward, and executes correct 10-bit choices after only 10 reward experiences \u2014 a learning rate 1000-fold higher than in 2AFC experiments. Many mice improve discontinuously from one minute to the next, suggesting moments of sudden insight about the structure of the labyrinth. The underlying search algorithm does not require a global memory of places visited and is largely explained by purely local turning rules.", "date": "2021-07-01", "date_type": "published", "publication": "eLife", "volume": "10", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e66175", "id_number": "CaltechAUTHORS:20210119-130811113", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210119-130811113", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "543015" }, { "agency": "Simons Foundation", "grant_number": "543025" }, { "agency": "NSF", "grant_number": "IIS-1564330" }, { "agency": "Google" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/eLife.66175", "pmcid": "PMC8294850", "primary_object": { "basename": "elife-66175-v2.pdf", "url": "https://authors.library.caltech.edu/records/85fpv-smk36/files/elife-66175-v2.pdf" }, "related_objects": [ { "basename": "2021.01.14.426746v1.full.pdf", "url": "https://authors.library.caltech.edu/records/85fpv-smk36/files/2021.01.14.426746v1.full.pdf" }, { "basename": "elife-66175-transrepform-v2.pdf", "url": "https://authors.library.caltech.edu/records/85fpv-smk36/files/elife-66175-transrepform-v2.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Rosenberg, Matthew; Zhang, Tony; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dkw5a-pk181", "eprint_id": 108202, "eprint_status": "archive", "datestamp": "2023-08-20 03:55:45", "lastmod": "2023-12-22 23:20:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Yang", "name": { "family": "Liu", "given": "Yang" }, "orcid": "0000-0002-8155-9134" }, { "id": "Bernstein-Jeremy-D", "name": { "family": "Bernstein", "given": "Jeremy" }, "orcid": "0000-0001-9110-7476" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Yue-Yisong", "name": { "family": "Yue", "given": "Yisong" }, "orcid": "0000-0001-9127-1989" } ] }, "title": "Learning by Turning: Neural Architecture Aware Optimisation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 by the authors.\n\nPublished - liu21c.pdf
Submitted - 2102.07227.pdf
", "abstract": "Descent methods for deep networks are notoriously capricious: they require careful tuning of step size, momentum and weight decay, and which method will work best on a new benchmark is a priori unclear. To address this problem, this paper conducts a combined study of neural architecture and optimisation, leading to a new optimiser called Nero: the neuronal rotator. Nero trains reliably without momentum or weight decay, works in situations where Adam and SGD fail, and requires little to no learning rate tuning. Also, Nero's memory footprint is square root that of Adam or LAMB. Nero combines two ideas: (1) projected gradient descent over the space of balanced networks; (2) neuron-specific updates, where the step size sets the angle through which each neuron's hyperplane turns. The paper concludes by discussing how this geometric connection between architecture and optimisation may impact theories of generalisation in deep learning.", "date": "2021-07", "date_type": "published", "publication": "Proceedings of Machine Learning Research", "volume": "139", "publisher": "ML Research Press", "pagerange": "6748-6758", "id_number": "CaltechAUTHORS:20210225-132711583", "issn": "2640-3498", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210225-132711583", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.48550/arXiv.2102.07227", "primary_object": { "basename": "2102.07227.pdf", "url": "https://authors.library.caltech.edu/records/dkw5a-pk181/files/2102.07227.pdf" }, "related_objects": [ { "basename": "liu21c.pdf", "url": "https://authors.library.caltech.edu/records/dkw5a-pk181/files/liu21c.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Liu, Yang; Bernstein, Jeremy; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/55fz4-f7f55", "eprint_id": 107327, "eprint_status": "archive", "datestamp": "2023-08-19 23:47:26", "lastmod": "2023-12-22 23:20:41", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qiao-Mu", "name": { "family": "Qiao", "given": "Mu" }, "orcid": "0000-0001-7309-4237" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Factorized linear discriminant analysis and its application in computational biology", "ispublished": "unpub", "full_text_status": "public", "note": "Submitted - 2010.02171.pdf
", "abstract": "A fundamental problem in computational biology is to find a suitable representation of the high-dimensional gene expression data that is consistent with the structural and functional properties of cell types, collectively called their phenotypes. This representation is often sought from a linear transformation of the original data, for the reasons of model interpretability and computational simplicity. Here we propose a novel method of linear dimensionality reduction to address this problem. This method, which we call factorized linear discriminant analysis (FLDA), seeks a linear transformation of gene expressions that varies highly with only one phenotypic feature and minimally with others. We further leverage our approach with a sparsity-based regularization algorithm, which selects a few genes important to a specific phenotypic feature or feature combination. We illustrated this approach by applying it to a single-cell transcriptome dataset of Drosophila T4/T5 neurons. A representation from FLDA captured structures in the data aligned with phenotypic features and revealed critical genes for each phenotype.", "date": "2021-01-06", "date_type": "published", "publisher": "arXiv", "id_number": "CaltechAUTHORS:20210105-133427535", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210105-133427535", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.48550/arXiv.2010.02171", "primary_object": { "basename": "2010.02171.pdf", "url": "https://authors.library.caltech.edu/records/55fz4-f7f55/files/2010.02171.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Qiao, Mu and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/38ne8-4rx67", "eprint_id": 106488, "eprint_status": "archive", "datestamp": "2023-08-20 00:35:24", "lastmod": "2023-12-22 23:20:35", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bernstein-J-D", "name": { "family": "Bernstein", "given": "Jeremy" }, "orcid": "0000-0001-9110-7476" }, { "id": "Zhao-Jiawei", "name": { "family": "Zhao", "given": "Jiawei" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Liu-Ming-Yu", "name": { "family": "Liu", "given": "Ming-Yu" }, "orcid": "0000-0002-2951-2398" }, { "id": "Anandkumar-A", "name": { "family": "Anandkumar", "given": "Anima" }, "orcid": "0000-0002-6974-6797" }, { "id": "Yue-Yisong", "name": { "family": "Yue", "given": "Yisong" }, "orcid": "0000-0001-9127-1989" } ] }, "title": "Learning compositional functions via multiplicative weight updates", "ispublished": "unpub", "full_text_status": "public", "note": "The authors would like to thank the anonymous reviewers for their helpful comments. \n\nJB was supported by an NVIDIA fellowship. The work was partly supported by funding from NASA.\n\nPublished - NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Paper.pdf
Supplemental Material - NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Supplemental.pdf
", "abstract": "Compositionality is a basic structural feature of both biological and artificial neural networks. Learning compositional functions via gradient descent incurs well known problems like vanishing and exploding gradients, making careful learning rate tuning essential for real-world applications. This paper proves that multiplicative weight updates satisfy a descent lemma tailored to compositional functions. Based on this lemma, we derive Madam\u2014a multiplicative version of the Adam optimiser\u2014and show that it can train state of the art neural network architectures without learning rate tuning. We further show that Madam is easily adapted to train natively compressed neural networks by representing their weights in a logarithmic number system. We conclude by drawing connections between multiplicative weight updates and recent findings about synapses in biology.", "date": "2020-12", "date_type": "published", "publisher": "Advances in Neural Information Processing Systems", "id_number": "CaltechAUTHORS:20201106-120208748", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201106-120208748", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NVIDIA Corporation" }, { "agency": "NASA" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "contributors": { "items": [ { "id": "Larochelle-H", "name": { "family": "Larochelle", "given": "H." } }, { "id": "Ranzato-M", "name": { "family": "Ranzato", "given": "M." } }, { "id": "Hadsell-R", "name": { "family": "Hadsell", "given": "R." } }, { "id": "Balcan-M-F", "name": { "family": "Balcan", "given": "M. F." } }, { "id": "Lin-H", "name": { "family": "Lin", "given": "H." } } ] }, "doi": "10.48550/arXiv.2006.14560", "primary_object": { "basename": "NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Paper.pdf", "url": "https://authors.library.caltech.edu/records/38ne8-4rx67/files/NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Paper.pdf" }, "related_objects": [ { "basename": "NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Supplemental.pdf", "url": "https://authors.library.caltech.edu/records/38ne8-4rx67/files/NeurIPS-2020-learning-compositional-functions-via-multiplicative-weight-updates-Supplemental.pdf" } ], "resource_type": "book_section", "pub_year": "2020", "author_list": "Bernstein, Jeremy; Zhao, Jiawei; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pkq4n-ytp93", "eprint_id": 99595, "eprint_status": "archive", "datestamp": "2023-08-19 23:17:29", "lastmod": "2023-12-22 23:20:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Ya-tang", "name": { "family": "Li", "given": "Ya-tang" }, "orcid": "0000-0003-2763-1534" }, { "id": "Turan-Zeynep", "name": { "family": "Turan", "given": "Zeynep" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Functional Architecture of Motion Direction in the Mouse Superior Colliculus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Elsevier Inc. \n\nReceived 9 December 2019, Revised 12 April 2020, Accepted 5 June 2020, Available online 10 July 2020. \n\nM.M. was supported by grants from NIH (R01 NS111477) and from the Simons Foundation (543015SPI). Y.-t.L was supported by a grant from the NEI (K99EY028640) and a Helen Hay Whitney Postdoctoral Fellowship. \n\nAuthor Contributions: Y.-t.L designed the study, performed all experiments, interpreted results, and wrote the manuscript. Z.T. provided partial-cortex mutant mice and validated their brain anatomy. M.M. helped design the study, interpret results, and write the manuscript. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1708240.pdf
Submitted - 825711.full.pdf
Supplemental Material - 1-s2.0-S0960982220308393-mmc1.pdf
", "abstract": "Motion vision is important in guiding animal behavior. Both the retina and the visual cortex process object motion in largely unbiased fashion: all directions are represented at all locations in the visual field. We investigate motion processing in the superior colliculus of the awake mouse by optically recording neural responses across both hemispheres. Within the retinotopic map, one finds large regions of \u223c500 \u03bcm size where neurons prefer the same direction of motion. This preference is maintained in depth to \u223c350 \u03bcm. The scale of these patches, \u223c30 degrees of visual angle, is much coarser than the animal's visual resolution (\u223c2 degrees). A global map of motion direction shows approximate symmetry between the left and right hemispheres and a net bias for upward-nasal motion in the upper visual field.", "date": "2020-09-07", "date_type": "published", "publication": "Current Biology", "volume": "30", "number": "17", "publisher": "Cell Press", "pagerange": "3304-3315", "id_number": "CaltechAUTHORS:20191031-141639740", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191031-141639740", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS111477" }, { "agency": "Simons Foundation", "grant_number": "543015SPI" }, { "agency": "NIH", "grant_number": "K99EY028640" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cub.2020.06.023", "pmcid": "PMC8221388", "primary_object": { "basename": "1-s2.0-S0960982220308393-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/pkq4n-ytp93/files/1-s2.0-S0960982220308393-mmc1.pdf" }, "related_objects": [ { "basename": "825711.full.pdf", "url": "https://authors.library.caltech.edu/records/pkq4n-ytp93/files/825711.full.pdf" }, { "basename": "nihms-1708240.pdf", "url": "https://authors.library.caltech.edu/records/pkq4n-ytp93/files/nihms-1708240.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Li, Ya-tang; Turan, Zeynep; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t3df1-gzb61", "eprint_id": 103461, "eprint_status": "archive", "datestamp": "2023-08-19 18:49:00", "lastmod": "2023-12-13 17:01:09", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Yang", "name": { "family": "Liu", "given": "Yang" } }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "PanDA: Panoptic Data Augmentation", "ispublished": "unpub", "full_text_status": "public", "keywords": "Data Augmentation, Panoptic Segmentation, Scene Understanding, Image Synthesis", "note": "Submitted - 1911.12317.pdf
", "abstract": "The recently proposed panoptic segmentation task presents a significant challenge of image understanding with computer vision by unifying semantic segmentation and instance segmentation tasks. In this paper we present an efficient and novel panoptic data augmentation (PanDA) method which operates exclusively in pixel space, requires no additional data or training, and is computationally cheap to implement. By retraining original state-of-the-art models on PanDA augmented datasets generated with a single frozen set of parameters, we show robust performance gains in panoptic segmentation, instance segmentation, as well as detection across models, backbones, dataset domains, and scales. Finally, the effectiveness of unrealistic-looking training images synthesized by PanDA suggest that one should rethink the need for image realism for efficient data augmentation.", "date": "2020-05-26", "date_type": "published", "publisher": "arXiv", "id_number": "CaltechAUTHORS:20200526-134149667", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200526-134149667", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.48550/arXiv.1911.12317", "primary_object": { "basename": "1911.12317.pdf", "url": "https://authors.library.caltech.edu/records/t3df1-gzb61/files/1911.12317.pdf" }, "resource_type": "monograph", "pub_year": "2020", "author_list": "Liu, Yang; Perona, Pietro; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wtr1r-4ds33", "eprint_id": 102664, "eprint_status": "archive", "datestamp": "2023-08-19 20:56:55", "lastmod": "2023-12-22 23:20:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Kyu-Hyung", "name": { "family": "Lee", "given": "Kyu Hyung" } }, { "id": "Tran-Alvita", "name": { "family": "Tran", "given": "Alvita" } }, { "id": "Turan-Z", "name": { "family": "Turan", "given": "Zeynep" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "The sifting of visual information in the superior colliculus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 Lee et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 30 July 2019; Accepted: 09 March 2020; Published: 14 April 2020. \n\nWe thank Sotiris Masmanidis (UCLA) for kindly providing us with silicon probes. The Pals1^(flox/flox) mouse strain was a gift from Seonhee Kim (Temple University) and Christopher A Walsh (Harvard Medical School). We also thank the members of Meister lab for valuable discussions and comments. \n\nThis work was supported by grants to MM from the Simons Foundation (543015SPI) and the NIH (R01NS111477) and a NSF Graduate Research Fellowship to AT. \n\nCompeting interests: Markus Meister: Reviewing editor, eLife. The other authors declare that no competing interests exist. \n\nAuthor contributions: Kyu Hyun Lee, Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Project administration; Alvita Tran, Data curation, Software, Formal analysis, Funding acquisition, Validation, Investigation, Visualization, Methodology; Zeynep Turan, Data curation, Validation, Investigation, Visualization, Methodology; Markus Meister, Conceptualization, Resources, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Project administration. \n\nEthics:\nAnimal experimentation: This study was performed according to approved institutional animal care and use committee (IACUC) protocols (#1656) of Caltech. All surgery was performed under isoflurane anesthesia and every effort was made to minimize suffering. \n\nData availability: The data used in the manuscript as well as the analysis codes have been made available on CaltechDATA, under the accession number 1401 (doi:10.22002/D1.1401).\n\nPublished - elife-50678-v2.pdf
Accepted Version - elife-50678-v1.pdf
Supplemental Material - elife-50678-supp-v1.zip
Supplemental Material - elife-50678-transrepform-v2.pdf
", "abstract": "Much of the early visual system is devoted to sifting the visual scene for the few bits of behaviorally relevant information. In the visual cortex of mammals, a hierarchical system of brain areas leads eventually to the selective encoding of important features, like faces and objects. Here, we report that a similar process occurs in the other major visual pathway, the superior colliculus. We investigate the visual response properties of collicular neurons in the awake mouse with large-scale electrophysiology. Compared to the superficial collicular layers, neuronal responses in the deeper layers become more selective for behaviorally relevant stimuli; more invariant to location of stimuli in the visual field; and more suppressed by repeated occurrence of a stimulus in the same location. The memory of familiar stimuli persists in complete absence of the visual cortex. Models of these neural computations lead to specific predictions for neural circuitry in the superior colliculus.", "date": "2020-04-14", "date_type": "published", "publication": "eLife", "volume": "9", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e50678", "id_number": "CaltechAUTHORS:20200420-134619006", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200420-134619006", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "543015SPI" }, { "agency": "NIH", "grant_number": "R01NS111477" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.50678", "primary_object": { "basename": "elife-50678-v2.pdf", "url": "https://authors.library.caltech.edu/records/wtr1r-4ds33/files/elife-50678-v2.pdf" }, "related_objects": [ { "basename": "elife-50678-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/wtr1r-4ds33/files/elife-50678-supp-v1.zip" }, { "basename": "elife-50678-transrepform-v2.pdf", "url": "https://authors.library.caltech.edu/records/wtr1r-4ds33/files/elife-50678-transrepform-v2.pdf" }, { "basename": "elife-50678-v1.pdf", "url": "https://authors.library.caltech.edu/records/wtr1r-4ds33/files/elife-50678-v1.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Lee, Kyu Hyung; Tran, Alvita; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/knyj1-fks47", "eprint_id": 103465, "eprint_status": "archive", "datestamp": "2023-08-19 20:22:52", "lastmod": "2023-12-22 23:20:37", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beery-S", "name": { "family": "Beery", "given": "Sara" }, "orcid": "0000-0002-2544-1844" }, { "id": "Liu-Yang", "name": { "family": "Liu", "given": "Yang" } }, { "id": "Morris-Dan", "name": { "family": "Morris", "given": "Dan" } }, { "id": "Piavis-J", "name": { "family": "Piavis", "given": "Jim" } }, { "id": "Kapoor-Ashish", "name": { "family": "Kapoor", "given": "Ashish" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Joshi-Neel", "name": { "family": "Joshi", "given": "Neel" } }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" } ] }, "title": "Synthetic Examples Improve Generalization for Rare Classes", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2020 IEEE. \n\nWe would like to thank the USGS and NPS for providing data. This work was supported by NSFG RFP Grant No. 1745301, the views are those of the authors and do not necessarily reflect the views of the NSF. Compute provided by Microsoft AI for Earth and AWS.\n\nSubmitted - 1904.05916.pdf
", "abstract": "The ability to detect and classify rare occurrences in images has important applications - for example, counting rare and endangered species when studying biodiversity, or detecting infrequent traffic scenarios that pose a danger to self-driving cars. Few-shot learning is an open problem: current computer vision systems struggle to categorize objects they have seen only rarely during training, and collecting a sufficient number of training examples of rare events is often challenging and expensive, and sometimes outright impossible. We explore in depth an approach to this problem: complementing the few available training images with ad-hoc simulated data.Our testbed is animal species classification, which has a real-world long-tailed distribution. We present two natural world simulators, and analyze the effect of different axes of variation in simulation, such as pose, lighting, model, and simulation method, and we prescribe best practices for efficiently incorporating simulated data for real-world performance gain. Our experiments reveal that synthetic data can considerably reduce error rates for classes that are rare, that as the amount of simulated data is increased, accuracy on the target class improves, and that high variation of simulated data provides maximum performance gain.", "date": "2020-03", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "852-862", "id_number": "CaltechAUTHORS:20200526-140034764", "isbn": "978-1-7281-6553-0", "book_title": "2020 IEEE Winter Conference on Applications of Computer Vision (WACV)", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200526-140034764", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" }, { "agency": "Microsoft AI for Earth" }, { "agency": "Amazon Web Services" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1109/WACV45572.2020.9093570", "primary_object": { "basename": "1904.05916.pdf", "url": "https://authors.library.caltech.edu/records/knyj1-fks47/files/1904.05916.pdf" }, "resource_type": "book_section", "pub_year": "2020", "author_list": "Beery, Sara; Liu, Yang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/k0ce8-q3067", "eprint_id": 99887, "eprint_status": "archive", "datestamp": "2023-08-19 18:43:59", "lastmod": "2023-10-20 22:09:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gjorgjieva-J", "name": { "family": "Gjorgjieva", "given": "Julijana" }, "orcid": "0000-0001-7118-4079" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } } ] }, "title": "Functional diversity among sensory neurons from efficient coding principles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Gjorgjieva et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: July 24, 2018; Accepted: October 10, 2019; Published: November 14, 2019. \n\nData Availability Statement: All relevant data are within the paper and its Supporting Information files. \n\nAll authors were supported by the NIH, the Gatsby Charitable Foundation and the Swartz Foundation. JG was supported by the Max Planck Society and a Burroughs-Wellcome Career Award at the Scientific Interface. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe thanks Shuai Shao for careful reading of the analytical calculations. \n\nAuthor Contributions: Conceptualization: Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky. Formal analysis: Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky. Funding acquisition: Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky. Investigation: Julijana Gjorgjieva. Methodology: Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky. Software: Julijana Gjorgjieva. Supervision: Markus Meister, Haim Sompolinsky. Visualization: Julijana Gjorgjieva. Writing \u2013 original draft: Julijana Gjorgjieva. Writing \u2013 review & editing: Julijana Gjorgjieva, Markus Meister, Haim Sompolinsky.\n\nPublished - journal.pcbi.1007476.pdf
Supplemental Material - journal.pcbi.1007476.s001.eps
Supplemental Material - journal.pcbi.1007476.s002.eps
Supplemental Material - journal.pcbi.1007476.s003.pdf
Supplemental Material - journal.pcbi.1007476.s004.pdf
Supplemental Material - journal.pcbi.1007476.s005.pdf
Supplemental Material - journal.pcbi.1007476.s006.pdf
Supplemental Material - journal.pcbi.1007476.s007.pdf
", "abstract": "In many sensory systems the neural signal is coded by the coordinated response of heterogeneous populations of neurons. What computational benefit does this diversity confer on information processing? We derive an efficient coding framework assuming that neurons have evolved to communicate signals optimally given natural stimulus statistics and metabolic constraints. Incorporating nonlinearities and realistic noise, we study optimal population coding of the same sensory variable using two measures: maximizing the mutual information between stimuli and responses, and minimizing the error incurred by the optimal linear decoder of responses. Our theory is applied to a commonly observed splitting of sensory neurons into ON and OFF that signal stimulus increases or decreases, and to populations of monotonically increasing responses of the same type, ON. Depending on the optimality measure, we make different predictions about how to optimally split a population into ON and OFF, and how to allocate the firing thresholds of individual neurons given realistic stimulus distributions and noise, which accord with certain biases observed experimentally.", "date": "2019-11-14", "date_type": "published", "publication": "PLOS Computational Biology", "volume": "15", "number": "11", "publisher": "Public Library of Science", "pagerange": "Art. No. e1007476", "id_number": "CaltechAUTHORS:20191118-080725855", "issn": "1553-7358", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191118-080725855", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Gatsby Charitable Foundation" }, { "agency": "Swartz Foundation" }, { "agency": "Max-Planck-Society" }, { "agency": "Burroughs-Wellcome Fund" } ] }, "doi": "10.1371/journal.pcbi.1007476", "pmcid": "PMC6890262", "primary_object": { "basename": "journal.pcbi.1007476.s002.eps", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s002.eps" }, "related_objects": [ { "basename": "journal.pcbi.1007476.s003.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s003.pdf" }, { "basename": "journal.pcbi.1007476.s004.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s004.pdf" }, { "basename": "journal.pcbi.1007476.s005.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s005.pdf" }, { "basename": "journal.pcbi.1007476.s006.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s006.pdf" }, { "basename": "journal.pcbi.1007476.s007.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s007.pdf" }, { "basename": "journal.pcbi.1007476.pdf", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.pdf" }, { "basename": "journal.pcbi.1007476.s001.eps", "url": "https://authors.library.caltech.edu/records/k0ce8-q3067/files/journal.pcbi.1007476.s001.eps" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Gjorgjieva, Julijana; Meister, Markus; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2ftqt-zd927", "eprint_id": 90520, "eprint_status": "archive", "datestamp": "2023-08-19 12:50:09", "lastmod": "2023-10-23 15:45:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Yang", "name": { "family": "Liu", "given": "Yang" }, "orcid": "0000-0002-8155-9134" }, { "id": "Stiles-N-R-B", "name": { "family": "Stiles", "given": "Noelle R. B." }, "orcid": "0000-0002-7352-5815" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Augmented Reality Powers a Cognitive Assistant for the Blind", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Liu et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 24 April 2018; Accepted: 27 October 2018; Published: 27 November 2018. \n\nData and materials availability: Data and code that produced the figures are available on the Dryad Digital Repository. \n\nData availability: All data generated or analysed during this study are included in the manuscript and supporting files. Source data files for all figures have been deposited in Dryad. Additional code is published on a Github repository (https://github.com/meisterlabcaltech/CARA_Public; copy archived at https://github.com/elifesciences-publications/CARA_Public). \n\nSupported by grant 103212 from the Shurl and Kay Curci Foundation. We thank Ralph Adolphs, David Anderson, and Shin Shimojo for comments on the manuscript, and Kristina Dylla for posing for Figure 1A and field testing all of the tasks. \n\nAuthor contributions: Yang Liu, Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing\u2014review and editing; Noelle RB Stiles, Resources, Validation, Investigation, Methodology; Markus Meister, Conceptualization, Supervision, Funding acquisition, Writing\u2014original draft, Project administration, Writing\u2014review and editing. \n\nEthics: Human subjects: All procedures involving human subjects were reviewed and approved by the Institutional Review Board at Caltech, Human Subjects Protocol 16-0663. All subjects gave their informed consent to the experiments, and where applicable to publication of videos that accompany this article.\n\nPublished - elife-37841-v1.pdf
Submitted - 321265.full.pdf
Supplemental Material - elife-37841-transrepform-v1.pdf
", "abstract": "To restore vision for the blind, several prosthetic approaches have been explored that convey raw images to the brain. So far, these schemes all suffer from a lack of bandwidth. An alternate approach would restore vision at the cognitive level, bypassing the need to convey sensory data. A wearable computer captures video and other data, extracts important scene knowledge, and conveys that to the user in compact form. Here, we implement an intuitive user interface for such a device using augmented reality: each object in the environment has a voice and communicates with the user on command. With minimal training, this system supports many aspects of visual cognition: obstacle avoidance, scene understanding, formation and recall of spatial memories, navigation. Blind subjects can traverse an unfamiliar multi-story building on their first attempt. To spur further development in this domain, we developed an open-source environment for standardized benchmarking of visual assistive devices.", "date": "2018-11-28", "date_type": "published", "publication": "eLife", "volume": "7", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e37841", "id_number": "CaltechAUTHORS:20181030-140944700", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-140944700", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Shurl and Kay Curci Foundation", "grant_number": "103212" } ] }, "doi": "10.7554/eLife.37841.001", "pmcid": "PMC6257813", "primary_object": { "basename": "elife-37841-transrepform-v1.pdf", "url": "https://authors.library.caltech.edu/records/2ftqt-zd927/files/elife-37841-transrepform-v1.pdf" }, "related_objects": [ { "basename": "elife-37841-v1.pdf", "url": "https://authors.library.caltech.edu/records/2ftqt-zd927/files/elife-37841-v1.pdf" }, { "basename": "321265.full.pdf", "url": "https://authors.library.caltech.edu/records/2ftqt-zd927/files/321265.full.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Liu, Yang; Stiles, Noelle R. B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0e7hj-w0v41", "eprint_id": 91278, "eprint_status": "archive", "datestamp": "2023-08-19 12:45:51", "lastmod": "2023-10-19 22:21:46", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qiao-Mu", "name": { "family": "Qiao", "given": "Mu" }, "orcid": "0000-0001-7309-4237" }, { "id": "Zhang-Tony", "name": { "family": "Zhang", "given": "Tony" } }, { "id": "Segalin-C", "name": { "family": "Segalin", "given": "Cristina" }, "orcid": "0000-0001-7219-7074" }, { "id": "Sam-Sarah", "name": { "family": "Sam", "given": "Sarah" } }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Mouse Academy: high-throughput automated training and trial-by-trial behavioral analysis during learning", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. \n\nWe thank Joshua Sanders for technical assistance in incorporating Bpod into our system. We thank Ann Kennedy for insightful comments and suggestions on analysis of the behavioral trajectories. We thank Oisin Mac Adoha and Yuxin Chen for helpful comments and discussions. This work was supported by a grant from the Simons Foundation (SCGB 543015, M.M. and P.P.) and a postdoctoral fellowship from the Swartz Foundation (M.Q.). \n\nAUTHOR CONTRIBUTIONS: M.Q. and M.M. designed the study; M.Q. and S.S. constructed the hardware setup and wrote the controlling software; M.Q. performed experiments and collected data for analysis; M.Q. developed the iterative generalized linear model with input from P.P. and M.M; C.S. developed the automated tracking software; T.Z. implemented animal tracking and behavioral trajectory analysis with input from M.Q., P.P. and M.M; M.Q. and M.M. wrote the manuscript with comments from all authors. \n\nDATA AVAILABILITY: The datasets analyzed during the current study are available in https://drive.google.com/open?id=1gkPbqGYKPGs7Rx1WNmubQW0dKyYE5YVR \n\nThe authors declare no competing financial interests.\n\nSubmitted - 467878.full.pdf
", "abstract": "Progress in understanding how individual animals learn will require high-throughput standardized methods for behavioral training but also advances in the analysis of the resulting behavioral data. In the course of training with multiple trials, an animal may change its behavior abruptly, and capturing such events calls for a trial-by-trial analysis of the animal's strategy. To address this challenge, we developed an integrated platform for automated animal training and analysis of behavioral data. A low-cost and space-efficient apparatus serves to train entire cohorts of mice on a decision-making task under identical conditions. A generalized linear model (GLM) analyzes each animal's performance at single-trial resolution. This model infers the momentary decision-making strategy and can predict the animal's choice on each trial with an accuracy of ~80%. We also introduce automated software to assess the animal's detailed trajectories and body poses within the apparatus. Unsupervised analysis of these features revealed unusual trajectories that represent hesitation in the response. This integrated hardware/software platform promises to accelerate the understanding of animal learning.", "date": "2018-11-28", "date_type": "published", "id_number": "CaltechAUTHORS:20181128-093526738", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526738", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "SCGB 543015" }, { "agency": "Swartz Foundation" } ] }, "doi": "10.1101/467878", "primary_object": { "basename": "467878.full.pdf", "url": "https://authors.library.caltech.edu/records/0e7hj-w0v41/files/467878.full.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Qiao, Mu; Zhang, Tony; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/egasq-d9c23", "eprint_id": 90498, "eprint_status": "archive", "datestamp": "2023-08-19 02:46:32", "lastmod": "2023-10-18 23:29:24", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gjorgjieva-J", "name": { "family": "Gjorgjieva", "given": "Julijana" }, "orcid": "0000-0001-7118-4079" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } } ] }, "title": "Optimal Sensory Coding By Populations Of ON And OFF Neurons", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nJG was supported by the Max Planck Society and a Burroughs-Wellcome Career Award at the Scientific Interface. All authors were supported by the NIH, the Gatsby Charitable Foundation and the Swartz Foundation.\n\nSubmitted - 131946.full.pdf
", "abstract": "In many sensory systems the neural signal is coded by multiple parallel pathways, suggesting an evolutionary fitness benefit of general nature. A common pathway splitting is that into ON and OFF cells, responding to stimulus increments and decrements, respectively. According to efficient coding theory, sensory neurons have evolved to an optimal configuration for maximizing information transfer given the structure of natural stimuli and circuit constraints. Using the efficient coding framework, we describe two aspects of neural coding: how to optimally split a population into ON and OFF pathways, and how to allocate the firing thresholds of individual neurons given realistic noise levels, stimulus distributions and optimality measures. We find that populations of ON and OFF neurons convey equal information about the stimulus regardless of the ON/OFF mixture, once the thresholds are chosen optimally, independent of stimulus statistics and noise. However, an equal ON/OFF mixture is the most efficient as it uses the fewest spikes to convey this information. The optimal thresholds and coding efficiency, however, depend on noise and stimulus statistics if information is decoded by an optimal linear readout. With non-negligible noise, mixed ON/OFF populations reap significant advantages compared to a homogeneous population. The best coding performance is achieved by a unique mixture of ON/OFF neurons tuned to stimulus asymmetries and noise. We provide a theory for how different cell types work together to encode the full stimulus range using a diversity of response thresholds. The optimal ON/OFF mixtures derived from the theory accord with certain biases observed experimentally.", "date": "2018-10-30", "date_type": "published", "id_number": "CaltechAUTHORS:20181030-105013410", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-105013410", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Max Planck Society" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH" }, { "agency": "Gatsby Charitable Foundation" }, { "agency": "Swartz Foundation" } ] }, "doi": "10.1101/131946", "primary_object": { "basename": "131946.full.pdf", "url": "https://authors.library.caltech.edu/records/egasq-d9c23/files/131946.full.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Gjorgjieva, Julijana; Meister, Markus; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0ma3g-zry11", "eprint_id": 79848, "eprint_status": "archive", "datestamp": "2023-08-19 04:15:08", "lastmod": "2023-10-26 17:22:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barnes-S", "name": { "family": "Barnes", "given": "Steven" } }, { "id": "Krieger-B", "name": { "family": "Krieger", "given": "Brenna" } }, { "id": "Qiao-Mu", "name": { "family": "Qiao", "given": "Mu" }, "orcid": "0000-0001-7309-4237" }, { "id": "Rousso-D-L", "name": { "family": "Rousso", "given": "David L." } }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Four alpha ganglion cell types in mouse retina: Function, structure, and molecular signatures", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Krieger et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nEditor: Steven Barnes, Dalhousie University, CANADA \n\nReceived: November 11, 2016. Accepted: June 11, 2017. Published: July 28, 2017. \n\nThanks to Max Joesch for contributing neural recording data. \n\nFunding: Supported by NIH grants 1U01NS090562 to M.M., NS029169 and EY022073 to J.R.S, and EY025119 to D.L.R. \n\nAuthor Contributions\nConceptualization: BK MQ JS MM.\nData curation: BK MQ DR MM.\nFormal analysis: BK MQ DR JS MM.\nFunding acquisition: DR JS MM.\nInvestigation: BK MQ DR.\nMethodology: BK DR JS MM.\nProject administration: JS MM.\nSoftware: BK DR MM.\nSupervision: JS MM.\nValidation: JS MM.\nVisualization: BK MM.\nWriting \u2013 original draft: BK MM.\nWriting \u2013 review & editing: BK MQ DR JS MM.\n\nPublished - journal.pone.0180091.pdf
Supplemental Material - pone.0180091.s001.tiff
", "abstract": "The retina communicates with the brain using \u226530 parallel channels, each carried by axons of distinct types of retinal ganglion cells. In every mammalian retina one finds so-called \"alpha\" ganglion cells (\u03b1RGCs), identified by their large cell bodies, stout axons, wide and mono-stratified dendritic fields, and high levels of neurofilament protein. In the mouse, three \u03b1RGC types have been described based on responses to light steps: On-sustained, Off-sustained, and Off-transient. Here we employed a transgenic mouse line that labels \u03b1RGCs in the live retina, allowing systematic targeted recordings. We characterize the three known types and identify a fourth, with On-transient responses. All four \u03b1RGC types share basic aspects of visual signaling, including a large receptive field center, a weak antagonistic surround, and absence of any direction selectivity. They also share a distinctive waveform of the action potential, faster than that of other RGC types. Morphologically, they differ in the level of dendritic stratification within the IPL, which accounts for their response properties. Molecularly, each type has a distinct signature. A comparison across mammals suggests a common theme, in which four large-bodied ganglion cell types split the visual signal into four channels arranged symmetrically with respect to polarity and kinetics.", "date": "2017-07-28", "date_type": "published", "publication": "PLOS ONE", "volume": "12", "number": "7", "publisher": "Public Library of Science", "pagerange": "Art. No. e0180091", "id_number": "CaltechAUTHORS:20170807-132930354", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170807-132930354", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1U01NS090562" }, { "agency": "NIH", "grant_number": "NS029169" }, { "agency": "NIH", "grant_number": "EY022073" }, { "agency": "NIH", "grant_number": "EY025119" } ] }, "doi": "10.1371/journal.pone.0180091", "pmcid": "PMC5533432", "primary_object": { "basename": "journal.pone.0180091.pdf", "url": "https://authors.library.caltech.edu/records/0ma3g-zry11/files/journal.pone.0180091.pdf" }, "related_objects": [ { "basename": "pone.0180091.s001.tiff", "url": "https://authors.library.caltech.edu/records/0ma3g-zry11/files/pone.0180091.s001.tiff" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Barnes, Steven; Krieger, Brenna; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1g4b3-nw108", "eprint_id": 73526, "eprint_status": "archive", "datestamp": "2023-08-22 19:34:08", "lastmod": "2023-10-24 15:26:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Real-E", "name": { "family": "Real", "given": "Esteban" } }, { "id": "Asari-Hiroki", "name": { "family": "Asari", "given": "Hiroki" } }, { "id": "Gollisch-T", "name": { "family": "Gollisch", "given": "Tim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Neural Circuit Inference from Function to Structure", "ispublished": "pub", "full_text_status": "public", "keywords": "vision; retina; ganglion cells; bipolar cells; brain circuit; neurophysiology; neural code; computational neuroscience; machine learning; circuit model", "note": "\u00a9 2016 Elsevier Ltd.\n\nReceived 12 September 2016, Revised 17 November 2016, Accepted 17 November 2016, Available online 5 January 2017\nPublished: January 5, 2017.\n\nWe would like to thank Ofer Mazor, Haim Sompolinsky, Arjun Krishnaswami, Yoram Burak, Uri Rokni, Andreas Liu, Evan Feinberg, Joel Greenwood, Stan Cotreau, Aravinthan Samuel, and especially Edward Soucy for many useful discussions. This work was supported by Harvard's Mind/Brain/Behavior Initiative (E.R.), a Gosney postdoctoral fellowship at Caltech (H.A.), and grants from the NIH (7R01EY014737 and 1U01NS090562 to M.M.).\n\nAuthor Contributions:\nE.R. performed the extracellular array recordings constituting the main dataset. H.A. performed the simultaneous intracellular and extracellular recordings\nused to test the models. M.M., E.R., and T.G. designed the models; E.R. coded the models and ran the simulations; and E.R. and H.A. analyzed the results. E.R., H.A., and M.M. wrote the manuscript.\n\nSupplemental Material - mmc1.pdf
", "abstract": "Advances in technology are opening new windows on the structural connectivity and functional dynamics of brain circuits. Quantitative frameworks are needed that integrate these data from anatomy and physiology. Here, we present a modeling approach that creates such a link. The goal is to infer the structure of a neural circuit from sparse neural recordings, using partial knowledge of its anatomy as a regularizing constraint. We recorded visual responses from the output neurons of the retina, the ganglion cells. We then generated a systematic sequence of circuit models that represents retinal neurons and connections and fitted them to the experimental data. The optimal models faithfully recapitulated the ganglion cell outputs. More importantly, they made predictions about dynamics and connectivity among unobserved neurons internal to the circuit, and these were subsequently confirmed by experiment. This circuit inference framework promises to facilitate the integration and understanding of big data in neuroscience.", "date": "2017-01-23", "date_type": "published", "publication": "Current Biology", "volume": "27", "number": "2", "publisher": "Cell Press", "pagerange": "189-198", "id_number": "CaltechAUTHORS:20170117-132604622", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170117-132604622", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Harvard University" }, { "agency": "Caltech" }, { "agency": "NIH", "grant_number": "7R01EY014737" }, { "agency": "NIH", "grant_number": "1U01NS090562" } ] }, "doi": "10.1016/j.cub.2016.11.040", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/1g4b3-nw108/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Real, Esteban; Asari, Hiroki; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/msp84-d8463", "eprint_id": 69815, "eprint_status": "archive", "datestamp": "2023-08-20 13:25:49", "lastmod": "2023-10-20 20:39:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Physical limits to magnetogenetics", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016, Meister. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived April 25, 2016. Accepted August 15, 2016. Published August 16, 2016. \n\nThe author thanks Bill Bialek, Justin Bois, Stephen J Royle, and an anonymous contributor on PubPeer for helpful comments on an earlier version. \n\nNo external funding was received for this work. \n\nAuthor contributions: MM, Did everything, Conception and design, Analysis and interpretation of data, Drafting or revising the article. \n\nThe author declares that no competing interests exist.\n\nPublished - e17210-download.pdf
", "abstract": "This is an analysis of how magnetic fields affect biological molecules and cells. It was prompted by a series of prominent reports regarding magnetism in biological systems. The first claims to have identified a protein complex that acts like a compass needle to guide magnetic orientation in animals (Qin et al., 2016). Two other articles report magnetic control of membrane conductance by attaching ferritin to an ion channel protein and then tugging the ferritin or heating it with a magnetic field (Stanley et al., 2015; Wheeler et al., 2016). Here I argue that these claims conflict with basic laws of physics. The discrepancies are large: from 5 to 10 log units. If the reported phenomena do in fact occur, they must have causes entirely different from the ones proposed by the authors. The paramagnetic nature of protein complexes is found to seriously limit their utility for engineering magnetically sensitive cells.", "date": "2016-08-16", "date_type": "published", "publication": "eLife", "volume": "5", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. 17210", "id_number": "CaltechAUTHORS:20160822-141245894", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160822-141245894", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.7554/eLife.17210", "pmcid": "PMC5016093", "primary_object": { "basename": "e17210-download.pdf", "url": "https://authors.library.caltech.edu/records/msp84-d8463/files/e17210-download.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7pc1r-9ng53", "eprint_id": 69022, "eprint_status": "archive", "datestamp": "2023-08-20 12:48:18", "lastmod": "2023-10-20 16:26:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Joesch-M", "name": { "family": "Joesch", "given": "Maximilian" } }, { "id": "Mankus-D", "name": { "family": "Mankus", "given": "David" } }, { "id": "Yamagata-M", "name": { "family": "Yamagata", "given": "Masahito" } }, { "id": "Shahbazi-A", "name": { "family": "Shahbazi", "given": "Ali" } }, { "id": "Shalek-R", "name": { "family": "Shalek", "given": "Richard" } }, { "id": "Suissa-Peleg-A", "name": { "family": "Suissa-Peleg", "given": "Adi" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Lichtman-J-W", "name": { "family": "Lichtman", "given": "Jeff W." } }, { "id": "Scheirer-W-J", "name": { "family": "Scheirer", "given": "Walter J" } }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "Reconstruction of genetically identified neurons imaged by serial-section electron microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Joesch et al. This article is distributed under the terms of the Creative Commons Attribution License. Received February 04, 2016. Accepted June 27, 2016. Published July 07, 2016.\n\nWe thank Alice Ting, Jeff Martell, and Stephanie Lam for advice and for providing the APX and APEX2 constructs. We also thank Chiao-Lin Chen and Norbert Perrimon for generating and providing the UAS-APEX-GFP fly and Benjamin de Bivort for support with the fly work. This work was supported by NIH grant NS76467 to M.M., J.L. and\nJ.R.S., an HHMI Collaborative Innovation Award to J.R.S., an IARPA contract #D16PC00002 to W.J.S. and by The International Human Frontier Science Program Organization fellowship to M.J. The authors declare no conflicts of interest.\n\nPublished - e15015-download.pdf
Supplemental Material - elife-15015-supp-v1.zip
", "abstract": "Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that enhances the electron-density of the labeled cells and while retaining quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that dramatically speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by at least two orders of magnitude, facilitating directed inquiry of circuit motifs.", "date": "2016-07-07", "date_type": "published", "publication": "eLife", "volume": "5", "publisher": "eLife Sciences Publications", "pagerange": "Art. NO. e15015", "id_number": "CaltechAUTHORS:20160714-081242660", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160714-081242660", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS76467" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Intelligence Advanced Research Projects Activity (IARPA)", "grant_number": "D16PC00002" }, { "agency": "Human Frontier Science Program" } ] }, "doi": "10.7554/eLife.15015", "pmcid": "PMC4959841", "primary_object": { "basename": "e15015-download.pdf", "url": "https://authors.library.caltech.edu/records/7pc1r-9ng53/files/e15015-download.pdf" }, "related_objects": [ { "basename": "elife-15015-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/7pc1r-9ng53/files/elife-15015-supp-v1.zip" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Joesch, Maximilian; Mankus, David; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7hj7a-7ng44", "eprint_id": 63183, "eprint_status": "archive", "datestamp": "2023-08-20 11:16:36", "lastmod": "2023-10-25 23:37:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Joesch-M", "name": { "family": "Joesch", "given": "Maximilian" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "A neuronal circuit for colour vision based on rod\u2013cone opponency", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nReceived 29 March 2015. Accepted 21 January 2016. Published online 06 April 2016. \n\nWe thank E. Soucy and J. Greenwood for technical support, J. Cauceglia for providing the urine post samples, J. R. Sanes and E. Soucy for comments on the manuscript. This work was supported by grants to M.M. from the NIH and to M.J. from The International Human Frontier Science Program Organization. \n\nAuthor Contributions: M.J. designed the study, performed all experiments, interpreted results, and wrote the manuscript. M.M. helped design the study, interpret results, and wrote the manuscript. \n\nThe authors declare no competing financial interests.\n\nSupplemental Material - nature17158-sf1.jpg
Supplemental Material - nature17158-sf2.jpg
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Supplemental Material - nature17158-sf6.jpg
Supplemental Material - nature17158-sf7.jpg
Supplemental Material - nature17158-sf8.jpg
Supplemental Material - nature17158-sf9.jpg
", "abstract": "In bright light, cone-photoreceptors are active and colour vision derives from a comparison of signals in cones with different visual pigments. This comparison begins in the retina, where certain retinal ganglion cells have 'colour-opponent' visual responses\u2014excited by light of one colour and suppressed by another colour. In dim light, rod-photoreceptors are active, but colour vision is impossible because they all use the same visual pigment. Instead, the rod signals are thought to splice into retinal circuits at various points, in synergy with the cone signals. Here we report a new circuit for colour vision that challenges these expectations. A genetically identified type of mouse retinal ganglion cell called JAMB (J-RGC), was found to have colour-opponent responses, OFF to ultraviolet (UV) light and ON to green light. Although the mouse retina contains a green-sensitive cone, the ON response instead originates in rods. Rods and cones both contribute to the response over several decades of light intensity. Remarkably, the rod signal in this circuit is antagonistic to that from cones. For rodents, this UV-green channel may play a role in social communication, as suggested by spectral measurements from the environment. In the human retina, all of the components for this circuit exist as well, and its function can explain certain experiences of colour in dim lights, such as a 'blue shift' in twilight. The discovery of this genetically defined pathway will enable new targeted studies of colour processing in the brain.", "date": "2016-04-14", "date_type": "published", "publication": "Nature", "volume": "532", "number": "7598", "publisher": "Nature Publishing Group", "pagerange": "236-239", "id_number": "CaltechAUTHORS:20151223-110847966", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151223-110847966", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Human Frontier Science Program" } ] }, "doi": "10.1038/nature17158", "primary_object": { "basename": "nature17158-sf2.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf2.jpg" }, "related_objects": [ { "basename": "nature17158-sf4.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf4.jpg" }, { "basename": "nature17158-sf6.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf6.jpg" }, { "basename": "nature17158-sf7.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf7.jpg" }, { "basename": "nature17158-sf1.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf1.jpg" }, { "basename": "nature17158-sf3.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf3.jpg" }, { "basename": "nature17158-sf5.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf5.jpg" }, { "basename": "nature17158-sf8.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf8.jpg" }, { "basename": "nature17158-sf9.jpg", "url": "https://authors.library.caltech.edu/records/7hj7a-7ng44/files/nature17158-sf9.jpg" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Joesch, Maximilian and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sbtd2-xt236", "eprint_id": 62495, "eprint_status": "archive", "datestamp": "2023-09-22 22:52:37", "lastmod": "2023-10-23 23:30:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Teeters-J-L", "name": { "family": "Teeters", "given": "Jeffery L." } }, { "id": "Godfrey-K", "name": { "family": "Godfrey", "given": "Keith" } }, { "id": "Young-R", "name": { "family": "Young", "given": "Rob" } }, { "id": "Dang-C", "name": { "family": "Dang", "given": "Chinh" } }, { "id": "Friedsam-C", "name": { "family": "Friedsam", "given": "Claudia" } }, { "id": "Wark-B", "name": { "family": "Wark", "given": "Barry" } }, { "id": "Asari-H", "name": { "family": "Asari", "given": "Hiroki" } }, { "id": "Peron-S", "name": { "family": "Peron", "given": "Simon" } }, { "id": "Li-Nuo", "name": { "family": "Li", "given": "Nuo" } }, { "id": "Peyrache-A", "name": { "family": "Peyrache", "given": "Adrien" } }, { "id": "Denisov-G", "name": { "family": "Denisov", "given": "Gennady" } }, { "id": "Siegle-J-H", "name": { "family": "Siegle", "given": "Joshua H." } }, { "id": "Olsen-S-R", "name": { "family": "Olsen", "given": "Shawn R." } }, { "id": "Martin-Christopher-Kavli", "name": { "family": "Martin", "given": "Christopher" }, "orcid": "0000-0002-8078-8859" }, { "id": "Chun-Miyoung", "name": { "family": "Chun", "given": "Miyoung" } }, { "id": "Tripathy-S", "name": { "family": "Tripathy", "given": "Shreejoy" } }, { "id": "Blanche-T-J", "name": { "family": "Blanche", "given": "Timothy J." } }, { "id": "Harris-K", "name": { "family": "Harris", "given": "Kenneth" } }, { "id": "Buzs\u00e1ki-G", "name": { "family": "Buzs\u00e1ki", "given": "Gy\u00f6rgy" } }, { "id": "Koch-C", "name": { "family": "Koch", "given": "Christof" }, "orcid": "0000-0001-6482-8067" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Svoboda-K", "name": { "family": "Svoboda", "given": "Karel" } }, { "id": "Sommer-F-T", "name": { "family": "Sommer", "given": "Friedrich T." } } ] }, "title": "Neurodata Without Borders: Creating a Common Data Format for Neurophysiology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Elsevier Inc.\n\nThe Kavli Foundation, General Electric, Howard Hughes Medical Institute, the Allen Institute for Brain Science, the National Science Foundation (grant 0855272), and the International Neuroinformatics Coordinating Facility provided the financial support for conducting the NWB: Neurophysiology pilot project. Janelia Research Campus administered and hosted the two project meetings. The project was heavily dependent on exchanges of the project team with external experts who provided critical input. We thank Jim Berg, Aleena Garner, and Kenji Mitzuseki for sharing experimental data; Jack Waters for help with defining the data model for optophysiology; David Feng and Lydia Ng for support with technical issues of HDF5; and Anton Arkhipov, Tsai-Wen Chen, Saskia De Vries, Severine Durand, Nathan Gouwens, and Zengcai Guo for reviewing the prototype version of the NWB format.\n\nSupplemental Material - mmc1.pdf
", "abstract": "The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.", "date": "2015-11-18", "date_type": "published", "publication": "Neuron", "volume": "88", "number": "4", "publisher": "Elsevier", "pagerange": "629-634", "id_number": "CaltechAUTHORS:20151201-102717877", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151201-102717877", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Kavli Foundation" }, { "agency": "General Electric" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Allen Institute for Brain Science" }, { "agency": "NSF", "grant_number": "0855272" }, { "agency": "International Neuroinformatics Coordinating Facility" } ] }, "local_group": { "items": [ { "id": "Koch-Laboratory" } ] }, "doi": "10.1016/j.neuron.2015.10.025", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/sbtd2-xt236/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Teeters, Jeffery L.; Godfrey, Keith; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/18scf-1be84", "eprint_id": 58791, "eprint_status": "archive", "datestamp": "2023-08-22 15:55:26", "lastmod": "2023-10-23 19:43:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "On the dimensionality of odor space", "ispublished": "pub", "full_text_status": "public", "keywords": "Research organism; Computational and systems biology; Neuroscience", "note": "\u00a9 2015, Meister. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived April 1, 2015. Accepted June 16, 2015. Published July 7, 2015.\n\nAuthor contributions: MM, Conception and design, Analysis and interpretation of data, Drafting or revising the article.\nFunding: No external funding was received for this work.\n\nAcknowledgements: Many thanks to Adam Shai for extended discussions.\n\nSupplementary file \u00b7Source code 1. Annotated Igor (Wavemetrics) code. DOI: 10.7554/eLife.07865.008\n\nPublished - e07865.full.pdf
Supplemental Material - media-1.zip
", "abstract": "There is great interest in understanding human olfactory experience from a principled and quantitative standpoint. The comparison is often made to color vision, where a solid framework with a three-dimensional perceptual space enabled a rigorous search for the underlying neural pathways, and the technological development of lifelike color display devices. A recent, highly publicized report claims that humans can discriminate at least 1 trillion odors, which exceeds by many orders of magnitude the known capabilities of color discrimination. This claim is wrong. I show that the failure lies in the mathematical method used to infer the size of odor space from a limited experimental sample. Further analysis focuses on establishing how many dimensions the perceptual odor space has. I explore the dimensionality of physical, neural, and perceptual spaces, drawing on results from bacteria to humans, and propose some experimental approaches to better estimate the number of discriminable odors.", "date": "2015-07-07", "date_type": "published", "publication": "eLife", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e07865", "id_number": "CaltechAUTHORS:20150707-114340163", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150707-114340163", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.7554/eLife.07865", "pmcid": "PMC4491593", "primary_object": { "basename": "e07865.full.pdf", "url": "https://authors.library.caltech.edu/records/18scf-1be84/files/e07865.full.pdf" }, "related_objects": [ { "basename": "media-1.zip", "url": "https://authors.library.caltech.edu/records/18scf-1be84/files/media-1.zip" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yv8jn-vp450", "eprint_id": 51897, "eprint_status": "archive", "datestamp": "2023-08-20 05:24:18", "lastmod": "2023-10-18 18:40:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Feinberg-E-H", "name": { "family": "Feinberg", "given": "Evan H." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Orientation columns in the mouse superior colliculus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a92014 Macmillan Publishers Limited. \n\nReceived 06 August 2014. Accepted 24 November 2014. Published online 17 December 2014. \n\nWe thank E. Soucy and J. Greenwood for assistance with instrumentation; M. Joesch, A. Krishnaswamy, D. Kostadinov, S. Pashkovski, A. Giessel, T. Dunn, G. Keller, P. Kaifosh, M. Amoroso, and H. Asari for software; M. Andermann, V. Bonin, and F. Engert for advice on microscope design; J. Cohen for headplate designs; D. Anderson, K. Blum, B. \u00d6lveckzy, and J. Sanes for critical reading of the manuscript; and J. Sanes for providing laboratory space and support to E.H.F. E.H.F. was supported by NIH T32 NS007484 and a Howard Hughes Medical Institute-Helen Hay Whitney Foundation fellowship. Additional support was provided by an NIH grant to M.M.\n\nSupplemental Material - nature14103-s1.pdf
", "abstract": "More than twenty types of retinal ganglion cells conduct visual information from the eye to the rest of the brain. Each retinal ganglion cell type tessellates the retina in a regular mosaic, so that every point in visual space is processed for visual primitives such as contrast and motion. This information flows to two principal brain centres: the visual cortex and the superior colliculus. The superior colliculus plays an evolutionarily conserved role in visual behaviours, but its functional architecture is poorly understood. Here we report on population recordings of visual responses from neurons in the mouse superior colliculus. Many neurons respond preferentially to lines of a certain orientation or movement axis. We show that cells with similar orientation preferences form large patches that span the vertical thickness of the retinorecipient layers. This organization is strikingly different from the randomly interspersed orientation preferences in the mouse's visual cortex; instead, it resembles the orientation columns observed in the visual cortices of large mammals. Notably, adjacent superior colliculus orientation columns have only limited receptive field overlap. This is in contrast to the organization of visual cortex, where each point in the visual field activates neurons with all preferred orientations. Instead, the superior colliculus favours specific contour orientations within ~30\u00b0 regions of the visual field, a finding with implications for behavioural responses mediated by this brain centre.", "date": "2015-03-12", "date_type": "published", "publication": "Nature", "volume": "519", "number": "7542", "publisher": "Nature Publishing Group", "pagerange": "229-232", "id_number": "CaltechAUTHORS:20141118-102008104", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141118-102008104", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 NS007484" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Helen Hay Whitney Foundation" } ] }, "doi": "10.1038/nature14103", "primary_object": { "basename": "nature14103-s1.pdf", "url": "https://authors.library.caltech.edu/records/yv8jn-vp450/files/nature14103-s1.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Feinberg, Evan H. and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/av68f-p9n77", "eprint_id": 56065, "eprint_status": "archive", "datestamp": "2023-08-20 05:20:54", "lastmod": "2023-10-20 23:36:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kunwar-P-S", "name": { "family": "Kunwar", "given": "Prabhat S." } }, { "id": "Zelikowski-M", "name": { "family": "Zelikowsky", "given": "Moriel" } }, { "id": "Remedios-R", "name": { "family": "Remedios", "given": "Ryan" } }, { "id": "Cai-Haijiang", "name": { "family": "Cai", "given": "Haijiang" } }, { "id": "Yilmaz-M", "name": { "family": "Yilmaz", "given": "Melis" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Anderson-D-J", "name": { "family": "Anderson", "given": "David J." }, "orcid": "0000-0001-6175-3872" } ] }, "title": "Ventromedial hypothalamic neurons control a defensive emotion state", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015, Kunwar et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived January 22, 2015. Accepted March 5, 2015. Published March 6, 2015.\n\nThe authors thank Monica McCardle, Heeju Kim, Jung-Sook Kim and Xiaolin Da for technical assistance; Celine Chiu and Gina Mancuso for administrative support; and Robert Robertson, Brian Duistermars and Allan Wong for assistance with Matlab programming. We thank all members of Anderson lab for sharing regents and constructive discussion, Dr. Todd Anthony for providing viral reagents and Dr. Brad Lowell for SF1-Cre mice. We thank Ann Kennedy for assistance with data analyses and comments on manuscript. A. Steele and P. Paterson laboratories for discussion, sharing reagents and providing technical help. Dr. Baer, Dr. Lencioni, Jennifer Constanza, Jeffrey Cochrane, ruben Bayon, Ana Colon & Sarah Fitzgerald for ensuring animal welfare, care and husbandry. We would also like to thank R. Mooney, R. Adolphs, M. S. Fanselow, R. Malenka and A. Choe for constructive comments on the manuscript. Lastly, we would like to dedicate this manuscript to D. Robert J. Blanchard (d. 2013), who inspired this project and many others.\n\nAuthor contributions:\nPSK, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or\nrevising the article; MZ, Analysis and interpretation of data, Drafting or revising the article; RR, HC,\nMY, Acquisition of data, Analysis and interpretation of data; MM, Analysis and interpretation of\nlooming data; DJA, Conception and design, Analysis and interpretation of data, Drafting or revising\nthe article.\n\nEthics:\nAnimal experimentation: This study was performed in accordance with the recommendations in the\nGuide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the\nanimals were handled according to approved institutional animal care and use committee (IACUC)\nprotocol 1602, 1552 & 1600.\n\nPublished - e06633.full.pdf
", "abstract": "Defensive behaviors reflect underlying emotion states, such as fear. The hypothalamus plays a role in such behaviors, but prevailing textbook views depict it as an effector of upstream emotion centers, such as the amygdala, rather than as an emotion center itself. We used optogenetic manipulations to probe the function of a specific hypothalamic cell type that mediates innate defensive responses. These neurons are sufficient to drive multiple defensive actions, and required for defensive behaviors in diverse contexts. The behavioral consequences of activating these neurons, moreover, exhibit properties characteristic of emotion states in general, including scalability, (negative) valence, generalization and persistence. Importantly, these neurons can also condition learned defensive behavior, further refuting long-standing claims that the hypothalamus is unable to support emotional learning and therefore is not an emotion center. These data indicate that the hypothalamus plays an integral role to instantiate emotion states, and is not simply a passive effector of upstream emotion centers.", "date": "2015-03-06", "date_type": "published", "publication": "eLife", "volume": "4", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e06633", "id_number": "CaltechAUTHORS:20150325-100540825", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150325-100540825", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "MH085082" }, { "agency": "NIH", "grant_number": "MH070053" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" }, { "agency": "Caltech Divisional Postdoctoral Fellowship" }, { "agency": "NSF Postdoctoral Research Fellowship" } ] }, "doi": "10.7554/eLife.06633", "pmcid": "PMC4379496", "primary_object": { "basename": "e06633.full.pdf", "url": "https://authors.library.caltech.edu/records/av68f-p9n77/files/e06633.full.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Kunwar, Prabhat S.; Zelikowsky, Moriel; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/h1qyg-dt397", "eprint_id": 49626, "eprint_status": "archive", "datestamp": "2023-08-22 13:36:49", "lastmod": "2023-10-17 21:35:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gjorgjieva-J", "name": { "family": "Gjorgjieva", "given": "Julijana" }, "orcid": "0000-0001-7118-4079" }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Benefits of Pathway Splitting in Sensory Coding", "ispublished": "pub", "full_text_status": "public", "keywords": "efficient coding; ON\u2013OFF; optimality; parallel pathways; retina; sensory processing", "note": "\u00a9 2014 the authors. For the first six months after publication SfN's license will be exclusive. Beginning six months after publication SfN's license will be non-exclusive and SfN grants the public the non-exclusive right to copy, distribute, or display the Work under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/. \n\nReceived March 14, 2014; revised July 3, 2014; accepted July 22, 2014.\n\nThis work was supported by a grant from the National Institutes of Health (J.G., H.S. and M.M.) and grants from\nthe Gatsby Charitable Foundation and the Swartz Foundation (H.S.). J.G. thanks Xaq Pitkow for providing help with\nthe sigmoidal nonlinearities from retinal data.\n\nAuthor contributions: J.G., H.S., and M.M. designed research; J.G., H.S., and M.M. performed research; J.G.\nanalyzed data; J.G., H.S., and M.M. wrote the paper.\n\nThe authors declare no competing financial interests.\n\nPublished - 12127.full.pdf
", "abstract": "In many sensory systems, the neural signal splits into multiple parallel pathways. For example, in the mammalian retina, \u223c20 types of retinal ganglion cells transmit information about the visual scene to the brain. The purpose of this profuse and early pathway splitting remains unknown. We examine a common instance of splitting into ON and OFF neurons excited by increments and decrements of light intensity in the visual scene, respectively. We test the hypothesis that pathway splitting enables more efficient encoding of sensory stimuli. Specifically, we compare a model system with an ON and an OFF neuron to one with two ON neurons. Surprisingly, the optimal ON\u2013OFF system transmits the same information as the optimal ON\u2013ON system, if one constrains the maximal firing rate of the neurons. However, the ON\u2013OFF system uses fewer spikes on average to transmit this information. This superiority of the ON\u2013OFF system is also observed when the two systems are optimized while constraining their mean firing rate. The efficiency gain for the ON\u2013OFF split is comparable with that derived from decorrelation, a well known processing strategy of early sensory systems. The gain can be orders of magnitude larger when the ecologically important stimuli are rare but large events of either polarity. The ON\u2013OFF system also provides a better code for extracting information by a linear downstream decoder. The results suggest that the evolution of ON\u2013OFF diversification in sensory systems may be driven by the benefits of lowering average metabolic cost, especially in a world in which the relevant stimuli are sparse.", "date": "2014-09-03", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "34", "number": "36", "publisher": "Society for Neuroscience", "pagerange": "12127-12144", "id_number": "CaltechAUTHORS:20140911-151331633", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140911-151331633", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Gatsby Charitable Foundation" }, { "agency": "Swartz Foundation" } ] }, "doi": "10.1523/JNEUROSCI.1032-14.2014", "pmcid": "PMC4152610", "primary_object": { "basename": "12127.full.pdf", "url": "https://authors.library.caltech.edu/records/h1qyg-dt397/files/12127.full.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Gjorgjieva, Julijana; Sompolinsky, Haim; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qx078-fk246", "eprint_id": 44410, "eprint_status": "archive", "datestamp": "2023-08-19 23:29:04", "lastmod": "2023-10-26 00:27:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Asari-Hiroki", "name": { "family": "Asari", "given": "Hiroki" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "The Projective Field of Retinal Bipolar Cells and Its Modulation by Visual Context", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Elsevier Inc. \n\nAccepted: November 21, 2013. Published: February 5, 2014. \n\nWe gratefully acknowledge Ed Soucy for assistance with experiments. This work was supported by a Postdoctoral Fellowship for Research Abroad from the Japan Society for the Promotion of Science (H.A.) and grants from the U.S. National Institutes of Health (M.M.). \n\nAuthor Contributions: H.A. and M.M. designed the study and wrote the manuscript. H.A. performed experiments and analysis.\n\nSupplemental Material - mmc1.pdf
", "abstract": "The receptive field of a sensory neuron spells out all the receptor inputs it receives. To understand a neuron's role in the circuit, one also needs to know its projective field, namely the outputs it sends to all downstream cells. Here we present the projective fields of the primary excitatory neurons in a sensory circuit. We stimulated single bipolar cells of the salamander retina and recorded simultaneously from a population of ganglion cells. Individual bipolar cell signals diverge through polysynaptic pathways into ganglion cells of many different types and over surprisingly large distance. However, the strength and polarity of the projection depend on the cell types involved. Furthermore, visual stimulation strongly modulates the bipolar cell projective field, in opposite direction for different cell types. In this way, the context from distant parts of the visual field can control the routing of signals in the inner retina.", "date": "2014-02-05", "date_type": "published", "publication": "Neuron", "volume": "81", "number": "3", "publisher": "Elsevier", "pagerange": "641-652", "id_number": "CaltechAUTHORS:20140320-111914365", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140320-111914365", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)" }, { "agency": "NIH" } ] }, "doi": "10.1016/j.neuron.2013.11.029", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/qx078-fk246/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Asari, Hiroki and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jfwjh-c3b32", "eprint_id": 75726, "eprint_status": "archive", "datestamp": "2023-08-19 22:08:27", "lastmod": "2023-10-25 15:14:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Clark-D-A", "name": { "family": "Clark", "given": "Damon A." } }, { "id": "Benichou-R", "name": { "family": "Benichou", "given": "Raphael" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "da-Silveira-R-A", "name": { "family": "da Silveira", "given": "Rava Azeredo" } } ] }, "title": "Dynamical Adaptation in Photoreceptors", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Clark et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived May 20, 2011; Accepted September 3, 2013; Published November 14, 2013. \n\nWe acknowledge Stephen Baccus, Michael J. Berry II, Tom Clandinin, Vincent Hakim, and Simon Laughlin for helpful discussions and comments on the manuscript. We thank Stephen Baccus for the salamander cone cell recordings. \n\nAuthor Contributions: Conceived and designed the experiments: DAC MM RAdS. Analyzed the data: DAC RB MM RAdS. Wrote the paper: DAC MM RAdS. \n\nThis work was supported by the Jane Coffin Childs Fund and a CNRS postdoctoral fellowship (DAC), the Ecole Polytechnique (RB), a grant from the NIH (MM), and the CNRS though UMR 8550, the Universit\u00e9 Pierre et Marie Curie, and the Universit\u00e9 Denis Diderot (RAdS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n \nThe authors have declared that no competing interests exist.\n\nPublished - journal.pcbi.1003289.PDF
Supplemental Material - File_S1.txt
Supplemental Material - File_S2.txt
", "abstract": "Adaptation is at the heart of sensation and nowhere is it more salient than in early visual processing. Light adaptation in photoreceptors is doubly dynamical: it depends upon the temporal structure of the input and it affects the temporal structure of the response. We introduce a non-linear dynamical adaptation model of photoreceptors. It is simple enough that it can be solved exactly and simulated with ease; analytical and numerical approaches combined provide both intuition on the behavior of dynamical adaptation and quantitative results to be compared with data. Yet the model is rich enough to capture intricate phenomenology. First, we show that it reproduces the known phenomenology of light response and short-term adaptation. Second, we present new recordings and demonstrate that the model reproduces cone response with great precision. Third, we derive a number of predictions on the response of photoreceptors to sophisticated stimuli such as periodic inputs, various forms of flickering inputs, and natural inputs. In particular, we demonstrate that photoreceptors undergo rapid adaptation of response gain and time scale, over \u223c 300 ms\u2014i. e., over the time scale of the response itself\u2014and we confirm this prediction with data. For natural inputs, this fast adaptation can modulate the response gain more than tenfold and is hence physiologically relevant.", "date": "2013-11", "date_type": "published", "publication": "PLOS Computational Biology", "volume": "9", "number": "11", "publisher": "Public Library of Science", "pagerange": "Art. No. e1003289", "id_number": "CaltechAUTHORS:20170405-092056680", "issn": "1553-7358", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-092056680", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" }, { "agency": "Centre National de la Recherche Scientifique (CNRS)", "grant_number": "UMR 8550" }, { "agency": "Ecole Polytechnique" }, { "agency": "NIH" }, { "agency": "Universit\u00e9 Pierre et Marie Curie" }, { "agency": "Universit\u00e9 Denis Diderot" } ] }, "doi": "10.1371/journal.pcbi.1003289", "pmcid": "PMC3828139", "primary_object": { "basename": "File_S1.txt", "url": "https://authors.library.caltech.edu/records/jfwjh-c3b32/files/File_S1.txt" }, "related_objects": [ { "basename": "File_S2.txt", "url": "https://authors.library.caltech.edu/records/jfwjh-c3b32/files/File_S2.txt" }, { "basename": "journal.pcbi.1003289.PDF", "url": "https://authors.library.caltech.edu/records/jfwjh-c3b32/files/journal.pcbi.1003289.PDF" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Clark, Damon A.; Benichou, Raphael; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/q05zd-xc516", "eprint_id": 42769, "eprint_status": "archive", "datestamp": "2023-08-22 10:40:29", "lastmod": "2023-10-25 23:00:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Leonardo-A", "name": { "family": "Leonardo", "given": "Anthony" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Nonlinear Dynamics Support a Linear Population Code in a Retinal Target-Tracking Circuit", "ispublished": "pub", "full_text_status": "public", "keywords": "TIGER SALAMANDER RETINA; GANGLION-CELL RESPONSES; NEURONAL POPULATION; CONTRAST ADAPTATION; PRIMATE RETINA; BIPOLAR CELLS; PREDICTION; PATTERNS; SIGNALS; IDENTIFICATION", "note": "\u00a9 2013 the authors.\nReceived May 27, 2013. \nRevision received August 20, 2013. \nAccepted September 13, 2013. \n\nAuthor contributions: A.L. and M.M. designed research; A.L. performed research; A.L. analyzed data; A.L. and\nM.M. wrote the paper.\n\nFunding for AL was provided by a Helen Hay Whitney postdoctoral fellowship and a Burroughs Wellcome Career\nAward in the Biological Sciences. We thank Vivek Jayaraman, Alla Karpova, and Bill Mowrey for comments on the\nmanuscript.\n\nPublished - 16971.full.pdf
", "abstract": "A basic task faced by the visual system of many organisms is to accurately track the position of moving prey. The retina is the first stage\nin the processing of such stimuli; the nature of the transformation here, from photons to spike trains, constrains not only the ultimate\nfidelity of the tracking signal but also the ease with which it can be extracted by other brain regions. Herewedemonstrate that a population\nof fast-OFF ganglion cells in the salamander retina, whose dynamics are governed by a nonlinear circuit, serve to compute the future\nposition of the target over hundreds of milliseconds. The extrapolated position of the target is not found by stimulus reconstruction but\nis instead computed by a weighted sum of ganglion cell outputs, the population vector average (PVA). The magnitude of PVA extrapolation\nvaries systematically with target size, speed, and acceleration, such that large targets are tracked most accurately at high speeds,\nand small targets at low speeds, just as is seen in the motion of real prey. Tracking precision reaches the resolution of single photoreceptors,\nand the PVA algorithm performs more robustly than several alternative algorithms. If the salamander brain uses the fast-OFF cell\ncircuit for target extrapolation as we suggest, the circuit dynamics should leave a microstructure on the behavior that may be measured\nin future experiments. Our analysis highlights the utility of simple computations that, while not globally optimal, are efficiently implemented\nand have close to optimal performance over a limited but ethologically relevant range of stimuli.", "date": "2013-10-23", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "33", "number": "43", "publisher": "Society for Neuroscience", "pagerange": "16971-16982", "id_number": "CaltechAUTHORS:20131202-102453212", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131202-102453212", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Helen Hay Whitney Foundation" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1523/JNEUROSCI.2257-13.2013", "pmcid": "PMC3807026", "primary_object": { "basename": "16971.full.pdf", "url": "https://authors.library.caltech.edu/records/q05zd-xc516/files/16971.full.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Leonardo, Anthony and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/17gmh-c2z94", "eprint_id": 41869, "eprint_status": "archive", "datestamp": "2023-08-19 21:58:05", "lastmod": "2023-10-25 14:51:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yilmaz-M", "name": { "family": "Yilmaz", "given": "Melis" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Rapid Innate Defensive Responses of Mice to Looming Visual Stimuli", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Elsevier Ltd.\n\nAvailable online 10 October 2013.\n\nWe thank Xavier Burgos-Artizzu for advice on video analysis, and David\nAnderson, Joshua Sanes, and Rachel Wilson for comments on the manuscript.\nThis work was supported by grants from the NIH to M.M.\n\nAccepted Version - nihms514919.pdf
Supplemental Material - MovieS1.mp4
Supplemental Material - MovieS2.mp4
Supplemental Material - mmc1.pdf
", "abstract": "Much of brain science is concerned with understanding the neural circuits that underlie specific behaviors. While the mouse has become a favorite experimental subject, the behaviors of this species are still poorly explored. For example, the mouse retina, like that of other mammals, contains \u223c20 different circuits that compute distinct features of the visual scene [1 and 2]. By comparison, only a handful of innate visual behaviors are known in this species\u2014the pupil reflex [3], phototaxis [4], the optomotor response [5], and the cliff response [6]\u2014two of which are simple reflexes that require little visual processing. We explored the behavior of mice under a visual display that simulates an approaching object, which causes defensive reactions in some other species [7 and 8]. We show that mice respond to this stimulus either by initiating escape within a second or by freezing for an extended period. The probability of these defensive behaviors is strongly dependent on the parameters of the visual stimulus. Directed experiments identify candidate retinal circuits underlying the behavior and lead the way into detailed study of these neural pathways. This response is a new addition to the repertoire of innate defensive behaviors in the mouse that allows the detection and avoidance of aerial predators.", "date": "2013-10-21", "date_type": "published", "publication": "Current Biology", "volume": "23", "number": "20", "publisher": "Cell Press", "pagerange": "2011-2015", "id_number": "CaltechAUTHORS:20131010-112717303", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131010-112717303", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "doi": "10.1016/j.cub.2013.08.015", "pmcid": "PMC3809337", "primary_object": { "basename": "MovieS1.mp4", "url": "https://authors.library.caltech.edu/records/17gmh-c2z94/files/MovieS1.mp4" }, "related_objects": [ { "basename": "MovieS2.mp4", "url": "https://authors.library.caltech.edu/records/17gmh-c2z94/files/MovieS2.mp4" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/17gmh-c2z94/files/mmc1.pdf" }, { "basename": "nihms514919.pdf", "url": "https://authors.library.caltech.edu/records/17gmh-c2z94/files/nihms514919.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Yilmaz, Melis and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t3yv8-r0a68", "eprint_id": 43162, "eprint_status": "archive", "datestamp": "2023-08-19 21:06:37", "lastmod": "2023-10-25 23:19:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Cox-D-J", "name": { "family": "Cox", "given": "David" } } ] }, "title": "Rats maintain a binocular field centered on the horizon", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Meister M et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \n\nFirst Published: 16 Aug 2013, 2:176 (doi:10.12688/f1000research.2-176.v1). First Indexed: 22 Aug 2013, 2:176 (doi: 10.12688/f1000research.2-176.v1).\n\nAuthor contributions: MM wrote the first version of the letter and corresponded with the paper's senior author for clarification. MM and DDC participated in the discussion and revision of the letter. \n\nNo competing interests were disclosed. \n\nGrant information: The author(s) declared that no grants were involved in supporting this work.\n\nPublished - Meister_2013.pdf
", "abstract": "In this letter, we attempt to correct a potentially serious misperception arising\nfrom the paper \"Rats maintain an overhead binocular field at the expense of\nconstant fusion\". While the authors repeatedly emphasize that the animal's\nbinocular field is overhead, the authors' own data show that the truth is quite\ndifferent, even orthogonal: the binocular field is in fact centered dead-ahead in\nfront of the animal, tapering to a sliver both above and below the animal. We\npredict that this paper will be widely cited for something that it does not\ndemonstrate, a concern that is borne out by the paper's earliest citation.", "date": "2013-08-16", "date_type": "published", "publication": "F1000Research", "volume": "2013", "number": "2", "publisher": "F1000 Research Ltd.", "pagerange": "Art. No. 176", "id_number": "CaltechAUTHORS:20131224-092551420", "issn": "2046-1402", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131224-092551420", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.12688/f1000research.2-176.v1", "pmcid": "PMC3790602", "primary_object": { "basename": "Meister_2013.pdf", "url": "https://authors.library.caltech.edu/records/t3yv8-r0a68/files/Meister_2013.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Meister, Markus and Cox, David" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ry7y4-b9x46", "eprint_id": 75733, "eprint_status": "archive", "datestamp": "2023-08-19 14:16:57", "lastmod": "2023-10-25 15:15:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "G\u00fctig-R", "name": { "family": "G\u00fctig", "given": "Robert" } }, { "id": "Gollisch-T", "name": { "family": "Gollisch", "given": "Tim" } }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Computing Complex Visual Features with Retinal Spike Times", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 G\u00fctig et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived August 26, 2012; Accepted November 28, 2012; Published January 2, 2013. \n\nThis research was supported by the Minerva Foundation and the German Research Foundation (RG); the Max Planck Society, the German Research Foundation SFB 889, and the International Human Frontier Science Program Organization (TG); the Israel Science Foundation, the Israeli Ministry of Defense, and the Gatsby Charitable Foundation (HS); and the National Institutes of Health (MM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nAuthor Contributions: Conceived and designed the experiments: RG TG HS MM. Performed the experiments: RG TG. Analyzed the data: RG TG. Wrote the paper: RG TG HS MM. \n\nThe authors have declared that no competing interests exist.\n\nPublished - journal.pone.0053063.PDF
", "abstract": "Neurons in sensory systems can represent information not only by their firing rate, but also by the precise timing of individual spikes. For example, certain retinal ganglion cells, first identified in the salamander, encode the spatial structure of a new image by their first-spike latencies. Here we explore how this temporal code can be used by downstream neural circuits for computing complex features of the image that are not available from the signals of individual ganglion cells. To this end, we feed the experimentally observed spike trains from a population of retinal ganglion cells to an integrate-and-fire model of post-synaptic integration. The synaptic weights of this integration are tuned according to the recently introduced tempotron learning rule. We find that this model neuron can perform complex visual detection tasks in a single synaptic stage that would require multiple stages for neurons operating instead on neural spike counts. Furthermore, the model computes rapidly, using only a single spike per afferent, and can signal its decision in turn by just a single spike. Extending these analyses to large ensembles of simulated retinal signals, we show that the model can detect the orientation of a visual pattern independent of its phase, an operation thought to be one of the primitives in early visual processing. We analyze how these computations work and compare the performance of this model to other schemes for reading out spike-timing information. These results demonstrate that the retina formats spatial information into temporal spike sequences in a way that favors computation in the time domain. Moreover, complex image analysis can be achieved already by a simple integrate-and-fire model neuron, emphasizing the power and plausibility of rapid neural computing with spike times.", "date": "2013-01-02", "date_type": "published", "publication": "PLoS ONE", "volume": "8", "number": "1", "publisher": "Public Library of Science", "pagerange": "Art. No. e53063", "id_number": "CaltechAUTHORS:20170405-103352974", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-103352974", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Minerva Foundation" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "SFB 889" }, { "agency": "Max Planck Society" }, { "agency": "Human Frontier Science Program" }, { "agency": "Israel Science Foundation" }, { "agency": "Ministry of Defense (Israel)" }, { "agency": "Gatsby Charitable Foundation" }, { "agency": "NIH" } ] }, "doi": "10.1371/journal.pone.0053063", "pmcid": "PMC3534662", "primary_object": { "basename": "journal.pone.0053063.PDF", "url": "https://authors.library.caltech.edu/records/ry7y4-b9x46/files/journal.pone.0053063.PDF" }, "resource_type": "article", "pub_year": "2013", "author_list": "G\u00fctig, Robert; Gollisch, Tim; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y91gw-ydf27", "eprint_id": 35732, "eprint_status": "archive", "datestamp": "2023-08-19 13:17:46", "lastmod": "2023-10-20 20:34:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Asari-Hiroki", "name": { "family": "Asari", "given": "Hiroki" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Divergence of visual channels in the inner retina", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. \n\nReceived 27 June; accepted 20 September; published online 21 October 2012.\n\nWe gratefully acknowledge E. Soucy for his extensive help with the experiments, as well as all of the members of the Meister laboratory for many useful discussions. This work was supported by a Postdoctoral Fellowship for Research Abroad from the Japan Society for the Promotion of Science (H.A.) and grants from the US National Institutes of Health (M.M.).\nAuthor Contributions: H.A. and M.M. designed the study and wrote the manuscript. H.A. performed the experiments and analysis.\n\nAccepted Version - nihms488915.pdf
Supplemental Material - nn.3241-S1.pdf
", "abstract": "Bipolar cells form parallel channels that carry visual signals from the outer to the inner retina. Each type of bipolar cell is thought to carry a distinct visual message to select types of amacrine cells and ganglion cells. However, the number of ganglion cell types exceeds that of the bipolar cells providing their input, suggesting that bipolar cell signals diversify on transmission to ganglion cells. We explored in the salamander retina how signals from individual bipolar cells feed into multiple ganglion cells and found that each bipolar cell was able to evoke distinct responses among ganglion cells, differing in kinetics, adaptation and rectification properties. This signal divergence resulted primarily from interactions with amacrine cells that allowed each bipolar cell to send distinct signals to its target ganglion cells. Our findings indicate that individual bipolar cell\u2013ganglion cell connections have distinct transfer functions. This expands the number of visual channels in the inner retina and enhances the computational power and feature selectivity of early visual processing.", "date": "2012-11", "date_type": "published", "publication": "Nature Neuroscience", "volume": "15", "number": "11", "publisher": "Nature Publishing Group", "pagerange": "1581-1589", "id_number": "CaltechAUTHORS:20121129-134641275", "issn": "1097-6256", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121129-134641275", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Japan Society for the Promotion of Science (JSPS)" }, { "agency": "NIH" } ] }, "doi": "10.1038/nn.3241", "pmcid": "PMC3717330", "primary_object": { "basename": "nn.3241-S1.pdf", "url": "https://authors.library.caltech.edu/records/y91gw-ydf27/files/nn.3241-S1.pdf" }, "related_objects": [ { "basename": "nihms488915.pdf", "url": "https://authors.library.caltech.edu/records/y91gw-ydf27/files/nihms488915.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Asari, Hiroki and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bqddp-kwa16", "eprint_id": 75700, "eprint_status": "archive", "datestamp": "2023-08-22 06:49:56", "lastmod": "2023-10-25 15:13:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Kim-In-Jung", "name": { "family": "Kim", "given": "In-Jung" } }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "The most numerous ganglion cell type of the mouse retina is a selective feature detector", "ispublished": "pub", "full_text_status": "public", "keywords": "electrophysiology; vision; neural processing; density recovery profile", "note": "\u00a9 2012 National Academy of Sciences. \n\nContributed by Joshua R. Sanes, July 7, 2012 (sent for review May 4, 2012). Published online before print August 13, 2012. \n\nWe thank Jeremy Kay for advice and sharing results on retinal gene expression patterns. This work was supported by National Institutes of Health Grants NS29169, EY020426, EY019355, EY010020, and EY014737 and a Charles A. King fellowship (to Y.Z.). \n\nAuthor contributions: Y.Z., J.R.S., and M.M. designed research; Y.Z. performed research; I.-J.K. contributed new reagents/analytic tools; Y.Z., J.R.S., and M.M. analyzed data; and Y.Z., J.R.S., and M.M. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nSee Author Summary on page 14297 (volume 109, number 36). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1211547109/-/DCSupplemental.\n\nPublished - PNAS-2012-Zhang-E2391-8.pdf
Supplemental Material - pnas.201211547SI.pdf
", "abstract": "The retina reports the visual scene to the brain through many parallel channels, each carried by a distinct population of retinal ganglion cells. Among these, the population with the smallest and densest receptive fields encodes the neural image with highest resolution. In human retina, and those of cat and macaque, these high-resolution ganglion cells act as generic pixel encoders: They serve to represent many different visual inputs and convey a neural image of the scene downstream for further processing. Here we identify and analyze high-resolution ganglion cells in the mouse retina, using a transgenic line in which these cells, called \"W3\", are labeled fluorescently. Counter to the expectation, these ganglion cells do not participate in encoding generic visual scenes, but remain silent during most common visual stimuli. A detailed study of their response properties showed that W3 cells pool rectified excitation from both On and Off bipolar cells, which makes them sensitive to local motion. However, they also receive unusually strong lateral inhibition, both pre- and postsynaptically, triggered by distant motion. As a result, the W3 cell can detect small moving objects down to the receptive field size of bipolar cells, but only if the background is featureless or stationary\u2014an unusual condition. A survey of naturalistic stimuli shows that W3 cells may serve as alarm neurons for overhead predators.", "date": "2012-09-04", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "36", "publisher": "National Academy of Sciences", "pagerange": "E2391-E2398", "id_number": "CaltechAUTHORS:20170404-135114672", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-135114672", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS29169" }, { "agency": "NIH", "grant_number": "EY020426" }, { "agency": "NIH", "grant_number": "EY019355" }, { "agency": "NIH", "grant_number": "EY010020" }, { "agency": "NIH", "grant_number": "EY014737" }, { "agency": "Charles A. King Fellowship" } ] }, "doi": "10.1073/pnas.1211547109", "pmcid": "PMC3437843", "primary_object": { "basename": "PNAS-2012-Zhang-E2391-8.pdf", "url": "https://authors.library.caltech.edu/records/bqddp-kwa16/files/PNAS-2012-Zhang-E2391-8.pdf" }, "related_objects": [ { "basename": "pnas.201211547SI.pdf", "url": "https://authors.library.caltech.edu/records/bqddp-kwa16/files/pnas.201211547SI.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Zhang, Yifeng; Kim, In-Jung; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1qk7e-zdk31", "eprint_id": 75723, "eprint_status": "archive", "datestamp": "2023-08-19 10:34:11", "lastmod": "2023-10-25 15:14:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pitkow-X", "name": { "family": "Pitkow", "given": "Xaq" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Decorrelation and efficient coding by retinal ganglion cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Macmillan Publishers Limited, part of Springer Nature. \n\nReceived 20 September 2011; accepted 13 February 2012; published online 11 March 2012. \n\nWe thank the members of the Meister laboratory, M. Berry, T. Toyozumi and J.-P. Nadal for helpful advice. This work was funded by grants from the US National Institutes of Health to M.M. \n\nAuthor Contributions: X.P. and M.M. designed the study. X.P. performed all of the experiments, analysis and modeling. X.P. and M.M. wrote the article. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms488914.pdf
Supplemental Material - nn.3064-S1.pdf
", "abstract": "An influential theory of visual processing asserts that retinal center-surround receptive fields remove spatial correlations in the visual world, producing ganglion cell spike trains that are less redundant than the corresponding image pixels. For bright, high-contrast images, this decorrelation would enhance coding efficiency in optic nerve fibers of limited capacity. We tested the central prediction of the theory and found that the spike trains of retinal ganglion cells were indeed decorrelated compared with the visual input. However, most of the decorrelation was accomplished not by the receptive fields, but by nonlinear processing in the retina. We found that a steep response threshold enhanced efficient coding by noisy spike trains and that the effect of this nonlinearity was near optimal in both salamander and macaque retina. These results offer an explanation for the sparseness of retinal spike trains and highlight the importance of treating the full nonlinear character of neural codes.", "date": "2012-04", "date_type": "published", "publication": "Nature Neuroscience", "volume": "15", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "628-635", "id_number": "CaltechAUTHORS:20170405-082056107", "issn": "1097-6256", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-082056107", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "doi": "10.1038/nn.3064", "pmcid": "PMC3725273", "primary_object": { "basename": "nihms488914.pdf", "url": "https://authors.library.caltech.edu/records/1qk7e-zdk31/files/nihms488914.pdf" }, "related_objects": [ { "basename": "nn.3064-S1.pdf", "url": "https://authors.library.caltech.edu/records/1qk7e-zdk31/files/nn.3064-S1.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Pitkow, Xaq and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yb6wh-4h691", "eprint_id": 75722, "eprint_status": "archive", "datestamp": "2023-08-19 08:35:46", "lastmod": "2023-10-25 15:14:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Samuel-M-A", "name": { "family": "Samuel", "given": "Melanie A." } }, { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "Age-Related Alterations in Neurons of the Mouse Retina", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 the authors. For the first six months after publication SfN's license will be exclusive. Beginning six months after publication the Work will be made freely available to the public on SfN's website to copy, distribute, or display under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived July 12, 2011; revised Aug. 29, 2011; accepted Sept. 15, 2011. \n\nThis work was supported by grants from the NIH to J.R.S and M.M. M.A.S. was a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-1990-08). We thank Z. He for rAAV-Cre, K. Kuchibohtla and B. Bacsai for the pAAV-CAG-YC3.6 vector, and I. Provencio for antibody to melanopsin.\n\nPublished - 16033.full.pdf
", "abstract": "The behavioral consequences of age-related alterations in neural function are well documented, but less is known about their cellular bases. To characterize such changes, we analyzed 14 molecularly identified subsets of mouse retinal projection neurons (retinal ganglion cells or RGCs) and interneurons (amacrine, bipolar, and horizontal cells). The retina thinned but expanded with age, maintaining its volume. There was minimal decline in the number of RGCs, interneurons, or photoreceptors, but the diameter of RGC dendritic arbors decreased with age. Together, the increased retinal area and the decreased dendritic area may lead to gaps in RGC coverage of the visual field. Axonal arbors of RGCs in the superior colliculus also atrophied with age, suggesting that the relay of visual information to central targets may decline over time. On the other hand, the laminar restriction of RGC dendrites and the interneuronal processes that synapse on them were not detectably disturbed, and RGC subtypes exhibited distinct electrophysiological responses to complex visual stimuli. Other neuronal types aged in different ways: amacrine cell arbors did not remodel detectably, whereas horizontal cell processes sprouted into the photoreceptor layer. Bipolar cells showed arbor-specific alterations: their dendrites sprouted but their axons remained stable. In summary, retinal neurons exhibited numerous age-related quantitative alterations (decreased areas of dendritic and axonal arbors and decreased density of cells and synapses), whereas their qualitative features (molecular identity, laminar specificity, and feature detection) were largely preserved. Together, these data reveal selective age-related alterations in neural circuitry, some of which could underlie declines in visual acuity.", "date": "2011-11-02", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "31", "number": "44", "publisher": "Society for Neuroscience", "pagerange": "16033-16044", "id_number": "CaltechAUTHORS:20170405-082004518", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-082004518", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1990-08" } ] }, "doi": "10.1523/JNEUROSCI.3580-11.2011", "pmcid": "PMC3238393", "primary_object": { "basename": "16033.full.pdf", "url": "https://authors.library.caltech.edu/records/yb6wh-4h691/files/16033.full.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Samuel, Melanie A.; Zhang, Yifeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5a3se-5bb26", "eprint_id": 75719, "eprint_status": "archive", "datestamp": "2023-08-19 07:07:47", "lastmod": "2023-10-25 15:14:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "de-Vries-S-E-J", "name": { "family": "de Vries", "given": "Saskia E. J." } }, { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "The Projective Field of a Retinal Amacrine Cell", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 the authors. Beginning six months after publication the Work will be made freely available to the public on SfN's website to copy, distribute, or display under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived Oct. 27, 2010; revised Feb. 20, 2011; accepted April 4, 2011. \n\nThis work was supported by a fellowship from the National Science Foundation (S.E.J.d.V.), the Pew Charitable Trust (S.A.B.), the McKnight Foundation (S.A.B.), and grants from NIH (M.M., S.A.B.). \n\nThe authors declare no competing financial interests.\n\nPublished - 8595.full.pdf
", "abstract": "In sensory systems, neurons are generally characterized by their receptive field, namely the sensitivity to activity patterns at the input of the circuit. To assess the role of the neuron in the system, one must also know its projective field, namely the spatiotemporal effects the neuron exerts on all of the outputs of the circuit. We studied both the receptive and projective fields of an amacrine interneuron in the salamander retina. This amacrine type has a sustained OFF response with a small receptive field, but its output projects over a much larger region. Unlike other amacrine cells, this type is remarkably promiscuous and affects nearly every ganglion cell within reach of its dendrites. Its activity modulates the sensitivity of visual responses in ganglion cells but leaves their kinetics unchanged. The projective field displays a center-surround structure: depolarizing a single amacrine suppresses the visual sensitivity of ganglion cells nearby and enhances it at greater distances. This change in sign is seen even within the receptive field of one ganglion cell; thus, the modulation occurs presynaptically on bipolar cell terminals, most likely via GABAB receptors. Such an antagonistic projective field could contribute to the mechanisms of the retina for predictive coding.", "date": "2011-06-08", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "31", "number": "23", "publisher": "Society for Neuroscience", "pagerange": "8595-8604", "id_number": "CaltechAUTHORS:20170405-073927798", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-073927798", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "Pew Charitable Trust" }, { "agency": "McKnight Foundation" }, { "agency": "NIH" } ] }, "doi": "10.1523/JNEUROSCI.5662-10.2011", "pmcid": "PMC3130123", "primary_object": { "basename": "8595.full.pdf", "url": "https://authors.library.caltech.edu/records/5a3se-5bb26/files/8595.full.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "de Vries, Saskia E. J.; Baccus, Stephen A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dedw5-ahe56", "eprint_id": 75711, "eprint_status": "archive", "datestamp": "2023-08-19 06:51:32", "lastmod": "2023-10-25 15:14:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kay-J-N", "name": { "family": "Kay", "given": "Jeremy N." } }, { "id": "De-la-Huerta-I", "name": { "family": "De la Huerta", "given": "Irina" } }, { "id": "Kim-In-Jung", "name": { "family": "Kim", "given": "In-Jung" } }, { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Yamagata-Masahito", "name": { "family": "Yamagata", "given": "Masahito" } }, { "id": "Chu-Monica-W", "name": { "family": "Chu", "given": "Monica W." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "Retinal Ganglion Cells with Distinct Directional Preferences Differ in Molecular Identity, Structure, and Central Projections", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 the authors. Beginning six months after publication the Work will be made freely available to the public on SfN's website to copy, distribute, or display under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived Feb. 19, 2011; accepted March 25, 2011. \n\nThis work was supported by grants from the NIH to I.-J.K., M.M., and J.R.S., a grant from NIH to J.R.S., Collaborative Innovation Award 43667 from HHMI, and fellowships from the Life Sciences Research Foundation to J.N.K. and from the Charles A. King Trust to Y.Z. We thank Sara Haddad, Debbie Pelusi, and Laura Stoppel for assistance.\n\nPublished - 7753.full.pdf
", "abstract": "The retina contains ganglion cells (RGCs) that respond selectively to objects moving in particular directions. Individual members of a group of ON-OFF direction-selective RGCs (ooDSGCs) detect stimuli moving in one of four directions: ventral, dorsal, nasal, or temporal. Despite this physiological diversity, little is known about subtype-specific differences in structure, molecular identity, and projections. To seek such differences, we characterized mouse transgenic lines that selectively mark ooDSGCs preferring ventral or nasal motion as well as a line that marks both ventral- and dorsal-preferring subsets. We then used the lines to identify cell surface molecules, including Cadherin 6, CollagenXXV\u03b11, and Matrix metalloprotease 17, that are selectively expressed by distinct subsets of ooDSGCs. We also identify a neuropeptide, CART (cocaine- and amphetamine-regulated transcript), that distinguishes all ooDSGCs from other RGCs. Together, this panel of endogenous and transgenic markers distinguishes the four ooDSGC subsets. Patterns of molecular diversification occur before eye opening and are therefore experience independent. They may help to explain how the four subsets obtain distinct inputs. We also demonstrate differences among subsets in their dendritic patterns within the retina and their axonal projections to the brain. Differences in projections indicate that information about motion in different directions is sent to different destinations.", "date": "2011-05-25", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "31", "number": "21", "publisher": "Society for Neuroscience", "pagerange": "7753-7762", "id_number": "CaltechAUTHORS:20170405-063019589", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-063019589", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Life Sciences Research Foundation" }, { "agency": "Charles A. King Trust" }, { "agency": "Howard Hughes Medical Institute (HHMI)", "grant_number": "43667" } ] }, "doi": "10.1523/JNEUROSCI.0907-11.2011", "pmcid": "PMC3108146", "primary_object": { "basename": "7753.full.pdf", "url": "https://authors.library.caltech.edu/records/dedw5-ahe56/files/7753.full.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Kay, Jeremy N.; De la Huerta, Irina; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cgg6d-tq552", "eprint_id": 22651, "eprint_status": "archive", "datestamp": "2023-08-19 05:22:44", "lastmod": "2023-10-23 17:06:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Szuts-T-A", "name": { "family": "Szuts", "given": "Tobi A." } }, { "id": "Fadeyev-V", "name": { "family": "Fadeyev", "given": "Vitaliy" } }, { "id": "Kachiguine-S", "name": { "family": "Kachiguine", "given": "Sergei" } }, { "id": "Sher-A", "name": { "family": "Sher", "given": "Alexander" } }, { "id": "Grivich-M-V", "name": { "family": "Grivich", "given": "Matthew V." } }, { "id": "Agroch\u00e3o-M", "name": { "family": "Agroch\u00e3o", "given": "Margarida" } }, { "id": "Hottowy-P", "name": { "family": "Hottowy", "given": "Pawel" } }, { "id": "Dabrowski-W", "name": { "family": "Dabrowski", "given": "Wladyslaw" } }, { "id": "Lubenov-E-V", "name": { "family": "Lubenov", "given": "Evgueniy V." }, "orcid": "0000-0002-1099-944X" }, { "id": "Siapas-A-G", "name": { "family": "Siapas", "given": "Athanassios G." }, "orcid": "0000-0001-8837-678X" }, { "id": "Uchida-Naoshige", "name": { "family": "Uchida", "given": "Naoshige" } }, { "id": "Litke-A-M", "name": { "family": "Litke", "given": "Alan M." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "A wireless multi-channel neural amplifier for freely moving animals", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Nature Publishing Group. \n\nReceived 21 October 2010; accepted 6 December 2010; published online 16 January 2011. \n\nWe thank A. Leifer and E. Soucy for technical assistance and O. Mazor and A. Biewener for advice. Funding was provided by the McKnight Foundation (M.M., T.A.S.) the Gordon and Betty Moore Foundation (M.M.), the Polish Ministry of Science and Higher Education (W.D., P.H.), the National Science Foundation (PHY-0750525, A.M.L.) and the Burroughs Wellcome Fund Career Award at the Scientific Interface (A.S.).\n\nAuthor Contributions: This manuscript was written by T.A.S. and M.M., with comments from all authors. The Neuroplat chip was designed by P.H., W.D. and A.M.L. The back and head boards were designed by A.M.L., V.F., S.K., A.S. and M.V.G. The wireless link was designed by T.A.S. and M.M. Implantations and experiments were performed by A.G.S. and E.V.L. (hippocampus), N.U. (frontal eye field), and T.A.S. and M.A. (V1). Analysis was performed by N.U. (FEF) and T.A.S. and M.M. (V1, hippocampus). M.M. and A.M.L. supervised the project.\n\nSupplemental Material - nn.2730-S1.pdf
", "abstract": "Conventional neural recording systems restrict behavioral experiments to a flat indoor environment compatible with the cable that tethers the subject to recording instruments. To overcome these constraints, we developed a wireless multi-channel system for recording neural signals from rats. The device takes up to 64 voltage signals from implanted electrodes, samples each at 20 kHz, time-division multiplexes them into one signal and transmits that output by radio frequency to a receiver up to 60 m away. The system introduces <4 \u03bcV of electrode-referred noise, comparable to wired recording systems, and outperforms existing rodent telemetry systems in channel count, weight and transmission range. This allows effective recording of brain signals in freely behaving animals. We report measurements of neural population activity taken outdoors and in tunnels. Neural firing in the visual cortex was relatively sparse, correlated even across large distances and was strongly influenced by locomotor activity.", "date": "2011-02", "date_type": "published", "publication": "Nature Neuroscience", "volume": "14", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "263-269", "id_number": "CaltechAUTHORS:20110303-161530587", "issn": "1097-6256", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110303-161530587", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "McKnight Foundation" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Ministry of Science and Higher Education (Poland)" }, { "agency": "NSF", "grant_number": "PHY-0750525" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1038/nn.2730", "primary_object": { "basename": "nn.2730-S1.pdf", "url": "https://authors.library.caltech.edu/records/cgg6d-tq552/files/nn.2730-S1.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Szuts, Tobi A.; Fadeyev, Vitaliy; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/acqe1-ycr80", "eprint_id": 75699, "eprint_status": "archive", "datestamp": "2023-08-22 01:21:20", "lastmod": "2023-10-25 15:13:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Burak-Y", "name": { "family": "Burak", "given": "Yoram" } }, { "id": "Rokni-U", "name": { "family": "Rokni", "given": "Uri" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } } ] }, "title": "Bayesian model of dynamic image stabilization in the visual system", "ispublished": "pub", "full_text_status": "public", "keywords": "computation; fixational eye motion; neural network; retina; cortex", "note": "\u00a9 2010 National Academy of Sciences. \n\nEdited by William T. Newsome, Stanford University, Stanford, CA, and approved September 17, 2010 (received for review May 8, 2010). Published online before print October 11, 2010. \n\nWe thank Dan Lee, Ofer Mazor, and Xaq Pitkow for helpful discussions and Eran Mukamel for comments on the manuscript. We acknowledge support from the Swartz Foundation (Y.B. and U.R.), the National Eye Institute (M.M.), the Israeli Science Foundation (H.S.), and the Israeli Ministry of Defense (H.S.). \n\nAuthor contributions: Y.B., U.R., M.M., and H.S. designed research; Y.B., U.R., and H.S. performed research; and Y.B., M.M., and H.S. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1006076107/-/DCSupplemental.\n\nPublished - PNAS-2010-Burak-19525-30.pdf
Supplemental Material - sapp.pdf
", "abstract": "Humans can resolve the fine details of visual stimuli although the image projected on the retina is constantly drifting relative to the photoreceptor array. Here we demonstrate that the brain must take this drift into account when performing high acuity visual tasks. Further, we propose a decoding strategy for interpreting the spikes emitted by the retina, which takes into account the ambiguity caused by retinal noise and the unknown trajectory of the projected image on the retina. A main difficulty, addressed in our proposal, is the exponentially large number of possible stimuli, which renders the ideal Bayesian solution to the problem computationally intractable. In contrast, the strategy that we propose suggests a realistic implementation in the visual cortex. The implementation involves two populations of cells, one that tracks the position of the image and another that represents a stabilized estimate of the image itself. Spikes from the retina are dynamically routed to the two populations and are interpreted in a probabilistic manner. We consider the architecture of neural circuitry that could implement this strategy and its performance under measured statistics of human fixational eye motion. A salient prediction is that in high acuity tasks, fixed features within the visual scene are beneficial because they provide information about the drifting position of the image. Therefore, complete elimination of peripheral features in the visual scene should degrade performance on high acuity tasks involving very small stimuli.", "date": "2010-11-09", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "107", "number": "45", "publisher": "National Academy of Sciences", "pagerange": "19525-19530", "id_number": "CaltechAUTHORS:20170404-134032704", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-134032704", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Swartz Foundation" }, { "agency": "National Eye Institute" }, { "agency": "Israeli Science Foundation" }, { "agency": "Ministry of Defense (Israel)" } ] }, "doi": "10.1073/pnas.1006076107", "pmcid": "PMC2984143", "primary_object": { "basename": "PNAS-2010-Burak-19525-30.pdf", "url": "https://authors.library.caltech.edu/records/acqe1-ycr80/files/PNAS-2010-Burak-19525-30.pdf" }, "related_objects": [ { "basename": "sapp.pdf", "url": "https://authors.library.caltech.edu/records/acqe1-ycr80/files/sapp.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Burak, Yoram; Rokni, Uri; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pp314-r3991", "eprint_id": 75721, "eprint_status": "archive", "datestamp": "2023-08-19 01:30:50", "lastmod": "2023-10-25 15:14:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gollisch-T", "name": { "family": "Gollisch", "given": "Tim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Eye Smarter than Scientists Believed: Neural Computations in Circuits of the Retina", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Elsevier Inc. \n\nAvailable online 27 January 2010. \n\nThis work was supported by the Max Planck Society (T.G.) and by grants from the National Eye Institute (M.M.).\n\nAccepted Version - nihms488912.pdf
", "abstract": "We rely on our visual system to cope with the vast barrage of incoming light patterns and to extract features from the scene that are relevant to our well-being. The necessary reduction of visual information already begins in the eye. In this review, we summarize recent progress in understanding the computations performed in the vertebrate retina and how they are implemented by the neural circuitry. A new picture emerges from these findings that helps resolve a vexing paradox between the retina's structure and function. Whereas the conventional wisdom treats the eye as a simple prefilter for visual images, it now appears that the retina solves a diverse set of specific tasks and provides the results explicitly to downstream brain areas.", "date": "2010-01-28", "date_type": "published", "publication": "Neuron", "volume": "65", "number": "2", "publisher": "Elsevier", "pagerange": "150-164", "id_number": "CaltechAUTHORS:20170405-081115721", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-081115721", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Max Planck Society" }, { "agency": "National Eye Institute" } ] }, "doi": "10.1016/j.neuron.2009.12.009", "pmcid": "PMC3717333", "primary_object": { "basename": "nihms488912.pdf", "url": "https://authors.library.caltech.edu/records/pp314-r3991/files/nihms488912.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Gollisch, Tim and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/aw4n6-tbm58", "eprint_id": 75713, "eprint_status": "archive", "datestamp": "2023-08-19 01:30:21", "lastmod": "2023-10-25 15:14:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kim-In-Jung", "name": { "family": "Kim", "given": "In-Jung" } }, { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "Laminar Restriction of Retinal Ganglion Cell Dendrites and Axons: Subtype-Specific Developmental Patterns Revealed with Transgenic Markers", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 the authors.Beginning six months after publication the Work will be made freely available to the public on SfN's website to copy, distribute, or display under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived Sept. 25, 2009; revised Dec. 1, 2009; accepted Dec. 5, 2009. \n\nThis study was supported by grants from National Institutes of Health to M.M., J.R.S., and I.-J.K., a Bushrod H. Campbell and Adah F. Hall Charity Fund Fellowship to I.-J.K, a Damon Runyon Fellowship to Y.Z., and a Merck Award for Genome-Related Research to I.-J.K. We thank Renate Hellmiss, Debbie Pelusi, Sara Haddad, and Laura Stoppel for advice and assistance.\n\nPublished - 1452.full.pdf
", "abstract": "Retinal ganglion cells (RGCs), which transfer information from the eye to the brain, are heterogeneous in structure and function, but developmental studies have generally treated them as a single group. Here, we investigate the development of RGC axonal and dendritic arbors using four mouse transgenic lines in which nonoverlapping subsets of RGCs are indelibly labeled with a fluorescent protein. Each subset has a distinct functional signature, size, and morphology. Dendrites of each subset are restricted to specific sublaminae within the inner plexiform layer in adulthood, but acquire their restriction in different ways: one subset has lamina-restricted dendrites from an early postnatal stage, a second remodels an initially diffuse pattern, and two others develop stepwise. Axons of each subset arborize in discrete laminar zones within the lateral geniculate nucleus or superior colliculus, demonstrating previously unrecognized subdivisions of retinorecipient layers. As is the case for dendrites, lamina-restricted axonal projections of RGC subsets develop in different ways. For example, while axons of two RGC subsets arborize in definite zones of the superior colliculus from an early postnatal stage, axons of another subset initially occupy a deep layer, then translocate to a narrow subpial zone. Together, these results show that RGC subsets use a variety of strategies to construct lamina-restricted dendritic and axonal arbors. Taking account of these subtype-specific features will facilitate identification of the molecules and cells that regulate arbor formation.", "date": "2010-01-27", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "30", "number": "4", "publisher": "Society for Neuroscience", "pagerange": "1452-1462", "id_number": "CaltechAUTHORS:20170405-065327156", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-065327156", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Bushrod H. Campbell and Adah F. Hall Charity Fund" }, { "agency": "Damon Runyon Cancer Research Foundation" }, { "agency": "Merck" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1523/JNEUROSCI.4779-09.2010", "pmcid": "PMC2822471", "primary_object": { "basename": "1452.full.pdf", "url": "https://authors.library.caltech.edu/records/aw4n6-tbm58/files/1452.full.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Kim, In-Jung; Zhang, Yifeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f6b4y-p7d54", "eprint_id": 14370, "eprint_status": "archive", "datestamp": "2023-08-21 20:51:30", "lastmod": "2023-10-18 16:48:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Geffen-M-N", "name": { "family": "Geffen", "given": "Maria N." } }, { "id": "Broome-B-M", "name": { "family": "Broome", "given": "Bede M." } }, { "id": "Laurent-G", "name": { "family": "Laurent", "given": "Gilles" }, "orcid": "0000-0002-2296-114X" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Neural encoding of rapidly fluctuating odors", "ispublished": "pub", "full_text_status": "public", "keywords": "Signaling; sysneuro", "note": "\u00a9 2009 Elsevier. \n\nAccepted 21 January 2009. Published: February 25, 2009. Available online 25 February 2009. \n\nThe authors thank members of the Laurent and Marcelo Magnasco groups for lively discussion and the group of Nate Lewis for guidance on electronic noses. This work was supported by a HHMI pre-doctoral fellowship (M.N.G.), Burroughs Wellcome Career at the Scientific Interface Award (M.N.G.), a pre-doctoral NRSA (B.M.B.), the National Institute of Deafness and Communication Disorders (G.L.), and the Gordon and Betty Moore Foundation (M.M.).\n\nSupplemental Material - PIIS0896627309000889.mmc1.pdf
", "abstract": "Olfactory processing in the insect antennal lobe is a highly dynamic process, yet it has been studied primarily with static step stimuli. To approximate the rapid odor fluctuations encountered in nature, we presented flickering \"white-noise\" odor stimuli to the antenna of the locust and recorded spike trains from antennal lobe projection neurons (PNs). The responses varied greatly across PNs and across odors for the same PN. Surprisingly, this diversity across the population was highly constrained, and most responses were captured by a quantitative model with just 3 parameters. Individual PNs were found to communicate odor information at rates up to ~4 bits/s. A small group of PNs was sufficient to provide an accurate representation of the dynamic odor time course, whose quality was maximal for fluctuations of frequency ~0.8 Hz. We develop a simple model for the encoding of dynamic odor stimuli that accounts for many prior observations on the population response.", "date": "2009-02-26", "date_type": "published", "publication": "Neuron", "volume": "61", "number": "4", "publisher": "Elsevier", "pagerange": "570-586", "id_number": "CaltechAUTHORS:20090605-114631504", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090605-114631504", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs Wellcome" }, { "agency": "NIH" }, { "agency": "National Institute on Deafness and Communication Disorders" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.neuron.2009.01.021", "primary_object": { "basename": "PIIS0896627309000889.mmc1.pdf", "url": "https://authors.library.caltech.edu/records/f6b4y-p7d54/files/PIIS0896627309000889.mmc1.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Geffen, Maria N.; Broome, Bede M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/c0mmc-xcn33", "eprint_id": 75716, "eprint_status": "archive", "datestamp": "2023-08-20 00:49:48", "lastmod": "2023-10-25 15:14:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Soucy-E-R", "name": { "family": "Soucy", "given": "Edward R." }, "orcid": "0000-0002-1187-5596" }, { "id": "Albeanu-D-F", "name": { "family": "Albeanu", "given": "Dinu F." } }, { "id": "Fantana-A-L", "name": { "family": "Fantana", "given": "Antoniu L." } }, { "id": "Murthy-V-N", "name": { "family": "Murthy", "given": "Venkatesh N." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Precision and diversity in an odor map on the olfactory bulb", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Nature America, Inc. \n\nReceived 24 September 2008; Accepted 18 December 2008; Published online 18 January 2009. \n\nWe thank P. Mombaerts for providing M72-EGFP mice and R. Wilson and N. Uchida for healthy critiques. \n\nAuthor Contributions: E.R.S., D.F.A., V.N.M. and M.M. designed the study, E.R.S., D.F.A. and A.L.F. performed experiments and analysis, E.R.S., D.F.A. and M.M. wrote the manuscript, and V.N.M. and M.M. supervised the project.\n\nSupplemental Material - nn.2262-S1.pdf
", "abstract": "We explored the map of odor space created by glomeruli on the olfactory bulb of both rat and mouse. Identified glomeruli could be matched across animals by their response profile to hundreds of odors. Their layout in different individuals varied by only ~ 1 glomerular spacing, corresponding to a precision of 1 part in 1,000. Across species, mouse and rat share many glomeruli with apparently identical odor tuning, arranged in a similar layout. In mapping the position of a glomerulus to its odor tuning, we found only a coarse relationship with a precision of ~ 5 spacings. No chemotopic order was apparent on a finer scale and nearby glomeruli were almost as diverse in their odor sensitivity as distant ones. This local diversity of sensory tuning stands in marked distinction from other brain maps. Given the reliable placement of the glomeruli, it represents a feature, not a flaw, of the olfactory bulb.", "date": "2009-02", "date_type": "published", "publication": "Nature Neuroscience", "volume": "12", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "210-220", "id_number": "CaltechAUTHORS:20170405-072611037", "issn": "1097-6256", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-072611037", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/nn.2262", "primary_object": { "basename": "nn.2262-S1.pdf", "url": "https://authors.library.caltech.edu/records/c0mmc-xcn33/files/nn.2262-S1.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Soucy, Edward R.; Albeanu, Dinu F.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z11ny-w1936", "eprint_id": 75702, "eprint_status": "archive", "datestamp": "2023-08-20 00:12:59", "lastmod": "2023-10-25 15:13:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lefebvre-J-L", "name": { "family": "Lefebvre", "given": "Julie L." } }, { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Wang-Xiaozhong", "name": { "family": "Wang", "given": "Xiaozhong" } }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "\u03b3-Protocadherins regulate neuronal survival but are dispensable for circuit formation in retina", "ispublished": "pub", "full_text_status": "public", "keywords": "Apoptosis, Interneuron, Laminar specificity, Receptive field, Mouse", "note": "\u00a9 2008 Company of Biologists. \n\nAccepted September 24, 2008. \n\nWe thank Joshua Weiner for sharing data. This work was supported by grants from the National Institutes of Health to M.M. and J.R.S, a NARSAD Young Investigator award to J.L., and Damon Runyon Cancer Research Foundation Fellowship to Y.-F.Z.\n\nPublished - 4141.full.pdf
Supplemental Material - 027912-figS1.pdf
Supplemental Material - 027912-figS2.pdf
Supplemental Material - 027912-figS3.pdf
", "abstract": "Twenty-two tandemly arranged protocadherin-\u03b3 (Pcdh-\u03b3) genes encode transmembrane proteins with distinct cadherin-related extracellular domains and a common intracellular domain. Genetic studies have implicated Pcdh-\u03b3 genes in the regulation of neuronal survival and synapse formation. Because mice lacking the Pcdh-\u03b3 cluster die perinatally, we generated conditional mutants to analyze roles of Pcdh-\u03b3 genes in the development and function of neural circuits. Retina-specific deletion of Pcdh-\u03b3s led to accentuation of naturally occurring death of interneurons and retinal ganglion cells (RGCs) during the first two postnatal weeks. Nonetheless, many neuronal subtypes formed lamina-specific arbors. Blocking apoptosis by deletion of the pro-apoptotic gene Bax showed that even neurons destined to die formed qualitatively and quantitatively appropriate connections. Moreover, electrophysiological analysis indicated that processing of visual information was largely normal in the absence of Pcdh-\u03b3 genes. These results suggest that Pcdh-\u03b3 genes are dispensable for elaboration of specific connections in retina, but play a primary role in sculpting neuronal populations to appropriate sizes or proportions during the period of naturally occurring cell death.", "date": "2008-12-15", "date_type": "published", "publication": "Development", "volume": "135", "number": "24", "publisher": "Company of Biologists", "pagerange": "4141-4151", "id_number": "CaltechAUTHORS:20170404-141850023", "issn": "0950-1991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-141850023", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Brain and Behavior Research Foundation" }, { "agency": "Damon Runyon Cancer Research Foundation" } ] }, "doi": "10.1242/dev.027912", "pmcid": "PMC2644426", "primary_object": { "basename": "027912-figS1.pdf", "url": "https://authors.library.caltech.edu/records/z11ny-w1936/files/027912-figS1.pdf" }, "related_objects": [ { "basename": "027912-figS2.pdf", "url": "https://authors.library.caltech.edu/records/z11ny-w1936/files/027912-figS2.pdf" }, { "basename": "027912-figS3.pdf", "url": "https://authors.library.caltech.edu/records/z11ny-w1936/files/027912-figS3.pdf" }, { "basename": "4141.full.pdf", "url": "https://authors.library.caltech.edu/records/z11ny-w1936/files/4141.full.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Lefebvre, Julie L.; Zhang, Yifeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/54dj2-f9024", "eprint_id": 75703, "eprint_status": "archive", "datestamp": "2023-08-22 13:31:07", "lastmod": "2023-10-25 15:13:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gollisch-T", "name": { "family": "Gollisch", "given": "Tim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Modeling convergent ON and OFF pathways in the early visual system", "ispublished": "pub", "full_text_status": "public", "keywords": "LN model extension; Multiple pathways; Spike-triggered analysis; Retina ON\u2013OFF ganglion cells", "note": "\u00a9 2008 The Author(s). This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. \n\nReceived: 19 February 2008 / Accepted: 25 August 2008. First Online: 15 November 2008. \n\nThis work was supported by grants from the National Eye Institute (M.M.) and the Human Frontier Science Program Organization (T.G.) and by the Max Planck Society.\n\nPublished - art_3A10.1007_2Fs00422-008-0252-y.pdf
", "abstract": "For understanding the computation and function of single neurons in sensory systems, one needs to investigate how sensory stimuli are related to a neuron's response and which biological mechanisms underlie this relationship. Mathematical models of the stimulus\u2013response relationship have proved very useful in approaching these issues in a systematic, quantitative way. A starting point for many such analyses has been provided by phenomenological \"linear\u2013nonlinear\" (LN) models, which comprise a linear filter followed by a static nonlinear transformation. The linear filter is often associated with the neuron's receptive field. However, the structure of the receptive field is generally a result of inputs from many presynaptic neurons, which may form parallel signal processing pathways. In the retina, for example, certain ganglion cells receive excitatory inputs from ON-type as well as OFF-type bipolar cells. Recent experiments have shown that the convergence of these pathways leads to intriguing response characteristics that cannot be captured by a single linear filter. One approach to adjust the LN model to the biological circuit structure is to use multiple parallel filters that capture ON and OFF bipolar inputs. Here, we review these new developments in modeling neuronal responses in the early visual system and provide details about one particular technique for obtaining the required sets of parallel filters from experimental data.", "date": "2008-11", "date_type": "published", "publication": "Biological Cybernetics", "volume": "99", "number": "4-5", "publisher": "Springer", "pagerange": "263-278", "id_number": "CaltechAUTHORS:20170404-143539566", "issn": "0340-1200", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-143539566", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Eye Institute" }, { "agency": "Human Frontier Science Program" }, { "agency": "Max Planck Society" }, { "agency": "NIH" } ] }, "doi": "10.1007/s00422-008-0252-y", "pmcid": "PMC2784078", "primary_object": { "basename": "art_3A10.1007_2Fs00422-008-0252-y.pdf", "url": "https://authors.library.caltech.edu/records/54dj2-f9024/files/art_3A10.1007_2Fs00422-008-0252-y.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Gollisch, Tim and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/359cn-5jq07", "eprint_id": 75720, "eprint_status": "archive", "datestamp": "2023-08-22 13:03:41", "lastmod": "2023-10-25 15:14:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fantana-A-L", "name": { "family": "Fantana", "given": "Antoniu L." } }, { "id": "Soucy-E-R", "name": { "family": "Soucy", "given": "Edward R." }, "orcid": "0000-0002-1187-5596" }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Rat Olfactory Bulb Mitral Cells Receive Sparse Glomerular Inputs", "ispublished": "pub", "full_text_status": "public", "keywords": "CELLBIO; MOLNEURO", "note": "\u00a9 2008 Elsevier Inc. \n\nAccepted 28 July 2008, Available online 10 September; 2008; Published: September 10, 2008. \n\nWe thank Catherine Dulac, John Kauer, Venki Murthy, Clay Reid, Carla Shatz, Rachel Wilson, and members of the Meister lab for support and many helpful discussions.\n\nSupplemental Material - mmc1.pdf
", "abstract": "Center-surround receptive fields are a fundamental unit of brain organization. It has been proposed that olfactory bulb mitral cells exhibit this functional circuitry, with excitation from one glomerulus and inhibition from a broad field of glomeruli within reach of the lateral dendrites. We investigated this hypothesis using a combination of in vivo intrinsic imaging, single-unit recording, and a large panel of odors. Assuming a broad inhibitory field, a mitral cell would be influenced by >100 contiguous glomeruli and should respond to many odors. Instead, the observed response rate was an order of magnitude lower. A quantitative model indicates that mitral cell responses can be explained by just a handful of glomeruli. These glomeruli are spatially dispersed on the bulb and represent a broad range of odor sensitivities. We conclude that mitral cells do not have center-surround receptive fields. Instead, each mitral cell performs a specific computation combining a small and diverse set of glomerular inputs.", "date": "2008-09-11", "date_type": "published", "publication": "Neuron", "volume": "59", "number": "5", "publisher": "Elsevier", "pagerange": "802-814", "id_number": "CaltechAUTHORS:20170405-080226964", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-080226964", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.neuron.2008.07.039", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/359cn-5jq07/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Fantana, Antoniu L.; Soucy, Edward R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z5729-j1f98", "eprint_id": 75715, "eprint_status": "archive", "datestamp": "2023-08-22 12:28:53", "lastmod": "2023-10-25 15:14:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "\u00d6lveczky-B-P", "name": { "family": "\u00d6lveczky", "given": "Bence P." } }, { "id": "Manu-M", "name": { "family": "Manu", "given": "Mihai" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "A Retinal Circuit That Computes Object Motion", "ispublished": "pub", "full_text_status": "public", "keywords": "neural coding; eye movements; motion processing; computational model; neural circuit; inhibition", "note": "\u00a9 2008 Society for Neuroscience. Beginning six months after publication the Work will be made freely available to the public on SfN's website to copy, distribute, or display under a Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived Sept. 13, 2007; revised April 1, 2008; accepted April 24, 2008. \n\nThis work was supported by a National Research Service Award postdoctoral fellowship (S.A.B.), a Harvard Junior Fellowship (B.P.\u00d6.), and grants from the National Institutes of Health (S.A.B., M. Meister).\n\nPublished - 6807.full.pdf
", "abstract": "Certain ganglion cells in the retina respond sensitively to differential motion between the receptive field center and surround, as produced by an object moving over the background, but are strongly suppressed by global image motion, as produced by the observer's head or eye movements. We investigated the circuit basis for this object motion sensitive (OMS) response by recording intracellularly from all classes of retinal interneurons while simultaneously recording the spiking output of many ganglion cells. Fast, transient bipolar cells respond linearly to motion in the receptive field center. The synaptic output from their terminals is rectified and then pooled by the OMS ganglion cell. A type of polyaxonal amacrine cell is driven by motion in the surround, again via pooling of rectified inputs, but from a different set of bipolar cell terminals. By direct intracellular current injection, we found that these polyaxonal amacrine cells selectively suppress the synaptic input of OMS ganglion cells. A quantitative model of these circuit elements and their interactions explains how an important visual computation is accomplished by retinal neurons and synapses.", "date": "2008-07-02", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "28", "number": "27", "publisher": "Society for Neuroscience", "pagerange": "6807-6817", "id_number": "CaltechAUTHORS:20170405-071558162", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-071558162", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship" }, { "agency": "Harvard University" } ] }, "doi": "10.1523/JNEUROSCI.4206-07.2008", "primary_object": { "basename": "6807.full.pdf", "url": "https://authors.library.caltech.edu/records/z5729-j1f98/files/6807.full.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Baccus, Stephen A.; \u00d6lveczky, Bence P.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/khzqm-d3g71", "eprint_id": 75731, "eprint_status": "archive", "datestamp": "2023-08-19 22:43:07", "lastmod": "2023-10-25 15:15:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Albeanu-D-F", "name": { "family": "Albeanu", "given": "Dinu F." } }, { "id": "Soucy-E-R", "name": { "family": "Soucy", "given": "Edward" }, "orcid": "0000-0002-1187-5596" }, { "id": "Sato-T-F", "name": { "family": "Sato", "given": "Tomokazu F." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Murthy-V-N", "name": { "family": "Murthy", "given": "Venkatesh N." } } ] }, "title": "LED Arrays as Cost Effective and Efficient Light Sources for Widefield Microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Albeanu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived September 21, 2007; Accepted April 3, 2008; Published May 14, 2008. \n\nSupport was only from start up funds provided by Harvard University to the senior authors. These funds have no restrictions and the University does not direct the research in any way. \n\nAuthor Contributions: Conceived and designed the experiments: VM MM DA ES. Performed the experiments: DA ES. Analyzed the data: DA TS. Contributed reagents/materials/analysis tools: VM MM. Wrote the paper: VM MM DA ES TS. \n\nThe authors have declared that no competing interests exist.\n\nPublished - journal.pone.0002146.PDF
", "abstract": "New developments in fluorophores as well as in detection methods have fueled the rapid growth of optical imaging in the life sciences. Commercial widefield microscopes generally use arc lamps, excitation/emission filters and shutters for fluorescence imaging. These components can be expensive, difficult to maintain and preclude stable illumination. Here, we describe methods to construct inexpensive and easy-to-use light sources for optical microscopy using light-emitting diodes (LEDs). We also provide examples of its applicability to biological fluorescence imaging.", "date": "2008-05-14", "date_type": "published", "publication": "PLoS ONE", "volume": "3", "number": "5", "publisher": "Public Library of Science", "pagerange": "Art. No. e2146", "id_number": "CaltechAUTHORS:20170405-101751665", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-101751665", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Harvard University" } ] }, "doi": "10.1371/journal.pone.0002146", "pmcid": "PMC2361193", "primary_object": { "basename": "journal.pone.0002146.PDF", "url": "https://authors.library.caltech.edu/records/khzqm-d3g71/files/journal.pone.0002146.PDF" }, "resource_type": "article", "pub_year": "2008", "author_list": "Albeanu, Dinu F.; Soucy, Edward; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ga0vx-et608", "eprint_id": 75728, "eprint_status": "archive", "datestamp": "2023-08-19 22:25:35", "lastmod": "2023-10-25 15:15:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kim-In-Jung", "name": { "family": "Kim", "given": "In-Jung" } }, { "id": "Zhang-Yifeng", "name": { "family": "Zhang", "given": "Yifeng" } }, { "id": "Yamagata-Masahito", "name": { "family": "Yamagata", "given": "Masahito" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Sanes-J-R", "name": { "family": "Sanes", "given": "Joshua R." } } ] }, "title": "Molecular identification of a retinal cell type that responds to upward motion", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Nature Publishing Group. \n\nReceived 13 September; accepted 24 January 2008. \n\nWe thank S. Dymecki for FlpE mice, A. Basbaum for WGA mice and U. Dr\u00e4ger, S. Haddad, B. Howell, A. Koizumi, T. Kummer, J. Livet, D. Pelusi and E. Soucy for advice and assistance. This work was supported by grants from the National Institutes of Health to M.M. and J.R.S., a Merck Award and a Bushrod H. Campbell and Adah F. Hall Charity Fund Fellowship to I.J.K., and a Damon Runyon fellowship to Y.Z. \n\nAuthor Contributions: I.J.K., Y.Z., M.Y., M.M. and J.R.S. conceived the experiments. I.J.K and M.Y. performed molecular and histological experiments. Y.Z. performed physiological experiments. Y.Z. and M.M. performed computational analysis. M.M. and J.R.S. wrote the paper.\n\nSupplemental Material - nature06739-s1.pdf
", "abstract": "The retina contains complex circuits of neurons that extract salient information from visual inputs. Signals from photoreceptors are processed by retinal interneurons, integrated by retinal ganglion cells (RGCs) and sent to the brain by RGC axons. Distinct types of RGC respond to different visual features, such as increases or decreases in light intensity (ON and OFF cells, respectively), colour or moving objects1, 2, 3, 4, 5. Thus, RGCs comprise a set of parallel pathways from the eye to the brain. The identification of molecular markers for RGC subsets will facilitate attempts to correlate their structure with their function, assess their synaptic inputs and targets, and study their diversification. Here we show, by means of a transgenic marking method, that junctional adhesion molecule B (JAM-B) marks a previously unrecognized class of OFF RGCs in mice. These cells have asymmetric dendritic arbors aligned in a dorsal-to-ventral direction across the retina. Their receptive fields are also asymmetric and respond selectively to stimuli moving in a soma-to-dendrite direction; because the lens reverses the image of the world on the retina, these cells detect upward motion in the visual field. Thus, JAM-B identifies a unique population of RGCs in which structure corresponds remarkably to function.", "date": "2008-03-27", "date_type": "published", "publication": "Nature", "volume": "452", "number": "7186", "publisher": "Nature Publishing Group", "pagerange": "478-482", "id_number": "CaltechAUTHORS:20170405-094857083", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-094857083", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Merck" }, { "agency": "Hall Charity Fund" }, { "agency": "Damon Runyon Cancer Research Foundation" } ] }, "doi": "10.1038/nature06739", "primary_object": { "basename": "nature06739-s1.pdf", "url": "https://authors.library.caltech.edu/records/ga0vx-et608/files/nature06739-s1.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Kim, In-Jung; Zhang, Yifeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sa23b-wj235", "eprint_id": 75712, "eprint_status": "archive", "datestamp": "2023-08-19 22:12:18", "lastmod": "2023-10-25 15:14:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gollisch-T", "name": { "family": "Gollisch", "given": "Tim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Rapid Neural Coding in the Retina with Relative Spike Latencies", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2008 American Association for the Advancement of Science. \n\n23 August 2007; accepted 11 December 2007.", "abstract": "Natural vision is a highly dynamic process. Frequent body, head, and eye movements constantly bring new images onto the retina for brief periods, challenging our understanding of the neural code for vision. We report that certain retinal ganglion cells encode the spatial structure of a briefly presented image in the relative timing of their first spikes. This code is found to be largely invariant to stimulus contrast and robust to noisy fluctuations in response latencies. Mechanistically, the observed response characteristics result from different kinetics in two retinal pathways (\"ON\" and \"OFF\") that converge onto ganglion cells. This mechanism allows the retina to rapidly and reliably transmit new spatial information with the very first spikes emitted by a neural population.", "date": "2008-02-22", "date_type": "published", "publication": "Science", "volume": "319", "number": "5866", "publisher": "American Association for the Advancement of Science", "pagerange": "1108-1111", "id_number": "CaltechAUTHORS:20170405-064514516", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-064514516", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.1149639", "resource_type": "article", "pub_year": "2008", "author_list": "Gollisch, Tim and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bpxdj-75n40", "eprint_id": 75725, "eprint_status": "archive", "datestamp": "2023-08-19 21:42:14", "lastmod": "2023-10-25 15:14:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Burr-D", "name": { "family": "Burr", "given": "David" } }, { "id": "Pitkow-X", "name": { "family": "Pitkow", "given": "Xaq" } }, { "id": "Sompolinsky-H", "name": { "family": "Sompolinsky", "given": "Haim" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "A Neural Computation for Visual Acuity in the Presence of Eye Movements", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 Pitkow et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived March 27, 2007; Accepted November 9, 2007; Published December 27, 2007. \n\nThe authors thank Ralf Engbert and Reinhold Kliegl for their eye movement data, and Daniel Fisher, Maneesh Sahani, and an anonymous referee for helpful conversations and suggestions. \n\nAuthor Contributions: XP, HS, and MM conceived and designed the experiments, analyzed the data, and wrote the paper. XP performed the experiments. \n\nXP and MM were supported by a National Institutes of Health grant. The work of HS was partially supported by a grant of the US-Israel Binational Science Foundation. \n\nThe authors have declared that no competing interests exist.\n\nPublished - journal.pbio.0050331.PDF
Supplemental Material - journal.pbio.0050331.sd001.PDF
", "abstract": "Humans can distinguish visual stimuli that differ by features the size of only a few photoreceptors. This is possible despite the incessant image motion due to fixational eye movements, which can be many times larger than the features to be distinguished. To perform well, the brain must identify the retinal firing patterns induced by the stimulus while discounting similar patterns caused by spontaneous retinal activity. This is a challenge since the trajectory of the eye movements, and consequently, the stimulus position, are unknown. We derive a decision rule for using retinal spike trains to discriminate between two stimuli, given that their retinal image moves with an unknown random walk trajectory. This algorithm dynamically estimates the probability of the stimulus at different retinal locations, and uses this to modulate the influence of retinal spikes acquired later. Applied to a simple orientation-discrimination task, the algorithm performance is consistent with human acuity, whereas naive strategies that neglect eye movements perform much worse. We then show how a simple, biologically plausible neural network could implement this algorithm using a local, activity-dependent gain and lateral interactions approximately matched to the statistics of eye movements. Finally, we discuss evidence that such a network could be operating in the primary visual cortex.", "date": "2007-12-27", "date_type": "published", "publication": "PLoS Biology", "volume": "5", "number": "12", "publisher": "Public Library of Science", "pagerange": "Art. No. e331", "id_number": "CaltechAUTHORS:20170405-083802627", "issn": "1545-7885", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-083802627", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Binational Science Foundation (USA-Israel)" } ] }, "doi": "10.1371/journal.pbio.0050331", "pmcid": "PMC2222970", "primary_object": { "basename": "journal.pbio.0050331.PDF", "url": "https://authors.library.caltech.edu/records/bpxdj-75n40/files/journal.pbio.0050331.PDF" }, "related_objects": [ { "basename": "journal.pbio.0050331.sd001.PDF", "url": "https://authors.library.caltech.edu/records/bpxdj-75n40/files/journal.pbio.0050331.sd001.PDF" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Burr, David; Pitkow, Xaq; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9kwym-t3p88", "eprint_id": 75718, "eprint_status": "archive", "datestamp": "2023-08-22 10:29:48", "lastmod": "2023-10-25 15:14:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "\u00d6lveczky-B-P", "name": { "family": "\u00d6lveczky", "given": "Bence P." } }, { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Retinal Adaptation to Object Motion", "ispublished": "pub", "full_text_status": "public", "keywords": "SYSNEURO; CELLBIO; SIGNALING", "note": "\u00a9 2007 Elsevier Inc. \n\nReceived 12 January 2007, Revised 14 May 2007, Accepted 26 September 2007, Available online 21 November 2007; Published: November 20, 2007. \n\nWe thank Dr Mihai Manu for help with bipolar cell recordings. This work was supported by the Harvard Society of Fellows (B.P.\u00d6.), an NRSA postdoctoral fellowship (S.A.B.), and grants from the NIH (M.M.).\n\nAccepted Version - nihms34816.pdf
", "abstract": "Due to fixational eye movements, the image on the retina is always in motion, even when one views a stationary scene. When an object moves within the scene, the corresponding patch of retina experiences a different motion trajectory than the surrounding region. Certain retinal ganglion cells respond selectively to this condition, when the motion in the cell's receptive field center is different from that in the surround. Here we show that this response is strongest at the very onset of differential motion, followed by gradual adaptation with a time course of several seconds. Different subregions of a ganglion cell's receptive field can adapt independently. The circuitry responsible for differential motion adaptation lies in the inner retina. Several candidate mechanisms were tested, and the adaptation most likely results from synaptic depression at the synapse from bipolar to ganglion cell. Similar circuit mechanisms may act more generally to emphasize novel features of a visual stimulus.", "date": "2007-11-21", "date_type": "published", "publication": "Neuron", "volume": "56", "number": "4", "publisher": "Elsevier", "pagerange": "689-700", "id_number": "CaltechAUTHORS:20170405-073838107", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-073838107", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Harvard Society of Fellows" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1016/j.neuron.2007.09.030", "pmcid": "PMC2117331", "primary_object": { "basename": "nihms34816.pdf", "url": "https://authors.library.caltech.edu/records/9kwym-t3p88/files/nihms34816.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "\u00d6lveczky, Bence P.; Baccus, Stephen A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hay5f-h3631", "eprint_id": 75701, "eprint_status": "archive", "datestamp": "2023-08-19 20:26:38", "lastmod": "2023-10-25 15:13:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Viney-T-J", "name": { "family": "Viney", "given": "Tim James" } }, { "id": "Balint-K", "name": { "family": "Balint", "given": "Kamill" } }, { "id": "Hillier-D", "name": { "family": "Hillier", "given": "Daniel" } }, { "id": "Siegert-S", "name": { "family": "Siegert", "given": "Sandra" } }, { "id": "Boldogkoi-Z", "name": { "family": "Boldogkoi", "given": "Zsolt" } }, { "id": "Enquist-L-W", "name": { "family": "Enquist", "given": "Lynn W." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Cepko-C-L", "name": { "family": "Cepko", "given": "Constance L." } }, { "id": "Roska-B", "name": { "family": "Roska", "given": "Botond" } } ] }, "title": "Local Retinal Circuits of Melanopsin-Containing Ganglion Cells Identified by Transsynaptic Viral Tracing", "ispublished": "pub", "full_text_status": "public", "keywords": "SYSNEURO", "note": "\u00a9 2007 Elsevier Under an Elsevier user license. \n\nReceived 11 January 2007, Revised 28 April 2007, Accepted 30 April 2007, Available online 24 May 2007Published online: May 24, 2007. \n\nWe are grateful for the assistance of Z. Springer and B. Gross Scherf. We thank F. Albeanu for his advice on building the two-photon microscope, F. Engert for providing us with the imaging software Tango, and P. Caroni for his comments on the paper. This study was supported by Office of Naval Research Multidisciplinary University Research Initiative [ONR MURI] and Naval International Cooperative Opportunities in Science and Technology Program [NICOP] grants, a Marie Curie Excellence Grant, a Human Frontier Science Program [HFSP] Young Investigator grant, and Friedrich Miescher Institute funds to B.R. I. Provencio kindly provided the melanopsin antibody. B.W. Banfield kindly provided PRV 614. Viral infections, electrophysiological recordings, and immunohistochemistry have been done at both Harvard and the Friedrich Miescher Institute. Two-photon time-lapse imaging, automatic confocal scanning, and automated image analysis were done at the Friedrich Miescher Institute. Membrane-bound-GFP-expressing PRV was developed at University of Szeged.\n\nSupplemental Material - mmc1.pdf
Supplemental Material - mmc2.mov
Supplemental Material - mmc3.mov
", "abstract": "Intrinsically photosensitive melanopsin-containing retinal ganglion cells (ipRGCs) control important physiological processes, including the circadian rhythm, the pupillary reflex, and the suppression of locomotor behavior (reviewed in [1]). ipRGCs are also activated by classical photoreceptors, the rods and cones, through local retinal circuits 2 ; 3. ipRGCs can be transsynaptically labeled through the pupillary-reflex circuit with the derivatives of the Bartha strain of the alphaherpesvirus pseudorabies virus(PRV) 4 ; 5 that express GFP 6; 7; 8; 9; 10; 11 ; 12. Bartha-strain derivatives spread only in the retrograde direction [13]. There is evidence that infected cells function normally for a while during GFP expression [7]. Here we combine transsynaptic PRV labeling, two-photon laser microscopy, and electrophysiological techniques to trace the local circuit of different ipRGC subtypes in the mouse retina and record light-evoked activity from the transsynaptically labeled ganglion cells. First, we show that ipRGCs are connected by monostratified amacrine cells that provide strong inhibition from classical-photoreceptor-driven circuits. Second, we show evidence that dopaminergic interplexiform cells are synaptically connected to ipRGCs. The latter finding provides a circuitry link between light\u2013dark adaptation and ipRGC function.", "date": "2007-06-05", "date_type": "published", "publication": "Current Biology", "volume": "17", "number": "11", "publisher": "Cell Press", "pagerange": "981-988", "id_number": "CaltechAUTHORS:20170404-140543270", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-140543270", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Office of Naval Research (ONR)" }, { "agency": "Naval International Cooperative Opportunities in Science and Technology Program (NICOP)" }, { "agency": "Marie Curie Fellowship" }, { "agency": "Human Frontier Science Program" }, { "agency": "Friedrich Miescher Institute" } ] }, "doi": "10.1016/j.cub.2007.04.058", "primary_object": { "basename": "mmc2.mov", "url": "https://authors.library.caltech.edu/records/hay5f-h3631/files/mmc2.mov" }, "related_objects": [ { "basename": "mmc3.mov", "url": "https://authors.library.caltech.edu/records/hay5f-h3631/files/mmc3.mov" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/hay5f-h3631/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Viney, Tim James; Balint, Kamill; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3ma24-1jm96", "eprint_id": 75724, "eprint_status": "archive", "datestamp": "2023-08-19 19:50:02", "lastmod": "2023-10-20 22:15:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Geffen-M-N", "name": { "family": "Geffen", "given": "Maria Neimark" } }, { "id": "de-Vries-S-E-J", "name": { "family": "de Vries", "given": "Saskia E. J" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 Geffen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived June 20, 2006; Accepted December 28, 2006; Published March 6, 2007. \n\nWe are grateful for many discussions with Haim Sompolinsky, Daniel Fisher, Stephen Baccus, Bence \u00d6lveczky, and members of the Meister laboratory. \n\nAuthor Contributions: MNG, SEJdV, and MM conceived and designed the experiments. MNG and SEJdV performed the experiments. MNG, SEJdV, and MM analyzed the data. MNG and MM wrote the paper. \n\nThe work was supported by predoctoral fellowships from the Howard Hughes Medical Institute (MNG) and the National Science Foundation (SEJDV), and grants EY10020 and EY14737 from the National Eye Institute (MM). \n\nThe authors have declared that no competing interests exist.\n\nPublished - journal.pbio.0050065.PDF
Erratum - journal.pbio.0050136.pdf
Erratum - journal.pbio.0050188.pdf
", "abstract": "Retinal ganglion cells are commonly classified as On-center or Off-center depending on whether they are excited predominantly by brightening or dimming within the receptive field. Here we report that many ganglion cells in the salamander retina can switch from one response type to the other, depending on stimulus events far from the receptive field. Specifically, a shift of the peripheral image\u2014as produced by a rapid eye movement\u2014causes a brief transition in visual sensitivity from Off-type to On-type for approximately 100 ms. We show that these ganglion cells receive inputs from both On and Off bipolar cells, and the Off inputs are normally dominant. The peripheral shift strongly modulates the strength of these two inputs in opposite directions, facilitating the On pathway and suppressing the Off pathway. Furthermore, we identify certain wide-field amacrine cells that contribute to this modulation. Depolarizing such an amacrine cell affects nearby ganglion cells in the same way as the peripheral image shift, facilitating the On inputs and suppressing the Off inputs. This study illustrates how inhibitory interneurons can rapidly gate the flow of information within a circuit, dramatically altering the behavior of the principal neurons in the course of a computation.", "date": "2007-03-06", "date_type": "published", "publication": "PLoS Biology", "volume": "5", "number": "3", "publisher": "Public Library of Science", "pagerange": "Art. No. e65", "id_number": "CaltechAUTHORS:20170405-082620129", "issn": "1545-7885", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-082620129", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" }, { "agency": "NIH", "grant_number": "EY10020" }, { "agency": "NIH", "grant_number": "EY14737" }, { "agency": "National Eye Institute" } ] }, "doi": "10.1371/journal.pbio.0050065", "pmcid": "PMC1808116", "primary_object": { "basename": "journal.pbio.0050065.PDF", "url": "https://authors.library.caltech.edu/records/3ma24-1jm96/files/journal.pbio.0050065.PDF" }, "related_objects": [ { "basename": "journal.pbio.0050136.pdf", "url": "https://authors.library.caltech.edu/records/3ma24-1jm96/files/journal.pbio.0050136.pdf" }, { "basename": "journal.pbio.0050188.pdf", "url": "https://authors.library.caltech.edu/records/3ma24-1jm96/files/journal.pbio.0050188.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Geffen, Maria Neimark; de Vries, Saskia E. J; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hcttx-t0a72", "eprint_id": 75727, "eprint_status": "archive", "datestamp": "2023-08-19 16:05:16", "lastmod": "2023-10-25 15:15:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hosoya-Toshihiko", "name": { "family": "Hosoya", "given": "Toshihiko" } }, { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Dynamic predictive coding by the retina", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 Nature Publishing Group. \n\nReceived 5 September 2004; Accepted 27 April 2005. \n\nWe thank members of the Meister laboratory, H. Sompolinsky and D. Fisher for advice. This work was supported by grants from the National Eye Institute (M.M. and S.A.B.) and the Human Frontier Science Program (T.H.). \n\nAuthor Contributions T.H. and M.M. planned the study, T.H. and S.A.B. performed the experiments, and T.H. and M.M. completed the analysis and wrote the manuscript.\n\nSupplemental Material - nature03689-s1.pdf
", "abstract": "Retinal ganglion cells convey the visual image from the eye to the brain. They generally encode local differences in space and changes in time rather than the raw image intensity. This can be seen as a strategy of predictive coding, adapted through evolution to the average image statistics of the natural environment. Yet animals encounter many environments with visual statistics different from the average scene. Here we show that when this happens, the retina adjusts its processing dynamically. The spatio-temporal receptive fields of retinal ganglion cells change after a few seconds in a new environment. The changes are adaptive, in that the new receptive field improves predictive coding under the new image statistics. We show that a network model with plastic synapses can account for the large variety of observed adaptations.", "date": "2005-07-07", "date_type": "published", "publication": "Nature", "volume": "436", "number": "7047", "publisher": "Nature Publishing Group", "pagerange": "71-77", "id_number": "CaltechAUTHORS:20170405-093657286", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-093657286", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Eye Institute" }, { "agency": "Human Frontier Science Program" }, { "agency": "NIH" } ] }, "doi": "10.1038/nature03689", "primary_object": { "basename": "nature03689-s1.pdf", "url": "https://authors.library.caltech.edu/records/hcttx-t0a72/files/nature03689-s1.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Hosoya, Toshihiko; Baccus, Stephen A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9xhs6-v3q44", "eprint_id": 75717, "eprint_status": "archive", "datestamp": "2023-08-19 13:26:35", "lastmod": "2023-10-25 15:14:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Retina versus Cortex: Contrast Adaptation in Parallel Visual Pathways", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2004 Cell Press. \n\nAvailable online 7 April 2004.", "abstract": "Human vision adapts to the contrast of patterns by changing its sensitivity, but the origins of this perceptual adaptation have been disputed. In this issue of Neuron, Solomon et al. show that contrast adaptation in the primate arises mostly in the retina for the magnocellular pathway and mostly in the cortex for the parvocellular pathway. It appears that adaptation arises most strongly at sites that pool over many inputs.", "date": "2004-04-08", "date_type": "published", "publication": "Neuron", "volume": "42", "number": "1", "publisher": "Elsevier", "pagerange": "5-7", "id_number": "CaltechAUTHORS:20170405-073120186", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-073120186", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0896-6273(04)00187-4", "resource_type": "article", "pub_year": "2004", "author_list": "Baccus, Stephen A. and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zqns6-b8s02", "eprint_id": 75736, "eprint_status": "archive", "datestamp": "2023-08-19 12:04:03", "lastmod": "2023-10-25 15:15:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Smallwood-P-M", "name": { "family": "Smallwood", "given": "Philip M." } }, { "id": "\u00d6lveczky-B-P", "name": { "family": "\u00d6lveczky", "given": "Bence P." } }, { "id": "Williams-G-L", "name": { "family": "Williams", "given": "Gary L." } }, { "id": "Jacobs-G-H", "name": { "family": "Jacobs", "given": "Gerald H." } }, { "id": "Reese-B-E", "name": { "family": "Reese", "given": "Benjamin E." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Nathans-J", "name": { "family": "Nathans", "given": "Jeremy" } } ] }, "title": "Genetically engineered mice with an additional class of cone photoreceptors: Implications for the evolution of color vision", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2003 National Academy of Sciences. \n\nContributed by Jeremy Nathans, July 25, 2003. Published online before print September 19, 2003. \n\nWe thank the Johns Hopkins University Transgenic Core Laboratory for blastocyst injections, Ms. Jennifer Macke and Dr. Edward Soucy for assistance during the early phases of this work, Dr. Yanshu Wang for advice, and an anonymous reviewer for helpful comments. This work was supported by the c (P.M.S. and J.N.) and the National Eye Institute [B.P.\u00d6., M.M., G.H.J. (Grant EY002052), and B.E.R.].\n\nPublished - PNAS-2003-Smallwood-11706-11.pdf
", "abstract": "Among eutherian mammals, only primates possess trichromatic color vision. In Old World primates, trichromacy was made possible by a visual pigment gene duplication. In most New World primates, trichromacy is based on polymorphic variation in a single X-linked gene that produces, by random X inactivation, a patchy mosaic of spectrally distinct cone photoreceptors in heterozygous females. In the present work, we have modeled the latter strategy in a nonprimate by replacing the X-linked mouse green pigment gene with one encoding the human red pigment. In the mouse retina, the human red pigment seems to function normally, and heterozygous female mice express the human red and mouse green pigments at levels that vary between animals. Multielectrode array recordings from heterozygous female retinas reveal significant variation in the chromatic sensitivities of retinal ganglion cells. The data are consistent with a model in which these retinal ganglion cells draw their inputs indiscriminately from a coarse-grained mosaic of red and green cones. These observations support the ideas that (i) chromatic signals could arise from stochastic variation in inputs drawn nonselectively from red and green cones and (ii) tissue mosaicism due to X chromosome inactivation could be one mechanism for driving the evolution of CNS diversity.", "date": "2003-09-30", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "100", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "11706-11711", "id_number": "CaltechAUTHORS:20170405-113339851", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-113339851", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "EY002052" }, { "agency": "National Eye Institute" } ] }, "doi": "10.1073/pnas.1934712100", "pmcid": "PMC208822", "primary_object": { "basename": "PNAS-2003-Smallwood-11706-11.pdf", "url": "https://authors.library.caltech.edu/records/zqns6-b8s02/files/PNAS-2003-Smallwood-11706-11.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Smallwood, Philip M.; \u00d6lveczky, Bence P.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/njcny-aq569", "eprint_id": 75705, "eprint_status": "archive", "datestamp": "2023-08-19 11:28:13", "lastmod": "2023-10-25 15:13:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "\u00d6lveczky-B-P", "name": { "family": "\u00d6lveczky", "given": "Bence P." } }, { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Segregation of object and background motion in the retina", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2003 Nature Publishing Group. \n\nReceived 20 December 2002; Accepted 18 March 2003; Published online 11 May 2003. \n\nWe thank members of the Meister laboratory for advice; P. Cavanagh, F. Engert, V. Murthy and K. Nakayama for comments on the manuscript; and H. van der Steen for providing the eye movement data in Fig. 1b. This work was supported by a grant from NEI (M.M.) and NRSA (S.A.B.). \n\nThe authors declare no competing financial interests.\n\nSupplemental Material - nature01652-s1.pdf
Supplemental Material - nature01652-s2.pdf
Supplemental Material - nature01652-s3.pdf
", "abstract": "An important task in vision is to detect objects moving within a stationary scene. During normal viewing this is complicated by the presence of eye movements that continually scan the image across the retina, even during fixation. To detect moving objects, the brain must distinguish local motion within the scene from the global retinal image drift due to fixational eye movements. We have found that this process begins in the retina: a subset of retinal ganglion cells responds to motion in the receptive field centre, but only if the wider surround moves with a different trajectory. This selectivity for differential motion is independent of direction, and can be explained by a model of retinal circuitry that invokes pooling over nonlinear interneurons. The suppression by global image motion is probably mediated by polyaxonal, wide-field amacrine cells with transient responses. We show how a population of ganglion cells selective for differential motion can rapidly flag moving objects, and even segregate multiple moving objects.", "date": "2003-05-22", "date_type": "published", "publication": "Nature", "volume": "423", "number": "6938", "publisher": "Nature Publishing Group", "pagerange": "401-408", "id_number": "CaltechAUTHORS:20170404-152615141", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-152615141", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Eye Institute" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1038/nature01652", "primary_object": { "basename": "nature01652-s3.pdf", "url": "https://authors.library.caltech.edu/records/njcny-aq569/files/nature01652-s3.pdf" }, "related_objects": [ { "basename": "nature01652-s1.pdf", "url": "https://authors.library.caltech.edu/records/njcny-aq569/files/nature01652-s1.pdf" }, { "basename": "nature01652-s2.pdf", "url": "https://authors.library.caltech.edu/records/njcny-aq569/files/nature01652-s2.pdf" } ], "resource_type": "article", "pub_year": "2003", "author_list": "\u00d6lveczky, Bence P.; Baccus, Stephen A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/b8hqx-bxp74", "eprint_id": 75697, "eprint_status": "archive", "datestamp": "2023-08-19 10:57:56", "lastmod": "2023-10-25 15:13:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schnitzer-M-J", "name": { "family": "Schnitzer", "given": "Mark J." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Multineuronal Firing Patterns in the Signal from Eye to Brain", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2003 Cell Press. \n\nReceived 12 March 2002, Revised 21 November 2002, Available online 8 February 2. \n\nThis work was supported by NIH grant EY10020 (M.M.) and by Bell Laboratories (M.J.S.). We thank the members of our group for comments on the manuscript.", "abstract": "Population codes in the brain have generally been characterized by recording responses from one neuron at a time. This approach will miss codes that rely on concerted patterns of action potentials from many cells. Here we analyze visual signaling in populations of ganglion cells recorded from the isolated salamander retina. These neurons tend to fire synchronously far more frequently than expected by chance. We present an efficient algorithm to identify what groups of cells cooperate in this way. Such groups can include up to seven or more neurons and may account for more than 50% of all the spikes recorded from the retina. These firing patterns represent specific messages about the visual stimulus that differ significantly from what one would derive by single-cell analysis.", "date": "2003-02-06", "date_type": "published", "publication": "Neuron", "volume": "37", "number": "3", "publisher": "Elsevier", "pagerange": "499-511", "id_number": "CaltechAUTHORS:20170404-132335746", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-132335746", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "EY10020" }, { "agency": "Bell Laboratories" } ] }, "doi": "10.1016/S0896-6273(03)00004-7", "resource_type": "article", "pub_year": "2003", "author_list": "Schnitzer, Mark J. and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zr676-gs486", "eprint_id": 75696, "eprint_status": "archive", "datestamp": "2023-08-19 10:25:30", "lastmod": "2023-10-25 15:13:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baccus-S-A", "name": { "family": "Baccus", "given": "Stephen A." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Fast and Slow Contrast Adaptation in Retinal Circuitry", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2002 Cell Press. \n\nReceived 12 June 2002, Revised 8 October 2002, Available online 10 December 2002. \n\nWe thank the members of our laboratory for insightful discussions, and Ed Soucy and Tim Holy for important technical contributions. S.A.B. was supported by an NRSA from NEI, and M.M. by a grant from NEI.", "abstract": "The visual system adapts to the magnitude of intensity fluctuations, and this process begins in the retina. Following the switch from a low-contrast environment to one of high contrast, ganglion cell sensitivity declines in two distinct phases: a fast change occurs in <0.1 s, and a slow decrease over \u223c10 s. To examine where these modulations arise, we recorded intracellularly from every major cell type in the salamander retina. Certain bipolar and amacrine cells, and all ganglion cells, adapted to contrast. Generally, these neurons showed both fast and slow adaptation. Fast effects of a contrast increase included accelerated kinetics, decreased sensitivity, and a depolarization of the baseline membrane potential. Slow adaptation did not affect kinetics, but produced a gradual hyperpolarization. This hyperpolarization can account for slow adaptation in the spiking output of ganglion cells.", "date": "2002-12-05", "date_type": "published", "publication": "Neuron", "volume": "36", "number": "5", "publisher": "Elsevier", "pagerange": "909-919", "id_number": "CaltechAUTHORS:20170404-131413153", "issn": "0896-6273", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-131413153", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship" }, { "agency": "National Eye Institute" } ] }, "doi": "10.1016/S0896-6273(02)01050-4", "resource_type": "article", "pub_year": "2002", "author_list": "Baccus, Stephen A. and Meister, Markus" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3cpz3-k3714", "eprint_id": 75714, "eprint_status": "archive", "datestamp": "2023-08-19 09:06:57", "lastmod": "2023-10-25 15:14:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stowers-L", "name": { "family": "Stowers", "given": "Lisa" } }, { "id": "Holy-T-E", "name": { "family": "Holy", "given": "Timothy E." } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" }, { "id": "Dulac-C", "name": { "family": "Dulac", "given": "Catherine" } }, { "id": "Koentges-G", "name": { "family": "Koentges", "given": "Georgy" } } ] }, "title": "Loss of Sex Discrimination and Male-Male Aggression in Mice Deficient for TRP2", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2002 American Association for the Advancement of Science. \n\n12 September 2001; accepted 16 January 2002. Published online 31 January 2002. \n\nWe thank M. A. Wilson for experimental advice; R. Hellmiss-Peralta for the illustration; T. C. Lee for help with the manuscript preparation; P. Jiang, J. Dubauskaite, and M. E. Klein for help with gene targeting; and D. Haig and members of the Dulac and Meister labs for helpful comments. Financially supported by the Howard Hughes Medical Institute (L.S.); NIH grant DC03903 (C.D.); and Office of Naval Research grant (M.M.), Human Frontier Science Program (G.K.), and Jane Coffin Childs Memorial Fund (T.E.H.) fellowships.", "abstract": "The mouse vomeronasal organ (VNO) is thought to mediate social behaviors and neuroendocrine changes elicited by pheromonal cues. The molecular mechanisms underlying the sensory response to pheromones and the behavioral repertoire induced through the VNO are not fully characterized. Using the tools of mouse genetics and multielectrode recording, we demonstrate that the sensory activation of VNO neurons requires TRP2, a putative ion channel of the transient receptor potential family that is expressed exclusively in these neurons. Moreover, we show that male mice deficient in TRP2 expression fail to display male-male aggression, and they initiate sexual and courtship behaviors toward both males and females. Our study suggests that, in the mouse, sensory activation of the VNO is essential for sex discrimination of conspecifics and thus ensures gender-specific behavior.", "date": "2002-02-22", "date_type": "published", "publication": "Science", "volume": "295", "number": "5559", "publisher": "American Association for the Advancement of Science", "pagerange": "1493-1500", "id_number": "CaltechAUTHORS:20170405-070334559", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170405-070334559", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "DC03903" }, { "agency": "Office of Naval Research (ONR)" }, { "agency": "Human Frontier Science Program" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" } ] }, "doi": "10.1126/science.1069259", "resource_type": "article", "pub_year": "2002", "author_list": "Stowers, Lisa; Holy, Timothy E.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/52v8v-xx364", "eprint_id": 118579, "eprint_status": "archive", "datestamp": "2023-08-19 02:06:31", "lastmod": "2023-10-24 23:24:50", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Berry-Michael-II", "name": { "family": "Berry", "given": "Michael, II" } }, { "id": "Meister-M", "name": { "family": "Meister", "given": "Markus" }, "orcid": "0000-0003-2136-6506" } ] }, "title": "Refractoriness and Neural Precision", "ispublished": "unpub", "full_text_status": "public", "note": "We would like to thank Mike DeWeese for many useful conversations. One of us, MJB, acknowledges the support of the National Eye Institute. The other, MM, acknowledges the support of the National Science Foundation.", "abstract": "The relationship between a neuron's refractory period and the precision of its response to identical stimuli was investigated. We constructed a model of a spiking neuron that combines probabilistic firing with a refractory period. For realistic refractoriness, the model closely reproduced both the average firing rate and the response precision of a retinal ganglion cell. The model is based on a \"free\" firing rate, which exists in the absence of refractoriness. This function may be a better description of a spiking neuron's response than the peri-stimulus time histogram.", "date": "1997-12", "date_type": "published", "publisher": "MIT Press", "place_of_pub": "Cambridge, MA", "pagerange": "110-116", "id_number": "CaltechAUTHORS:20221222-175402264", "isbn": "9780262100762", "book_title": "Advances in neural information processing systems 10 : proceedings of the 1997 conference", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221222-175402264", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "NSF" } ] }, "contributors": { "items": [ { "id": "Jordan-Michael-J", "name": { "family": "Jordan", "given": "Michael J." } }, { "id": "Kearns-Michael-J", "name": { "family": "Kearns", "given": "Michael J." } }, { "id": "Solla-Sara-A", "name": { "family": "Solla", "given": "Sara A." } } ] }, "resource_type": "book_section", "pub_year": "1997", "author_list": "Berry, Michael, II and Meister, Markus" } ]