ArticlePLoS biology2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem.
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Article in PLoS biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
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41citing papers in PubMed, 1 pooled it
7.4field-weighted citation impact, top 2% of its field
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- Lithium effects in the frontolimbic circuitry: a systematic review of neuroimaging findings in bipolar disorder.Translational psychiatry · 2026Pooled it
- Pyramidal cell types and circuit organization of the mouse insular cortex reveal functional specializations.Nature neuroscience · 2026Article
- A framework for comparative analysis of human and mouse cortical neuron dendrites in corresponding brain regions.Nature neuroscience · 2026Article
- Advances in the Comprehensive Tree Shrew Brain Atlas.Biomolecules · 2026Review
- A Community Standard Multispecies Cell Atlas of the Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Automated Proofreading of Digitally Reconstructed Neural Morphology Enhances Accuracy, Scalability, and Standardization.bioRxiv : the preprint server for biology · 2026Article
- A curvilinear coordinate flatmap for visualizing hippocampal structure and development.bioRxiv : the preprint server for biology · 2026Article
- From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science.GigaScience · 2026Review
- Advances and challenges in single-cell RNA sequencing data analysis: a comprehensive review.Briefings in bioinformatics · 2026Review
- Grand challenges for systems neuroscience: perspectives and opportunities.Frontiers in systems neuroscience · 2026Article
- Article
- multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data.bioRxiv : the preprint server for biology · 2025Article
- The ANTsX ecosystem for mapping the mouse brain.Nature communications · 2025Article
- Validation of structure tensor analysis for orientation estimation in brain tissue microscopy.Journal of neuroscience methods · 2025Article
- epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain.Nature communications · 2025Article
- Neuronal architecture of the mouse insular cortex underlying its diverse functions.bioRxiv : the preprint server for biology · 2025Article
- Warp analysis research pipelines: cloud-optimized workflows for biological data processing and reproducible analysis.Bioinformatics (Oxford, England) · 2025Article
- DeMBA: a developmental atlas for navigating the mouse brain in space and time.Nature communications · 2025Article
- Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools.bioRxiv : the preprint server for biology · 2025Article
- Spyglass: a framework for reproducible and shareable neuroscience research.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
103 authors at 20 institutions in 6 countries.
Michael HawrylyczAllen Institute for Brain Science, Seattle, Washington, United States of America.ORCID 0000-0002-5741-8024
Maryann E MartoneDepartment of Neuroscience, University of California San Diego, San Diego, California, United States of America.ORCID 0000-0002-8406-3871
Giorgio A AscoliBioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America.
Jan G BjaalieInstitute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
Hong-Wei DongUCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America.
Satrajit S GhoshMcGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
Jesse GillisDepartment of Physiology, University of Toronto, Toronto, Ontario, Canada.
Ronna HertzanoDepartment of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
David R HaynorDepartment of Radiology, University of Washington, Seattle, Washington, United States of America.
Patrick R HofNash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Yongsoo KimDepartment of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America.
Ed LeinAllen Institute for Brain Science, Seattle, Washington, United States of America.
Yufeng LiuSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Jeremy A MillerAllen Institute for Brain Science, Seattle, Washington, United States of America.
Partha P MitraCold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Eran MukamelDepartment of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America.
Lydia NgAllen Institute for Brain Science, Seattle, Washington, United States of America.
David Osumi-SutherlandEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Hanchuan PengSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Patrick L RayAllen Institute for Brain Science, Seattle, Washington, United States of America.
Raymond SanchezAllen Institute for Brain Science, Seattle, Washington, United States of America.
Aviv RegevGenentech, South San Francisco, California, United States of America.
Alex RopelewskiPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.
Richard H ScheuermannJ. Craig Venter Institute, La Jolla, California, United States of America.
Shawn Zheng Kai TanEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Carol L ThompsonAllen Institute for Brain Science, Seattle, Washington, United States of America.
Timothy TickleData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Hagen TilgnerFeil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America.
Merina VargheseNash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Brock WesterResearch and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America.
Owen WhiteInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Hongkui ZengAllen Institute for Brain Science, Seattle, Washington, United States of America.
Brian AevermannChan Zuckerberg Initiative, Redwood City, California, United States of America.
David AllemangKitware Inc., Albany, New York, United States of America.
Seth AmentInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Thomas L AtheyDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
Cody BakerCatalystNeuro, Benicia, California, United States of America.
Katherine S BakerAllen Institute for Brain Science, Seattle, Washington, United States of America.
Pamela M BakerAllen Institute for Brain Science, Seattle, Washington, United States of America.
Anita BandrowskiDepartment of Neuroscience, University of California San Diego, San Diego, California, United States of America.
Samik BanerjeeCold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Prajal BishwakarmaAllen Institute for Brain Science, Seattle, Washington, United States of America.
Ambrose CarrChan Zuckerberg Initiative, Redwood City, California, United States of America.
Min ChenDepartment of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Roni ChoudhuryKitware Inc., Albany, New York, United States of America.
Jonah CoolChan Zuckerberg Initiative, Redwood City, California, United States of America.
Heather CreasyInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Florence D'OraziChan Zuckerberg Initiative, Redwood City, California, United States of America.
Kylee DegatanoData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Benjamin DichterCatalystNeuro, Benicia, California, United States of America.
Song-Lin DingAllen Institute for Brain Science, Seattle, Washington, United States of America.
Tim DolbeareAllen Institute for Brain Science, Seattle, Washington, United States of America.
Joseph R EckerGenomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America.
Rongxin FangBioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America.
Jean-Christophe Fillion-RobinKitware Inc., Albany, New York, United States of America.
Timothy P FlissAllen Institute for Brain Science, Seattle, Washington, United States of America.
James GeeDepartment of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Tom GillespieDepartment of Neuroscience, University of California San Diego, San Diego, California, United States of America.
Nathan GouwensAllen Institute for Brain Science, Seattle, Washington, United States of America.
Guo-Qiang ZhangTexas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America.
Yaroslav O HalchenkoDepartment of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America.
Nomi L HarrisEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Brian R HerbInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Houri HintiryanUCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America.
Gregory HoodPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.
Sam HorvathKitware Inc., Albany, New York, United States of America.
Bingxing HuoCold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Dorota JareckaMcGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
Shengdian JiangSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Farzaneh KhajoueiData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Elizabeth A KiernanData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Huseyin KirEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Lauren KruseAllen Institute for Brain Science, Seattle, Washington, United States of America.
Changkyu LeeAllen Institute for Brain Science, Seattle, Washington, United States of America.
Boudewijn LelieveldtDepartment of Intelligent Systems, Delft University of Technology, Delft, the Netherlands.
Yang LiCenter for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America.
Hanqing LiuGenomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America.
Lijuan LiuSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Anup MarkuharInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
James MathewsAllen Institute for Brain Science, Seattle, Washington, United States of America.
Kaylee L MathewsData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Chris MeziasCold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Michael I MillerDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
Tyler MollenkopfAllen Institute for Brain Science, Seattle, Washington, United States of America.
Shoaib MuftiAllen Institute for Brain Science, Seattle, Washington, United States of America.
Christopher J MungallEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Joshua OrvisInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Maja A PuchadesInstitute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
Lei QuSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Joseph P ReceveurInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Bing RenCenter for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America.
Nathan SjoquistMicrosoft Corporation, Seattle, Washington, United States of America.
Brian StaatsAllen Institute for Brain Science, Seattle, Washington, United States of America.
Daniel TwardUCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America.
Cindy T J van VelthovenAllen Institute for Brain Science, Seattle, Washington, United States of America.
Quanxin WangAllen Institute for Brain Science, Seattle, Washington, United States of America.
Fangming XieDepartment of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America.
Hua XuSchool of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America.
Zizhen YaoAllen Institute for Brain Science, Seattle, Washington, United States of America.
Zhixi YunSEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China.
Yun Renee ZhangJ. Craig Venter Institute, La Jolla, California, United States of America.
W Jim ZhengSchool of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America.
Brian ZinggUCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America.
Allen Institute for Brain Science · USUniversity of Maryland, Baltimore · USSoutheast University · CNUniversity of California San Diego · USBroad Institute · USUniversity of California, Los Angeles · USChan Zuckerberg Initiative (United States) · USCold Spring Harbor Laboratory · USEuropean Bioinformatics Institute · GBThe University of Texas Health Science Center at Houston · USJ. Craig Venter Institute · USJohns Hopkins University · USLawrence Berkeley National Laboratory · USMcGovern Institute for Brain Research · USPittsburgh Supercomputing Center · USSalk Institute for Biological Studies · USUniversity of Oslo · NOUniversity of Pennsylvania · USCornell University · USDartmouth College · US
Funding
Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI NGAI, JOHN J. · 2017 to 2021
$64.7MTool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI ARLOTTA, PAOLA, HUANG, Z JOSH · 2017 to 2021
$64.5MAnatomical characterization of neuronal cell types of the mouse brainU01MH114829 · NIMH · UNIVERSITY OF SOUTHERN CALIFORNIA · PI ASCOLI, GIORGIO A, DONG, HONG-WEI · 2017 to 2021
$13.9MCollaboratory for atlasing cell type anatomy in the female and male mouse brainU01MH114824 · NIMH · COLD SPRING HARBOR LABORATORY · PI MITRA, PARTHA PRATIM · 2017 to 2021
$11.7MDANDI: Distributed Archives for Neurophysiology Data IntegrationR24MH117295 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Satrajit Sujit Ghosh, Yaroslav O Halchenko · 2019 to 2026
$11.6MMulti-Omic and Functional Analyses for Hearing Preservation and RestorationZIADC000094 · NIDCD · NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS · PI HERTZANO, RONNA · 2023 to 2025
$10.3MA Confocal Fluorescence Microscopy Brain Data ArchiveR24MH114793 · NIMH · CARNEGIE-MELLON UNIVERSITY · PI ALEXANDER J ROPELEWSKI, Alan Michael Watson · 2017 to 2026
$10.1MImaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain Admin SupplementU01MH117023 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI BOAS, DAVID A, FISCHL, BRUCE · 2018 to 2022
$7.6MThe Mouse Connectome Project Phase III: Assembling the global neural networks of the mouse brainR01MH094360 · NIMH · UNIVERSITY OF SOUTHERN CALIFORNIA · PI DONG, HONG-WEI · 2012 to 2021
$7.4MGeneration and Description of Neuronal Morphology and ConnectivityR01NS039600 · NINDS · GEORGE MASON UNIVERSITY · PI ASCOLI, GIORGIO A · 1999 to 2024
$6.9MBoss: A cloud-based data archive for electron microscopy and x-ray microtomographyR24MH114785 · NIMH · JOHNS HOPKINS UNIVERSITY · PI BROCK A. WESTER · 2018 to 2026
$6.9MEngagement and outreach to achieve a FAIR data ecosystem for the BICANU24MH130988 · NIMH · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI HUA XU, Guo-Qiang ZHANG · 2022 to 2026
$4.6MNIMH NIH HHS R01 MH094360NIMH NIH HHS R01 MH113005NIMH NIH HHS R01MH123220NIMH NIH HHS R24 MH114785NIMH NIH HHS R24 MH114793NIMH NIH HHS R24 MH117295NIMH NIH HHS RF1 MH123220NIMH NIH HHS RF1 MH124605NIMH NIH HHS RF1 MH128693NIMH NIH HHS U01 MH114824NIMH NIH HHS U01 MH114829NIMH NIH HHS U01 MH117023NIMH NIH HHS U19 MH114821NIMH NIH HHS U19MH114824NIMH NIH HHS U19 MH114830NIMH NIH HHS U24 MH130988NINDS NIH HHS R01 NS039600NINDS NIH HHS R01 NS086082NINDS NIH HHS R01 NS096720
Abstract
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
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BrainNeurosciencesAnimalsEcosystemHumansMiceNeurons
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