A guide to the BRAIN Initiative Cell Census Network data ecosystem

PLoS Biology, vol. 21, pp. e3002133

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.

Authors 98

1. Michael Hawrylycz corresponding

   Allen Institute for Brain Science

   Affiliation as printed

   Allen Institute for Brain Science, Seattle, Washington, United States of America

2. Maryann Elizabeth Martone corresponding

   San Francisco VA Medical Center · University of California San Diego

   Affiliation as printed

   Department of Neuroscience, University of California San Diego, San Diego, California, United States of America

   San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America

3. Giorgio A. Ascoli corresponding

   George Mason University

   Affiliation as printed

   Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America

4. Jan Gunnar Bjaalie corresponding

   University of Oslo

   Affiliation as printed

   Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

5. Hong‐Wei Dong corresponding

   University of California, Los Angeles

   Affiliation as printed

   UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America

6. Satrajit Ghosh corresponding

   McGovern Institute for Brain Research · Massachusetts Institute of Technology

   Affiliation as printed

   McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

7. Jesse A Gillis corresponding

   University of Toronto

   Affiliation as printed

   Department of Physiology, University of Toronto, Toronto, Ontario, Canada

8. Ronna P. Hertzano corresponding

   University of Maryland, Baltimore

   Affiliation as printed

   Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

   Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

   Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

9. David R. Haynor corresponding

   University of Washington

   Affiliation as printed

   Department of Radiology, University of Washington, Seattle, Washington, United States of America

10. Patrick R. Hof corresponding

    Icahn School of Medicine at Mount Sinai

    Affiliation as printed

    Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

11. Yongsoo Kim corresponding

    Pennsylvania State University

    Affiliation as printed

    Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America

12. Ed S. Lein corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

13. Yufeng Liu corresponding

    Southeast University

    Affiliation as printed

    SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China

14. Jeremy A. Miller corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

15. Partha P. Mitra corresponding

    Cold Spring Harbor Laboratory

    Affiliation as printed

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

16. Eran A. Mukamel corresponding

    University of California San Diego

    Affiliation as printed

    Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America

17. Lydia Ng corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

18. David Osumi-Sutherland corresponding

    European Bioinformatics Institute · Wellcome Trust

    Affiliation as printed

    European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

19. Patrick Lloyd Ray corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

20. Raymond E.A. Sanchez corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

21. Aviv Regev corresponding

    Genentech

    Affiliation as printed

    Genentech, South San Francisco, California, United States of America

22. Alex Ropelewski corresponding

    Pittsburgh Supercomputing Center · Carnegie Mellon University

    Affiliation as printed

    Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

23. Richard H. Scheuermann corresponding

    J. Craig Venter Institute

    Affiliation as printed

    J. Craig Venter Institute, La Jolla, California, United States of America

24. Shawn Zheng Kai Tan corresponding

    European Bioinformatics Institute · Wellcome Trust

    Affiliation as printed

    European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

25. Carol L. Thompson corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

26. Timothy L. Tickle corresponding

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

27. Hagen Tilgner corresponding

    Weill Cornell Medicine

    Affiliation as printed

    Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America

28. Merina Varghese corresponding

    Icahn School of Medicine at Mount Sinai

    Affiliation as printed

    Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

29. Brock A. Wester corresponding

    Johns Hopkins University · Johns Hopkins University Applied Physics Laboratory

    Affiliation as printed

    Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America

30. Owen R. White corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

31. Hongkui Zeng corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

32. Brian D. Aevermann corresponding

    Chan Zuckerberg Initiative (United States)

    Affiliation as printed

    Chan Zuckerberg Initiative, Redwood City, California, United States of America

33. David Allemang corresponding

    Kitware (United States)

    Affiliation as printed

    Kitware Inc., Albany, New York, United States of America

34. Seth A. Ament corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

35. Thomas L. Athey corresponding

    Johns Hopkins University

    Affiliation as printed

    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America

36. C L Baker corresponding

    CatalystNeuro

    Affiliation as printed

    CatalystNeuro, Benicia, California, United States of America

37. Katherine S. Baker corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

38. Pamela M. Baker corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

39. Anita E. Bandrowski corresponding

    University of California San Diego

    Affiliation as printed

    Department of Neuroscience, University of California San Diego, San Diego, California, United States of America

40. Samik Banerjee corresponding

    Cold Spring Harbor Laboratory

    Affiliation as printed

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

41. Prajal Bishwakarma corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

42. Ambrose Carr corresponding

    Chan Zuckerberg Initiative (United States)

    Affiliation as printed

    Chan Zuckerberg Initiative, Redwood City, California, United States of America

43. Min Chen corresponding

    University of Pennsylvania

    Affiliation as printed

    Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

44. Roni Choudhury corresponding

    Kitware (United States)

    Affiliation as printed

    Kitware Inc., Albany, New York, United States of America

45. Jonah Cool corresponding

    Chan Zuckerberg Initiative (United States)

    Affiliation as printed

    Chan Zuckerberg Initiative, Redwood City, California, United States of America

46. Heather Huot Creasy corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

47. Florence D. D’Orazi corresponding

    Chan Zuckerberg Initiative (United States)

    Affiliation as printed

    Chan Zuckerberg Initiative, Redwood City, California, United States of America

48. Kylee Degatano corresponding

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

49. Ben Dichter corresponding

    CatalystNeuro

    Affiliation as printed

    CatalystNeuro, Benicia, California, United States of America

50. Song‐Lin Ding corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

51. Tim A. Dolbeare corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

52. Joseph R. Ecker corresponding

    Salk Institute for Biological Studies · Howard Hughes Medical Institute

    Affiliation as printed

    Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America

53. Rongxin Fang corresponding

    University of California San Diego

    Affiliation as printed

    Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America

54. Jean‐Christophe Fillion‐Robin corresponding

    Kitware (United States)

    Affiliation as printed

    Kitware Inc., Albany, New York, United States of America

55. Timothy P. Fliss corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

56. James C. Gee corresponding

    University of Pennsylvania

    Affiliation as printed

    Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

57. Tom Gillespie corresponding

    University of California San Diego

    Affiliation as printed

    Department of Neuroscience, University of California San Diego, San Diego, California, United States of America

58. Nathan W. Gouwens corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

59. Guo‐Qiang Zhang corresponding

    The University of Texas Health Science Center at Houston

    Affiliation as printed

    Texas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America

60. Yaroslav O. Halchenko corresponding

    Dartmouth College

    Affiliation as printed

    Department of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America

61. Nomi L. Harris corresponding

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America

62. Brian R. Herb corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

63. Houri Hintiryan corresponding

    University of California, Los Angeles

    Affiliation as printed

    UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America

64. Greg Hood corresponding

    Pittsburgh Supercomputing Center · Carnegie Mellon University

    Affiliation as printed

    Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

65. Sam Horvath corresponding

    Kitware (United States)

    Affiliation as printed

    Kitware Inc., Albany, New York, United States of America

66. Bing‐Xing Huo corresponding

    Cold Spring Harbor Laboratory

    Affiliation as printed

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

67. Dorota Jarecka corresponding

    McGovern Institute for Brain Research · Massachusetts Institute of Technology

    Affiliation as printed

    McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

68. Shengdian Jiang corresponding

    Southeast University

    Affiliation as printed

    SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China

69. Farzaneh Khajouei corresponding

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

70. Elizabeth A. Kiernan corresponding

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

71. Hüseyin Kır corresponding

    European Bioinformatics Institute · Wellcome Trust

    Affiliation as printed

    European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

72. Lauren Kruse corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

73. Changkyu Lee corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

74. Boudewijn P. F. Lelieveldt corresponding Aachen Department of Radiology, Leiden University Medical Center

    Leiden University Medical Center · Delft University of Technology

    Affiliation as printed

    Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands

    Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands

75. Yang Eric Li corresponding

    University of California San Diego

    Affiliation as printed

    Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America

76. Hanqing Liu corresponding

    Salk Institute for Biological Studies · Howard Hughes Medical Institute

    Affiliation as printed

    Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America

77. Lijuan Liu corresponding

    Southeast University

    Affiliation as printed

    SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China

78. Anup Markuhar corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

79. Kaylee L. Mathews corresponding

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

80. Christopher Mezias corresponding

    Cold Spring Harbor Laboratory

    Affiliation as printed

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America

81. Michael I. Miller corresponding

    Johns Hopkins University

    Affiliation as printed

    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America

82. Tyler S. Mollenkopf corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

83. Shoaib Mufti corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

84. Chris Mungall corresponding

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America

85. Joshua Orvis corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

86. Maja Amedjkouh Puchades corresponding

    University of Oslo

    Affiliation as printed

    Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

87. Lei Qu corresponding

    Southeast University

    Affiliation as printed

    SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China

88. Joseph P. Receveur corresponding

    University of Maryland, Baltimore

    Affiliation as printed

    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

89. Bing Ren corresponding

    Ludwig Cancer Research · University of California San Diego · Ludwig Cancer Research

    Affiliation as printed

    Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America

    Ludwig Institute for Cancer Research, La Jolla, California, United States of America

90. Nathan Sjoquist corresponding

    Microsoft (United States)

    Affiliation as printed

    Microsoft Corporation, Seattle, Washington, United States of America

91. Brian J Staats corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

92. Daniel Jacob Tward corresponding

    University of California, Los Angeles

    Affiliation as printed

    UCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America

93. Cindy T. J. van Velthoven corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

94. Quanxin Wang corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

95. Fangming Xie corresponding

    University of California, Los Angeles

    Affiliation as printed

    Department of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America

96. Hua Xu corresponding

    The University of Texas Health Science Center at Houston

    Affiliation as printed

    School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America

97. Zizhen Yao corresponding

    Allen Institute for Brain Science

    Affiliation as printed

    Allen Institute for Brain Science, Seattle, Washington, United States of America

98. Zhixi Yun corresponding

    Southeast University

    Affiliation as printed

    SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China