News & Activities


December 2023


Whole Mouse Brain Atlas

A collection of nine new papers (and one previously published) from BICCN researchers reports the first complete cell type atlas of a mammalian brain, with over 30 million cells profiled from the adult mouse brain using a combination of single-cell transcriptomic, epigenomic, and spatial transcriptomic approaches, identifying over 5,300 cell types in the entire mouse brain. These studies achieve brain-wide cross-modality integration between transcriptomic profiles and epigenomic, spatial, or connectional properties, as well as certain aspects of evolutionary conservation and divergence, and uncover multitudes of organizing principles of the extraordinary cell type diversity across the brain. Read more about the Whole Mouse Brain Atlas at BICCN, at the Allen Institute and at Nature.


October 2023


Human and Non-Human Primate Cell Atlas

The human brain contains more than 100 billion cells, but exactly how these cells are organized into types and how these cell types differ between brain regions and species is an open question.  BICCN researchers coordinately worked on a collection of studies  defining and characterizing the underlying gene expression, gene regulatory, and morphoelectric features of cell types in the human and non-human primate (NHP) brain.  Read more about the Human and Non-Human Primate Cell Atlas and this includes several packages of data now available at the Human Cell Atlas site as well.


March 2022


Cell Types Knowledge Explorer

The Cell Types Knowledge Explorer is an interactive tool that aggregates rich, multimodal BICCN data at the level of individual cell types across mouse, human and marmoset. Developed in collaboration with the Allen Institute for Brain Science, the J. Craig Venter Institute, and the European Bioinformatics Institute, the Cell Types Explorer integrates the work of many BICCN laboratories and presents knowledge about cell types from the primary motor cortex in the form of intuitive data visualizations and text summaries. The Cell Types Explorer also serves as an entry point to the BICCN’s many freely available datasets and analysis tools and is powered by a data-driven ontology linking BICCN data to a well-established body of knowledge on neurobiology.  To learn more, watch this video.


October 2021


Cell Census of the Primary Motor Cortex

A major milestone in the effort to create a census of all brain cell types has been achieved. Dozens of research teams supported by the National Institutes of Health’s BRAIN Initiative Cell Census Network (BICCN) built a highly-detailed map of the motor cortex (MOp or M1). The resulting open-access data collection includes multimodal details of the cells found in the human, marmoset and mouse motor cortex including coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. The results establish a unified and mechanistic framework of neuronal cell type organization.


September 2020


New BICCN Awardees

Congratulations to the awardees of eight new BICCN grants! Stay tuned for more information on the Teams page.




Hawrylycz, Michael (Contact); Mungall, Christopher J; Scheuermann, Richard H; Parkinson, Helen Elizabeth; Lein, Ed ALLEN INSTITUTE

A Community Framework for Data-driven Brain Transcriptomic Cell Type Definition, Ontology, and Nomenclature


Multiplexed Nanoscale Protein Mapping Through Expansion Microscopy and Immuno-SABER


A high-resolution molecular and lineage atlas of the mouse brain using Slide-seq


Development of a scalable strategy for reconstructing cell-type determined connectome of the mammalian brain



Establishing Common Coordinate Framework for Quantitative Cell Census in Developing Mouse Brains


Developmental cell census of human and non-human primate brain



July 2020


Controlled access to human sequencing data available

BICCN includes a growing number of datasets providing RNA sequence-level information in human brain,  which is considered potentially identifiable. The consortium encourages use of tissue that is collected with the least restrictive consents, but datasets may consist of tissue collected under different patient consent conditions. Some datasets may be accessed without restrictions, including gene expression summarized as gene counts or otherwise aggregated to anonymize base sequences, and may be accessed directly from the NeMO data archive. Human sequence data collected under open access consent language may also be obtained directly from NeMO archive.

For human sequence level datasets collected under controlled access consent language, we announce a new process for data access. NeMO data archive has partnered with the NIMH Data Archive to provide a platform for application for and approval of human data access. Data access approvals will be managed at a dataset level by the NeMO data archive, and work is in progress to get each of the restricted access human datasets into the NDA platform. Please see detailed instructions here.



January 2020


BICCN Highlighted as Collaborative Neuroscience "Method to Watch"

BICCN was highlighted in a recent "Methods to Watch" article from Nature Methods:

"Large-scale initiatives like these generate a wealth of data, resources and tools, and making these available to the community is bound to multiply their impact. We look forward to these efforts bearing fruit."

Vogt, N. Collaborative neuroscience. Nat Methods 17, 22 (2020).



October 2019


Transcriptomics Explorer Launch

The Transcritpomics Explorer is a new tool that allows users to easily access cell-type information from mouse and human brains and to explore several custom-built visualizations of the data. Data supported by the U19 Zeng and U01 Lein BICCN grants is now available for visualization and analysis in the Transcriptomics Explorer.

Read more in the Allen Institute for Brain Science press release: Characterizing cell types in the mammalian brain.


BICCN Steering Committee Meeting

The fourth BICCN Steering Committee meeting was held at the Marriott Marquis Chicago on October 18, 2019 in advance of the Society for Neuroscience conference. Attendees heard progress updates from across the consortium, as well as presentations from the new BICCN grant awardees for 2019. Breakout sessions focused on topics including renewable antibody resources for proteomic phenotyping of the brain, consortium data infrastructure, and future planning for joint analysis opportunities.


September 2019


New Awardees

Congratulations to the awardees of eight new BICCN grants! Stay tuned for more information on the Teams page.




Snyder-Mackler, Noah  (Contact); Platt, Michael L; Shendure, Jay Ashok

University of Washington Single cell transcriptional and epigenomic atlas of the macaque brain across the lifespan
Ecker, Joseph R (Contact); Behrens, M Margarita Salk Institute for Biological Studies Epigenomic cell-type classification and regulatory element identification in the human brain
Tilgner, Hagen Weill Medical Coll of Cornell Univ Single cell isoform expression across mouse brain regions and development
Nowakowski, Tomasz

University of California, San Francisco

Mapping Developmental Lineage Relationships in the Cerebral Cortex
Chung, Kwanghun  (Contact); Eichinger, Daniel J; Pino, Ignacio ; Zhu, Heng Massachusetts Institute of Technology Highly specific, renewable, and cost-effective antibody toolbox for 3D proteomic phenotyping of the brain
Tasic, Bosiljka Allen Institute Cell class- or type-specific viruses for brain-wide labeling and neural circuit examination
Regev, Aviv  (Contact); Eldar, Yonina Broad Institute Scaling up spatial RNA profiling with compressed sensing
Mueller, Ulrich  (Contact); Miller, Michael I Johns Hopkins University Accessible technologies for high-throughput, whole-brain reconstructions of molecularly characterized mammalian neurons


BICCN Workshop

A workshop was held September 23-25, 2019 in Jackson Hole, WY to facilitate joint analysis of anatomical and morphological data from across the BICCN. Co-organized by Dr. Pavel Osten and the BCDC, the workshop brought together BICCN researchers and external experts in neuroanatomy to tackle the challenge of establishing standardized data analysis approaches.


July 2019


New Awardee

A new data archive joins the BICCN consortium! “Distributed Archives for Neurophysiology Data Integration” (DANDI), led by Dr. Satrajit Ghosh at MIT, will house BICCN neurophysiology and MR data. More information to follow soon on the Teams page!


May 2019


Cell Registry Launch

The Cell Registry, a new tool for exploring BICCN data, was publicly launched in early May. See the announcement in the Allen Institute for Brain Science newsletter.


April 2019


BICCN Steering Committee Meeting & Workshop

The third BICCN Steering Committee meeting was held on NIH Campus in Bethesda, MD on April 10, 2019 in advance of the 5th annual BRAIN Initiative Investigators Meeting. Additionally, the BCDC lead coordination of a concurrent Data Mapping Workshop. In addition to moderated presentations and discussion from each major group within BICCN, the Steering Committee meeting included breakout sessions on: transgenic and viral tools; human and non-human primate progress and planning; and cloud-native pipelines.

The Data Mapping Workshop was a hands-on hack-a-thon style event to address the myriad challenges in accurate image modality definition, registration, and mapping, with the specific outcome of getting spatial features suitable to support inclusion of BICCN data into the Integrated Data Set.


November 2018


BICCN Steering Committee Meeting

Over 100 BICCN members and affiliates assembled for the biannual BICCN Steering Committee meeting on November 2, 2018 on the UC San Diego campus. With coordination by the BCDC, the agenda included sessions on the Mini-Atlas projects; the Common Coordinate Framework; BCDC roadmap; BICCN challenges; Data workflow challenges; and outreach efforts. Breakout sessions on Mouse CCF, human and non-human primate research, and BCDC Infrastructure/Service Ingestion facilitated focused, stakeholder-lead discussion.


August 2018


BICCN Portal Debut

The BICCN Portal debuted in August 2018, supporting the first public release of BICCN data. The BICCN Portal serves as a community entry page for all BICCN related data; it features an overview of the consortium and its mission, profiling each of the major BICCN groups, as well as description of the primary data modalities and scope generated.
See the NIH announcement for the BICCN Portal debut.


April 2018


BRAIN Initiative Meeting

BICCN members were key participants of the 4th annual BRAIN Initiative Investigators Meeting held in Bethesda, MD on April 9-12, 2018.


March 2018


BICCN Workshop

On March 22-23, 2018 the BCDC and Allen Institute held a workshop with over 50 BICCN affiliated scientists with the intent to inform, educate, and collaborate with BICCN members in the areas of data analysis and integration.


November 2017


BICCN Kickoff

The BICCN Kickoff Meeting was held November 11, 2017 at the Howard Hughes Janelia Farms Research Campus. Organized by the BCDC, the meeting brought together the BICCN Steering Committee for initial planning for BICCN collaborations and strategy.