Revealing the Mammalian Motor Cortex: BICCN Flagship Release

Revealing the Mammalian Motor Cortex: Brain Initiative Cell Census Network (BICCN) Flagship Release Webinar

The Brain Initiative Cell Census Network (BICCN) is a collaborative consortium of many labs interested in the cellular composition of the mammalian brain. BICCN has recently published a flagship publication describing the overall project, along with a companion package of papers describing the cell types, connectivity, anatomy and other properties of the mammalian primary motor cortex (MOp or M1). At this webinar, learn about this multimodal research from leaders of some of the research teams involved.

Read a scientific overview and press release about the BICCN flagship publication and companion package.

A series of tutorials demonstrating how other researchers can use the open data, tools, and other resources produced by the BICCN will begin in November. More information about the tutorials is coming soon and will be shared with webinar registrants.

The Allen Institute for Brain Science is proud to be an organizing center for the BICCN by contributing data, serving as the Brain Cell Data Center (BCDC) to coordinate consortium working groups, and hosting the web portal and searchable inventory of data produced by the BICCN.

Webinar details

Wednesday, October 27, 2021
10:00-11:30am Pacific Time

The webinar will be livestreamed on Zoom and YouTube.

View recording




Time: Eastern

Time: Pacific

Welcome and introduction to the BICCN, the flagship publication, and companion package of papers

John Ngai, NIH, and Mike Hawrylycz, Allen Institute for Brain Science



Short talks by BICCN Members




Characterization of cell types in mouse primary motor cortex

Hongkui Zeng, Allen Institute for Brain Science



Epigenetic diversity of neurons in the mouse

Zhuzhu Zhang, Salk Institute

1:15-1:20pm 10:15-10:20am

Mapping the mouse primary motor cortex with MERFISH

Xiaowei Zhuang, Harvard University

1:20-1:25pm 10:20-10:25am

Cell classification across species

Ed Lein, Allen Institute for Brain Science 1:25-1:30pm


Emergence of cell types across development

Arnold Kriegstein, University of California, San Francisco

1:30-1:35pm 10:30-10:35am

Single-cell data analytics

Jesse Gillis, Cold Spring Harbor Laboratory



Archives and data access

Carol Thompson, Allen Institute for Brain Science

1:40-1:45pm 10:40-10:45am

Panel discusion and Q&A

All short talk presenters with moderator Maryann Martone, University of California San Diego



Speaker details

John J. Ngai, PhD

John J. Ngai, Ph.D., is the Director of the NIH’s Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative, where he oversees the long-term strategy and day-to-day operations of this ground-breaking enterprise. Dr. Ngai earned his bachelor’s degree in chemistry and biology from Pomona College, Claremont, California, and Ph.D. in biology from the California Institute of Technology (Caltech) in Pasadena.  Prior to joining NIH, as a UC Berkeley faculty member for over 25 years Dr. Ngai trained 20 undergraduate students, 24 graduate students and 15 postdoctoral fellows in addition to teaching well over 1,000 students in the classroom. His work has led to the publication of more than 75 scientific articles in some of the field’s most prestigious journals and 10 U.S. and international patents.



Mike Hawrylycz, PhD

Mike Hawrylycz joined the Allen Institute in 2003. Hawrylycz has worked in a variety of applied mathematics and computer science areas, addressing challenges in consumer and investment finance, electrical engineering and image processing, and computational biology and genomics. Hawrylycz received his Ph.D. in applied mathematics at the Massachusetts Institute of Technology. He subsequently was a post-doctoral researcher in the Computer Research and Applications Group at the Los Alamos National Laboratory.



Hongkui Zeng, PhD

Dr. Hongkui Zeng is Executive Vice President and Director of Allen Institute for Brain Science. She leads multidisciplinary teams to develop large-scale, high-throughput transcriptomic, connectomic and multimodal platforms and use them to characterize and classify the wide variety of cell types that constitute the mammalian brain, laying the foundation for unraveling the cell type basis of brain function. Her work has led to widely adopted community resources and standards, including transgenic mouse lines, Allen Mouse Brain Connectivity Atlas, the Common Coordinate Framework (CCF) and the brain-wide transcriptomic cell type taxonomy in mice.

Short talk:
Transcriptomic, morphological and connectional characterization of cell types in mouse primary motor cortex.



Zhuzhu Zhang, PhD

Zhuzhu Zhang is a postdoctoral research fellow at the Salk Institute for Biological Studies. She is broadly interested in understanding the epigenetic regulation in the mammalian brain at single-cell resolution, using both experimental and computational approaches. Specifically, Zhang studies the neuronal cell types and functions in the brain and investigates their epigenetic signatures in the context of neural pathways and circuits by developing and deploying novel single cell genomics approaches.

Short talk:
Epigenetic diversity of neurons in the mouse.



Xiaowei Zhuang, PhD

Xiaowei Zhuang is the David B. Arnold Professor of Science and the director of the Center for Advanced Imaging at Harvard University, and an investigator of Howard Hughes Medical Institute.

Short talk:
We used a single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH), to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (MOp). We further integrated MERFISH with retrograde labeling to map the projection targets of molecularly defined neuronal cell types in the MOp.



Ed Lein, PhD

Ed Lein is Senior Investigator at the Allen Institute for Brain Science and an Affiliate Professor in the Department of Neurological Surgery at the University of Washington.  He leads the Human Cell Types program at the Allen Institute, focused on creating a cellular atlas of the human brain, understanding conserved and specialized features of human brain, developing tools for genetic access to specific cell types in non-genetically tractable organisms including human, and understanding cellular and molecular consequences of Alzheimer’s disease.

Short talk:
Our genomic paradigm for cell classification reveals conserved and specialized features of cell types in mouse, monkey and human cortex.



Arnold Kriegstein, MD, PhD

Arnold Richard Kriegstein M.D., PhD., is a neurologist and developmental neuroscientist who works in the fields of neural stem cell research and brain development. He was the founding Director of the UCSF Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research. He is a member of the National Academy of Medicine.

Short talk:
We used single cell RNA sequencing and spatial gene mapping to learn how the dozens of functional areas of the human cerebral cortex emerge during early development.



Jesse Gillis, PhD

Jesse Gillis is an Associate Professor and Cancer Center Member at Cold Spring Harbor Laboratory. He received his PhD from the University of Toronto in 2007.  As functional genomics data has continued to increase in abundance and specificity, my lab has benefited from the opportunities to provide organizing frameworks, grounded in both biology and statistical insight. A particular focus within my lab is the analysis of gene co-expression, or the shared expression profile of genes across conditions. Genes which express under similar conditions will tend to share functions, and by tailoring data and methods, this can usefully model biological systems from cells to organisms to species.

Short talk:
The BICCN single cell data is unusual in both breadth and depth, representing a coordinated effort across many labs. Integration, quality control, and assessment of replicability are essential tasks undertaken as part of collaborative analyses within the BICCN to ensure the availability and utility of the data generated.



Carol Thompson, PhD

Carol Thompson has provided scientific leadership and management at the Allen Institute for Brain Science for the past 15 years. She is currently coordinating community-generated data for the Brain Cell Data Center as part of the BRAIN Initiative Cell Census Network (BICCN). Carol holds a BS in Biology from the University of Richmond and a PhD in Biochemistry from the University of North Carolina at Chapel Hill, where she studied cryptochromes under the guidance of Nobel laureate Aziz Sancar, MD, PhD.

Short talk:
The BICCN consortium is a distributed ecosystem of data archives and the Brain Cell Data Center to provide access to the various data assets. BICCN currently involves three archives: NeMO, BIL, and DANDI. Users can access data from the archives, including the data that underlie the flagship and companion papers, and use them in their own work.