Webinar Description:
The brain is by far the most complex organ, posing enormous challenges in understanding its normal function and what goes wrong in brain disorders that now represent the largest cause of ill health worldwide.  New cellular and molecular technologies are quickly accelerating the field and can now be used to create cellular maps or atlases of the brain at unprecedented resolution.  The NIH BRAIN Initiative Brain Atlas Network (BICAN) is supporting major efforts to use these techniques to create brain-wide cell atlases in human and model organisms important for biomedical research as catalytic foundational resources in the spirit of the Human Genome.

This webinar will present results on mapping the structural, cellular and molecular architecture of the basal ganglia, structures involved in motor control, cognition and reward, and affected in a range of motor, addictive and psychiatric disorders.  The Human and Mammalian Brain Atlas (HMBA) consortium, a program within BICAN, involves a coordinated effort to create a harmonized atlas of basal ganglia structures and cell types in human and non-human primate brain.  This includes the creation of structural coordinate frameworks, cross-species maps of cell types and their spatial architecture using single cell genomics and spatial transcriptomics methods, and characterization of the morphological and physiological properties of basal ganglia cell types.  Together these data comprise a new foundational cell atlas that comprehensively describe the cellular organization of the basal ganglia, molecular and epigenetic underpinnings of their properties, and both conserved and species-specialized features of this organization.

These cell atlases are created to be foundational community resources. Effective open access tools for visualization, exploration and data mining are essential to realize the potential of these resources to standardize and accelerate efforts across the field to understand brain function and disease.  A rich suite of tools to visualize and mine these data and for users to map their own data against will be introduced and described. 

Learning Goals

Cell atlas of the basal ganglia:
What are the basal ganglia? 
What is a cell atlas?
What are single cell and spatial genomics methods?
What did we learn from the atlas? 

HMBA -omics
What is single cell epigenomics/multiome analysis?  What can we learn from that?
How is it possible to scale up to map the basal ganglia structures?
How can we map across species and why is that important? 

HMBA spatial:
What is spatial transcriptomics and why is that important?  What can we learn from that?

HMBA cell phenotyping
What is Patch-seq analysis?  What can we learn from that? 

Tools to use atlases:
What online tools are available, and how can they be used? 

Speakers

Trygve Bakken, M.D, Ph.D.
Trygve Bakken maps the diversity of cell types in the human brain and compares them to other species to understand how our brains have evolved. By pairing large-scale single-cell genomics with genetic tools for precise circuit access, his work lays the groundwork for new approaches to study and treat brain disorders. 

David Van Essen, Ph.D.
David Van Essen has carried out pioneering studies of the structure, function, connectivity, development, and evolution of cerebral cortex in humans and nonhuman primates. This includes widely cited maps of cortical organization and connectivity in the macaque monkey plus a multi-modal surface-based human cortical parcellation. He co-led the Human Connectome Project (HCP), a large-scale effort that acquired, analyzed, and freely shared high-quality neuroimaging data from 1200 healthy adults. The VanEssen/Glasser lab has been heavily involved in the BICAN project since its inception.  

Yuanyun Fu, Ph.D.
Yuanyuan Fu is a scientist at the Allen Institute for Brain Science working on single-cell genomics analysis of human and non-human primate brains. Prior to joining the Institute in 2024, Yuanyuan received her PhD at Tsinghua University, where she studied the development of the human brain. 

Madeleine Hewitt, Ph.D.
Madeleine Hewitt is a Scientist I at the Allen Institute working on spatial transcriptomics analysis of human and non-human primate brains. Prior to joining the Institute in 2023, Madeleine received her PhD at the University of Washington, where she studied cell shape of zebrafish sensory organs. 

Megan Turner, Ph.D.
Meghan Turner is a scientist at the Allen Institute for Brain Science working on the analysis of spatial transcriptomics data in human and non-human primate brains. Prior to joining the Institute in 2023, Meghan earned her Ph.D. in Biophysics from the University of California, Berkeley, where she studied the molecular mechanisms of transcriptional regulation during embryonic development. 

Xiao-Ping Liu, Ph.D.
Xiao-Ping Liu is a member of the Human Cell Types team where she performs quantitative analysis on patch-seq data, which provide multimodal scRNA-seq, electrophysiological, and morphological characterization of neuronal cells. Previously, she completed her Ph.D. in the joint Harvard/MIT Health Sciences Technology program. She has studied neural processing of auditory stimuli, maturation of mechanotransduction and electrophysiological properties in inner ear sensory cells, and ion channels of inner ear sensory neurons.  

Boudewijn Lelieveldt, Ph.D.
Boudewijn Lelieveldt is professor of Biomedical Imaging at the Dept of Radiology, Leiden University Medical Center, and at the Pattern Recognition and Bioinformatics lab at Delft University of Technology, the Netherlands. His team focuses on the development of fast algorithms and software for highly interactive visual analytics of integrated single-cell and spatially resolved -omics data (Manivault Studio, Cytosplore Viewer).  For HMBA, his team developed several data viewers for cross-species comparison, data integration and cross-modal visualization of HMBA data. Links for talk: viewer.cytosplore.org, manivault.studio 

Rachel Hostetler, Ph.D
She joined the Allen Institute in 2023, as part of the Scientific and Public Outreach of Cell Type Taxonomies team. In her role, she provides training, technical support, and outreach to scientific users of Allen’s cell type taxonomy data and tools.

This webinar is part of the BRAIN Initiative® Cell Atlas Network (BICAN), which is a collaborative effort between neuroscientists, computational biologists and software engineers to create a comprehensive atlas of the human brain. Supported by the U.S. BRAIN Initiative, we are dedicated to advancing our knowledge of the brain by gathering and sharing new data that allows us to develop the “parts list” of the brain, detailing the vast array of neurons and non-neuronal cells in the human brain. The BICAN continues the work of the BICCN consortium.

To learn more about this webinar and BICAN, visit their website.

This webinar will highlight new features and data in the Brain Knowledge Platform. More details to come.

This beginner-friendly webinar will focus on installation, set-up, and common questions related to using Jupyter notebooks (Python) for accessing and analyzing ABC Atlas transcriptomic data. 

More details to come

This webinar will focus on the creation of a new cross-species spinal cord taxonomy, featuring transcriptomic data from human, macaque, and mouse. 

 More details to come