Upcoming Webinars
"Describe Your Neurons like the Allen Institute” Workshop Q&A Session
June 12th, 11:00am-12:00pm
This Q&A session will cover topics presented during the annual “Describe Your Neurons like the Allen Institute” workshop, held on April 6th-8th. Our goal is to provide access to resources and content for those who were unable to join us in-person. We also encourage previous workshop attendees to share any updates or developments on how they are using Allen Institute tools and/or data in their work. Please submit any questions and/or comments in advance through the registration form.
Open Access Tools for Exploring the Mammalian Basal Ganglia
June 16th, 10:30-11:45am
Join us for an interactive, live Q&A session, focused on using tools to explore cellular basal ganglia data from the BRAIN Initiative Cell Atlas Network (BICAN). We will start with a brief introduction of available tools (including the Allen Brain Cell Atlas, MapMyCells, Cytosplore Viewer, and Connectome Workbench), followed by a deep-dive into the Epigenome Explorer and Genetic Tools Atlas. Please submit any questions and/or comments in advance through the registration form.
Past Webinars
Mapping the cellular architecture of the mammalian basal ganglia
December 2, 2025, 9 - 10:30 am PST
New cellular advances allow us to map basal ganglia’s structure and function in both humans and model organisms. We will present major advances by the HMBA consortium on basal ganglia mapping—including cross-species cellular mapping and open-access visualization tools.
This event has passed.
New Frontiers in Understanding Brain Development
December 9, 2025, 10 - 12:00 pm PST
How does the brain build itself? What sparks the transformation from a handful of cells into a complex organ that powers thought, emotion, and behavior? We will present the findings from 12 coordinated papers aimed at mapping brain development in extraordinary detail.
This event has passed.
Exploring the New Brain Knowledge Platform
January 14, 2026, 11 - 12pm PST
This webinar will highlight new features and data in the Brain Knowledge Platform.
This event has passed.
Getting Started with Programmatic Access to ABC Atlas Data
February 11, 2026 10 - 11am PST
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.
This event has passed.
Creating a Cross-species Spinal Cord Taxonomy
March 13, 2026 10:30 - 11:30am PST
This webinar will focus on the creation of a new cross-species spinal cord taxonomy, featuring transcriptomic data from human, macaque, and mouse.
details
Upcoming Webinars
"Describe Your Neurons like the Allen Institute” Workshop Q&A Session
June 12th, 11:00am-12:00pm
The Allen Institute has created multiple large-scale transcriptomic cell type taxonomies aimed at identifying the “parts list” of the brain in various species, regions, and disease states, with more datasets currently in development. As the number, size, and complexity of these datasets continue to grow, there is an urgent need to share these taxonomies following findable, accessible, interoperable, and reusable (FAIR) principles, and to develop tools supporting their use.
To increase the accessibility and usage of cell type taxonomies and their associated tools, the Scientific and Public Outreach of Cell Type Taxonomies (SPOCTT) program has created opportunities and resources for users through workshops, webinars, user guides, tutorials, presentations, office hours, and more. The goals of the “Describe Your Neurons like the Allen Institute” workshop are to introduce attendees to cell type taxonomies and their associated tools, provide a deeper understanding of how these datasets and tools are developed, and facilitate the usage of these datasets and tools in attendee’s own work.
In this live Q&A session, workshop co-organizers Jeremy Miller, Ph.D. and Rachel Hostetler, Ph.D. will cover relevant topics, datasets, and tools. Attendees will have the opportunity to ask questions, share feedback, and share any updates or use-case examples of Allen data in their own work.
Open Access Tools for Exploring the Mammalian Basal Ganglia
June 16th, 10:30-11:45am
The BRAIN Initiative Cell Atlas Network (BICAN) is mapping the architecture of the mammalian basal ganglia at single cell-resolution. This work includes transcriptomic, morphological, and electrophysiological cell type characterization and cross-species mapping of the human and non-human primate brain. BICAN tools to explore data include those which enable:
- Viewing the human-macaque-marmoset consensus cellular atlas and spatial components -- Allen Brain Cell (ABC) Atlas,
- Mapping single-cell transcriptomic datasets to the atlas -- MapMyCells.
- Accessing electrophysiological (patch-seq) data -- Cytosplore
- Accessing common coordinate frameworks for individual species -- Connectome Workbench.
- Viewing epigenetic data -- Epigenome Browser
- Finding viral tools for targeting basal ganglia cell types --Genetic Tools Atlas.
Rachel Hostetler, Ph.D. (Allen Institute) will provide a brief overview of all the tools. Daofeng Li, Ph.D. and Wenjin Zhang (Washington University in St. Louis) presenting on the Epigenome Browser. Sharon Way, Ph.D., Yoav Ben-Simon Ph.D., and Sven Otto (Allen Institute) will present on the Genetic Tools Atlas. All presentations will include introductions to the tools, demos on how to use them, and ample time for questions. The goals of this session are to inform the community of these open access tools, demonstrate tool useability and use-cases, and provide an interactive opportunity for questions and feedback.
Past Webinars
Mapping the cellular architecture of the mammalian basal ganglia | Dec 2, 9-10:30am PST
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.
Meghan 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.
New Frontiers in Understanding Brain Development | Dec 9, 10-11am PST
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.
Exploring the new Brain Knowledge Platform | Jan 14, 11am-12pm PST
This webinar will highlight new features and data in the Brain Knowledge Platform. More details to come.
Getting Started with Programmatic Access to ABC Atlas Data | Feb 11, 10-11:30am PST
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
Creating a Cross-species Spinal Cord Taxonomy | March 11, 10:30-11:30am PST
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
webinar overview
Browse upcoming and past sessions focused on the Allen Institute’s open data tools, with registration links and highlights below. Additional details for select webinars are available further down the page—use the quick link to jump ahead.
You must register separately for each webinar you wish to attend.
