This workshop highlights the Brain Knowledge Platform, which features the Cell Type Knowledge Explorer, Allen Brain Cell (ABC) Atlas, MapMyCells, and additional tools. These tools include definitions and taxonomies of cell types, cell properties used in those definitions, and resources for applying these types to your cells.
No prior experience with Allen Institute tools, methods or techniques is required. Note: This workshop does not require programming or computational knowledge. If you are interested in studying cell types from a computational perspective, please apply to our “Computational Cell Types” workshop.
Applications are now closed. Applicants will be notified on January 23.
We will provide up to $1500 in travel & accommodation support for accepted participants. There is no application fee.
About This Event
In this workshop, participants will gain in-depth exposure on how the Allen Institute defines “cell types” and walk away with direct, applicable examples on using our free, open tools for their research. Allen Institute for Brain Science has created a treasure trove of data and variety of tools. This workshop will help you navigate these resources and give you example cases to apply them to your work.
This workshop is geared toward early-career scientists, especially graduate students, postdocs, research associates, and data analysts, who are interested in developing their understanding of cell types and how to refine their research with the techniques taught. However, faculty and senior scientists are welcome to apply.
Workshop highlights
Learn how to leverage the power of cell types in your research with these featured events:
- Meet some of the creators behind the Cell Type Knowledge Explorer, ABC Atlas, and MapMyCells
- Attend hands-on tutorials with example cases and one-on-one troubleshooting
- Hear from researchers who have used this data in their own work
- Learn about BICAN and available resources from across the consortium
- Give feedback and influence development of the ABC Atlas
- Visit the Allen Institute and our labs, and the scientists behind the science
ABOUT THE TOOLS
The Brain Knowledge Platform (BKP) combines high-quality neuroscience data with advanced software tools, enabling trust-worthy discovery and analysis. Below are some of the tools within the BKP:
Cell Type Knowledge Explorer is an award-winning entry point tool to explore cell type properties and taxonomies for human, marmoset, and mouse primary motor cortex. Over 3.5 million cells & nuclei are collected and characterized across multiple techniques, including single-cell RNA sequencing, DNA methylation, patch-seq, cellular morphology & projection, inter-areal circuit mapping, and more. Cell Type Knowledge Explorer was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and described in detail in the BICCN flagship publication.
ABC Atlas is a multimodal platform for visualizing and exploring multiple single cell transcriptomic datasets. Over 20 million cells are featured in the ABC Atlas, through spatial and single cell/nucleus data from whole adult mouse, aging mouse, human-marmoset-macaque basal ganglia, human Parkinson’s, whole human, and human Alzheimer’s brains with more datasets being added in the future.
MapMyCells is a tool that lets researchers map their own single cell data onto many of cell type taxonomy datasets listed above, allowing for cell types to be identifiable by a common nomenclature. Comparing data to large and robust reference cell type datasets enables users to annotate their cell types faster with trusted cell type labels.
Workshop Details
Workshop dates: April 6-8th, 2026
Cost: Allen Institute will provide up to $1500 in travel support for accepted workshop participants. Food will be provided at the workshop at no additional charge. There is no application fee.
Applicant notification: All applications will be notified of the decision on their application by January 23rd, 2026.
This workshop was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under Award Number U24NS133077. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Questions? Email rachel.hostetler@alleninstitute.org
