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Workshop: Describe Your Neurons Like the Allen Institute


GABAergic, glutamatergic, dopaminergic – if this is how you classify your cell types, this workshop is for you!

In this workshop, participants will gain in-depth exposure on how Allen Institute defines “cell types” and work with direct, applicable examples of how to use the Allen Institute’s free, open resources & tools for research. The highlighted tools featured at the workshop are Cell Types Knowledge Explorer and Allen Brain Cell (ABC) Atlas, both of which 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. We highly encourage non-R1, translational research, undergraduate-focused, and small labs to apply.

We will provide up to $1500 in travel & accommodation support for accepted participants. There is no application fee.

Applications are open until January 8th, 2024.

Apr 8 - 10, 2024

Allen Institute, Seattle WA


Graduate, Postdocs, Scientists

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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 review article by our EVP & Director of Allen Institute of Brain Science, Hongkui Zeng, explains cell types and how to define them.

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
  • 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


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 to visualize and explore multiple single cell datasets. Currently there are two data collections from Allen Institute and Harvard University. From the Allen Institute, there are two datasets: (1) spatial transcriptomics of the entire mouse brain with 500-gene panel from ~4 million cells via MERSCOPE and (2) non-spatial transcriptomics of the entire mouse brain with ~5,200 clusters from ~4 million cells via scRNA-seq. From Harvard University, there are both coronal and sagittal datasets of spatial transcriptomics of the entire mouse brain with 1122-gene panel from ~8 million cells total via MERFISH.

Application FOR WORKSHOP

Workshop Details

Workshop dates: April 8 – 10, 2024

Application deadline: Monday, January 8, 2024, at 11:50pm Pacific Time.

The Allen Institute recognizes that people of color, women, LGTBQ+ people, and people with disadvantaged backgrounds are underrepresented in science. We are especially interested in supporting the career development of scientists in one or more of these groups, and strongly encourage individuals with these backgrounds, as well as individuals working at non-R1 institutions, to apply.

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 February 1, 2024.

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 [email protected]