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 for 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. 

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.