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.

ABOUT THE TOOLS

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.