Thursday, November 21, 2024
11/21/2024
Project Summary Single cell transcriptomics has transformed the field of brain cell type classification, allowing simultaneous measurement of enough molecular features from enough cells to categorize neurons quantitively and with high conservation across brain areas and species. Furthermore, cells classified by their genes have largely coherent shapes, electrical properties, spatial locations, and projects targets, bringing the dream of multimodal cell type definitions ever closer to reality, but also introducing major challenges of sifting through all this disparate information to learn any given thing. To address these challenges the Allen Institute has developed a series of high-quality reference data sets, a standard format for organizing and sharing their associated cell type classifications, and a host of web tools for exploring these cell types. The Cell Type Knowledge Explorer (CTKE), released in December 2021, is designed for exploration of transcriptomics, electrophysiology, morphology, spatial localization, and epigenetics of individual cell types in the primary motor cortex of mouse, marmoset, and human. The Allen Brain Cell (ABC) Atlas, to be initially released in late 2022, will enable users to explore a cell type taxonomy and spatial map of the whole mouse brain, dramatically increasing the breadth of cell types covered by the CTKE, while continuing to enable user-friendly data exploration. Both resources present cell type taxonomies in a manner unique to the field of neuroscience. These data, standards, and web tools continue the open science practices that have been a keystone of the Allen Institute since the release of the Allen Mouse Brain Atlas almost two decades ago. To enable users not just to find, but also to successfully utilize these tools, the Allen Institute has an established Training, Education, and Outreach program to support users of its resources at various career and learning stages. Cell type and taxonomy scientific resources, in particular, rely on skills spanning neurobiology, genetics, applied math, and computer science, posing challenges for both students and professionals, and extending this program to support such tools would be particularly valuable to the neuroscience community. The goal of the Scientific and Public Outreach of Cell Type Taxonomies (SPOCTT) initiative is to make these public resources more widely accessible to the general and scientific communities, through a combination of consolidation, collaboration, training, education, and outreach efforts. By offering both scalable training resources and personalized support to prospective users of taxonomies and tools, we will (1) promote use of cell type taxonomies and associated tools (specifically the CTKE in year 1 and the ABC Atlas in year 2), (2) set BRAIN Initiative Cell Census Network (BICCN) and Allen Institute taxonomies as scientific standards for studying the brain in health and disease, and (3) broaden the reach of the Allen Institute to a younger and more diverse neuroscience community.
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