U24NS133077

Scientific and Public Outreach of Cell Type Taxonomies (SPOCTT) Initiative - 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 quantitatively 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.

Allen Institute

(1) TO SUPPORT EXTRAMURAL RESEARCH FUNDED BY THE NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE (NINDS) INCLUDING: BASIC RESEARCH THAT EXPLORES THE FUNDAMENTAL STRUCTURE AND FUNCTION OF THE BRAIN AND THE NERVOUS SYSTEM, RESEARCH TO UNDERSTAND THE CAUSES AND ORIGINS OF PATHOLOGICAL CONDITIONS OF THE NERVOUS SYSTEM WITH THE GOAL OF PREVENTING THESE DISORDERS, RESEARCH ON THE NATURAL COURSE OF NEUROLOGICAL DISORDERS, IMPROVED METHODS OF DISEASE PREVENTION, NEW METHODS OF DIAGNOSIS AND TREATMENT, DRUG DEVELOPMENT, DEVELOPMENT OF NEURAL DEVICES, CLINICAL TRIALS, AND RESEARCH TRAINING IN BASIC, TRANSLATIONAL AND CLINICAL NEUROSCIENCE. THE INSTITUTE IS THE LARGEST FUNDER OF BASIC NEUROSCIENCE IN THE US AND SUPPORTS RESEARCH ON TOPICS INCLUDING BUT NOT LIMITED TO: DEVELOPMENT OF THE NERVOUS SYSTEM, INCLUDING NEUROGENESIS AND PROGENITOR CELL BIOLOGY, SIGNAL TRANSDUCTION IN DEVELOPMENT AND PLASTICITY, AND PROGRAMMED CELL DEATH, SYNAPSE FORMATION, FUNCTION, AND PLASTICITY, LEARNING AND MEMORY, CHANNELS, TRANSPORTERS, AND PUMPS, CIRCUIT FORMATION AND MODULATION, BEHAVIORAL AND COGNITIVE NEUROSCIENCE, SENSORIMOTOR LEARNING, INTEGRATION AND EXECUTIVE FUNCTION, NEUROENDOCRINE SYSTEMS, SLEEP AND CIRCADIAN RHYTHMS, AND SENSORY AND MOTOR SYSTEMS. IN ADDITION, THE INSTITUTE SUPPORTS BASIC, TRANSLATIONAL AND CLINICAL STUDIES ON A NUMBER OF DISORDERS OF THE NERVOUS SYSTEM INCLUDING (BUT NOT LIMITED TO): STROKE, TRAUMATIC INJURY TO THE BRAIN, SPINAL CORD AND PERIPHERAL NERVOUS SYSTEM, NEURODEGENERATIVE DISORDERS, MOVEMENT DISORDERS, BRAIN TUMORS, CONVULSIVE DISORDERS, INFECTIOUS DISORDERS OF THE BRAIN AND NERVOUS SYSTEM, IMMUNE DISORDERS OF THE BRAIN AND NERVOUS SYSTEM, INCLUDING MULTIPLE SCLEROSIS, DISORDERS RELATED TO SLEEP, AND PAIN. PROGRAMMATIC AREAS, WHICH ARE PRIMARILY SUPPORTED BY THE DIVISION OF NEUROSCIENCE, ARE ALSO SUPPORTED BY THE DIVISION OF EXTRAMURAL ACTIVITIES, THE DIVISION OF TRANSLATIONAL RESEARCH, THE DIVISION OF CLINICAL RESEARCH, THE OFFICE OF TRAINING AND WORKFORCE DEVELOPMENT, THE OFFICE OF PROGRAMS TO ENHANCE NEUROSCIENCE WORKFORCE DEVELOPMENT, AND THE OFFICE OF INTERNATIONAL ACTIVITIES. (2) TO EXPAND AND IMPROVE THE SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. TO UTILIZE THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM, TO STIMULATE AND FOSTER SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION.

93.372 - 21st Century Cures Act - Brain Research through Advancing Innovative Neurotechnologies

National Institute of Neurological Disorders and Stroke (NNDS) [HHS - NIH]

Washington United States

State-Wide

BRAIN Initiative: Research Resource Grants for Technology Integration and Dissemination (U24 Clinical Trial Not Allowed) (RFA-NS-23-026)

Amendment Since initial award the End Date has been extended from 08/31/25 to 08/31/29 and the total obligations have increased 177% from $1,107,724 to $3,066,674.