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

项目摘要 单细胞转录学已经改变了脑细胞类型分类的领域，允许同时 从足够多的细胞中测量足够的分子特征来对神经元进行定量和高质量的分类 跨大脑区域和物种的保护。此外，根据基因分类的细胞在很大程度上 连贯的形状、电气属性、空间位置和项目目标，带来了多式联运的梦想 细胞类型的定义越来越接近现实，但也带来了筛选这一切的主要挑战 不同的信息来学习任何给定的东西。为了应对这些挑战，艾伦研究所开发了一种 一系列高质量的参考数据集，用于组织和共享其关联单元的标准格式 类型分类，以及用于探索这些细胞类型的大量网络工具。单元类型知识资源管理器 (CTKE)于2021年12月发布，旨在探索转录学、电生理学、 小鼠初级运动皮质单个细胞类型的形态、空间定位和表观遗传学， 绒猴和人类。将于2022年底首次发布的艾伦脑细胞(ABC)图谱将使用户能够 探索整个小鼠大脑的细胞类型分类和空间图谱，显著增加了广度 CTKE覆盖的单元格类型，同时继续支持用户友好的数据探索。这两种资源 以神经科学领域独有的方式介绍细胞类型分类。 这些数据、标准和网络工具延续了作为基石的开放科学实践 自从近二十年前艾伦老鼠脑图谱发布以来，他一直是艾伦研究所的研究员。要启用用户 不仅是为了找到这些工具，而且为了成功地利用这些工具，艾伦研究所有一个既定的培训， 教育和外联计划，以支持其资源的用户在不同的职业和学习阶段。细胞 特别是类型和分类科学资源，依赖于跨越神经生物学、遗传学、应用 数学和计算机科学，这对学生和专业人员都构成了挑战，并扩展了这一点 支持这类工具的计划对神经科学界来说特别有价值。 细胞类型分类科学和公共推广(SPOCTT)倡议的目标是 使公众和科学界更广泛地获取这些公共资源， 通过整合、协作、培训、教育和外展努力相结合。通过 为分类和分类的潜在用户提供可扩展的培训资源和个性化支持 工具，我们将(1)推广细胞类型分类和相关工具的使用(特别是第一年和 2)、(2)建立大脑倡议细胞普查网络(BICCN)和艾伦研究所的分类 作为研究健康和疾病大脑的科学标准，以及(3)扩大艾伦的研究范围 建立一个更年轻、更多元化的神经科学社区。

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.