Virtual observatory of the cortex: organelles, cells, circuits, and dynamics

皮质虚拟观察站：细胞器、细胞、回路和动力学

• 批准号: 10440183
• 负责人: Forrest Christie Collman
• 金额: $ 159.38万
• 依托单位: ALLEN INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10440183
• 关键词: Address; Area; Astronomy; Basic Science; Brain; Brain Diseases; Calcium; Cells; Cellular biology; Classification; Communities; Computer Analysis; Computer software; Data; Data Set; Dependence; Doctor of Philosophy; Drosophila genus; Education and Outreach; Educational workshop; Event; Frequencies; Funding; Human; Image; Institutes; Internet; Knowledge; Link; Location; Manuals; Mechanics; Morphology; Mus; Neurobiology; Neuroglia; Neurons; Neurosciences; Organelles; Persons; Physiology; Procedures; Quality Control; Research; Research Personnel; Resource Sharing; Resources; Schedule; Scientist; Site; Slice; Specialist; Stimulus; Structure; Synapses; Techniques; Testing; Time; Update; Visual Cortex; area V1; automated segmentation; base; cell type; clinically relevant; cortex mapping; cost; data access; data sharing; design; experimental study; extrastriate visual cortex; fly; imaging Segmentation; instrument; learning materials; millimeter; nanoscale; network models; neural circuit; novel strategies; outreach; petabyte; programs; reconstruction; recruit; response; simulation; social media; success; theories; virtual; visual coding; visual stimulus; wasting

We propose to create VOrtex, a Virtual Observatory for the Cortex: Spanning the Scales of Organelles, Cells, Circuits, and Dynamics. The observatory will disseminate an existing dataset: an automated reconstruction of all cells in a cubic millimeter of mouse visual cortex, along with the synaptic connectivity of the neurons and calcium-imaged responses to video stimuli. The cubic millimeter volume spans all layers of cortex and four visual areas (V1, LM, AL, RL). A team of human proofreaders will detect and correct the remaining errors in the automated segmentation. Such semiautomated reconstruction by “proofreading” is much faster than manual tracing of neurons. Considerable human proofreading effort is still required, however, due to the enormous scale of the data. Our cubic millimeter volume is 35x larger than an entire Drosophila brain, and 70x larger than the Janelia fly “hemibrain.” The proofreading team can be viewed as a new kind of scientific instrument. Just as a telescope is directed by the astronomy community, proofreading efforts should be directed by the neuroscience community. Based on requests from users (target cells, scientific rationale), the proofreading schedule will be decided by a scientific steering committee. The committee will consist of representatives from five subfields: neuronal cell biology, glial cell biology, cortical cell types, cortical circuits, and theory/simulation. Our novel approach of centralized labor, but distributed governance, combined with fast public releases of proofreading updates, should accelerate scientific discovery. The proofreading team will follow established quality control procedures, and quantitative metrics of accuracy will be maintained. Updates to the reconstructed wiring diagram will be made on an at least quarterly basis. Interactive viewing of the EM images and automated segmentation will be possible from any site with an internet connection. Users may execute large-scale computational analyses on their local clusters or commercial cloud through programmatic downloading of the data using our CloudVolume software. A community manager will solicit proofreading requests from the user community, design a proofreading schedule that maximizes fulfillment of requests, and propose the schedule to the steering committee. The manager will also recruit users and help them with the mechanics of accessing the data. The Allen Institute will continue to educate in the use of this data at The Summer Workshop on the Dynamic Brain. The VOrtex will provide fundamental knowledge about the cortex. The cell biology of neurons and glia is relevant for brain diseases, and the normal wiring diagram of the cortex could be relevant to the search for connectopathies.

我们建议创建 VOrtex，一个皮质虚拟观测站：跨越细胞器、细胞、 电路和动力学天文台将传播现有的数据集：自动重建 小鼠视觉皮层一立方毫米中的所有细胞，以及神经元的突触连接和 对视频刺激的钙成像反应 立方毫米体积跨越所有皮层和四层。 视觉区域（V1、LM、AL、RL）。 人工校对团队将检测并纠正自动化中剩余的错误 这种通过“校对”进行的半自动重建比手动追踪要快得多。 然而，由于规模巨大，仍然需要大量的人工校对工作。 我们的立方毫米体积比整个果蝇大脑大 35 倍，比 Janelia 大 70 倍。 飞“半脑”。 校对小组可以被视为一种新型科学仪器，就像望远镜一样。 由天文学界指导，校对工作应由神经科学界指导。 根据用户的要求（目标细胞、科学原理），校对时间表将由 科学指导委员会将由来自五个子领域的代表组成：神经细胞 生物学、神经胶质细胞生物学、皮质细胞类型、皮质回路和理论/模拟。 集中的劳动力，但分布式的治理，结合快速公开发布的校对更新， 应加速科学发现。 校对团队将遵循既定的质量控制程序和定量指标 重建接线图的更新将至少每季度进行一次。 可以从任何具有 EM 图像的站点进行交互式查看和自动分割。 用户可以在本地集群上执行大规模计算分析或 商业云，通过使用我们的 CloudVolume 软件以编程方式下载数据。 社区管理员会向用户社区征求校对请求，设计校对方案 最大限度地满足请求的时间表，并向指导委员会提出时间表。 经理还将招募用户并帮助他们访问数据。 继续在动态大脑夏季研讨会上教育如何使用这些数据。 Vortex 将提供有关皮质、神经元和神经胶质细胞生物学的基础知识。 与脑部疾病相关，并且皮质的正常接线图可能与寻找相关 连接病。