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

基本信息

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
项目类别：
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

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

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项目摘要

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.

我们建议创建涡流，这是皮层的虚拟天文台：跨越细胞器，细胞，，电路和动态。该观察结果将传播现有数据集：自动重建小鼠视觉皮层的立方毫米中的所有细胞，以及神经元和神经元的合成连通性钙成像对视频刺激的反应。立方毫米的体积跨越所有层皮质和四层视觉区域（V1，LM，AL，RL）。一组人类校对者将检测并纠正自动化的剩余错误分割。通过“校对”进行的这种半小矩的重建速度要比手动跟踪的速度要快得多神经元。但是，由于大规模的人类校对工作仍然需要数据。我们的立方毫米体积比整个果蝇大脑大35倍，比Janelia大70倍飞行“半脑”。校对团队可以看作是一种新型的科学工具。就像望远镜一样由天文学界的指导，校对工作应由神经科学社区指导。根据用户的请求（目标细胞，科学基本原理），校对时间表将由科学指导委员会。该委员会将包括来自五个子场：神经元细胞的代表生物学，神经胶质细胞生物学，皮质细胞类型，皮质回路和理论/模拟。我们的新颖方法集中的劳动力，但分配治理，结合了快速的公开校对更新，应该加速科学发现。校对团队将遵循既定的质量控制程序，以及定量指标将保持准确性。重建的接线图的更新将在至少季度上进行基础。从任何站点都可以使用EM图像和自动分割的交互式查看互联网连接。用户可以对其本地群集进行大规模计算分析或通过使用我们的CloudVolume软件的数据下载通过程序化下载商业云。一个社区经理将征集用户社区的校对请求，设计校对安排最大化请求的实现，并向指导委员会提出时间表。这经理还将招募用户并帮助他们访问数据的机制。艾伦学院将在夏季动态大脑的夏季研讨会上，继续教育有关此数据的使用。涡流将提供有关皮质的基本知识。神经元和神经胶质的细胞生物学与脑部疾病有关，皮质的正常接线图可能与搜索有关连接疗法。