Structure and Function of a Cubic Millimeter of Cortex: Crowdsourcing for Proofreading and Discovery

立方毫米皮质的结构和功能：用于校对和发现的众包

• 批准号: 10025901
• 负责人: Hyunjune SEBASTIAN SEUNG
• 金额: $ 635.05万
• 依托单位: PRINCETON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-20 至 2024-08-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10025901
• 关键词: 3-Dimensional; Area; Artificial Intelligence; Brain; Calcium; Caring; Cellular biology; Classification; Code; Communities; Computer software; Continuing Education; Data; Data Set; Dependence; Detection; Educational workshop; Electron Microscopy; Engineering; Event; Funding; Future; Hand; Human; Image; Infrastructure; Knowledge; Learning; Location; Machine Learning; Mental disorders; Mus; Neuroglia; Neurons; Pythons; Reproducibility; Research Personnel; Resources; Science; Source; Stimulus; Structure; Synapses; System; Training; Update; Visual; Visual Cortex; Visualization; Work; automated algorithm; automated segmentation; base; cell type; cognitive load; connectome; crowdsourcing; deep learning; design; heuristics; imaging Segmentation; improved; large datasets; microscopic imaging; millimeter; mouse model; online community; peer; programs; reconstruction; recruit; response; tool; visual coding; volunteer

At the end of 2020, the IARPA MICrONS program will conclude with an automated reconstruction of all neurons in a cubic millimeter of mouse visual cortex, along with the neurons’ synaptic connectivity and calcium-imaged responses to video stimuli. We believe that this dataset could become the most widely used resource in the field of cortical circuits, but more work is required to realize this potential. We propose to create an online community called Pyr (pronounced “peer”) that takes the result of MICrONS as its starting point. We propose to detect and correct the remaining errors in the automated segmentation through automated algorithms and human proofreading working in tandem. Automated error detection and correction will utilize hand-designed heuristics as well as deep learning and deep metric learning. Proofreading will be crowdsourced to nonscientist volunteers, a concept pioneered by Eyewire, but updated to handle a 1000x larger dataset and far more accurate artificial intelligence. We expect that Pyr will generate more cortical connections than any previous study, by orders of magnitude. This information will be accompanied by calcium-imaged visual responses of 80,000 neurons. With such an enormous and rich dataset, the primary bottleneck will become scientific discovery. We propose to crowdsource discovery by assembling a community of researchers who collaborate with Pyr and each other. Discovery infrastructure will include a “Science API” that allows programmatic access to the primary and derived data through Python functions, an automated system for “materializing” the connectome that makes the result of proofreading available to researchers with essentially zero delay, and a versioning system will insure that analyses are reproducible. We will create a framework enabling the community to contribute their own kinds of annotations, which will be included in materialization. Finally, we will build interactive discovery tools that couple Science API queries with visualization. We envision a community of researchers who will build upon the above discovery infrastructure, creating and sharing analysis tools of their own. They will investigate diverse questions about cortical structure and function, including many that we cannot foresee at all. In the future, Pyr could incorporate other cortical datasets as they become available, with much less engineering effort than the original MICrONS dataset. As with MICrONS, software will be developed in the open in public github repos. This software could be reused by others to build systems similar to Pyr.

到2020年底，IARPA的微米计划将完成所有的自动重建

项目成果

FlyWire: online community for whole-brain connectomics.

• DOI: 10.1038/s41592-021-01330-0
• 发表时间: 2022-01
• 期刊: Nature methods
• 影响因子: 48
• 作者: Dorkenwald S;McKellar CE;Macrina T;Kemnitz N;Lee K;Lu R;Wu J;Popovych S;Mitchell E;Nehoran B;Jia Z;Bae JA;Mu S;Ih D;Castro M;Ogedengbe O;Halageri A;Kuehner K;Sterling AR;Ashwood Z;Zung J;Brittain D;Collman F;Schneider-Mizell C;Jordan C;Silversmith W;Baker C;Deutsch D;Encarnacion-Rivera L;Kumar S;Burke A;Bland D;Gager J;Hebditch J;Koolman S;Moore M;Morejohn S;Silverman B;Willie K;Willie R;Yu SC;Murthy M;Seung HS
• 通讯作者: Seung HS

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity.

• DOI: 10.1016/j.cell.2022.01.023
• 发表时间: 2022-03-17
• 期刊: CELL
• 影响因子: 64.5
• 作者: Turner, Nicholas L.;Macrina, Thomas;Bae, J. Alexander;Yang, Runzhe;Wilson, Alyssa M.;Schneider-Mizell, Casey;Lee, Kisuk;Lu, Ran;Wu, Jingpeng;Bodor, Agnes L.;Bleckert, Adam A.;Brittain, Derrick;Froudarakis, Emmanouil;Dorkenwald, Sven;Collman, Forrest;Kemnitz, Nico;Ih, Dodam;Silversmith, William M.;Zung, Jonathan;Zlateski, Aleksandar;Tartavull, Ignacio;Yu, Szi-chieh;Popovych, Sergiy;Mu, Shang;Wong, William;Jordan, Chris S.;Castro, Manuel;Buchanan, JoAnn;Bumbarger, Daniel J.;Takeno, Marc;Torres, Russel;Mahalingam, Gayathri;Elabbady, Leila;Li, Yang;Cobos, Erick;Zhou, Pengcheng;Suckow, Shelby;Becker, Lynne;Paninski, Liam;Polleux, Franck;Reimer, Jacob;Tolias, Andreas S.;Reid, R. Clay;da Costa, Nuno Macarico;Seung, H. Sebastian
• 通讯作者: Seung, H. Sebastian

Petascale pipeline for precise alignment of images from serial section electron microscopy.

• DOI: 10.1038/s41467-023-44354-0
• 发表时间: 2024-01-04
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Popovych, Sergiy;Macrina, Thomas;Kemnitz, Nico;Castro, Manuel;Nehoran, Barak;Jia, Zhen;Bae, J. Alexander;Mitchell, Eric;Mu, Shang;Trautman, Eric T.;Saalfeld, Stephan;Li, Kai;Seung, H. Sebastian
• 通讯作者: Seung, H. Sebastian

Structure and function of axo-axonic inhibition.

• DOI: 10.7554/elife.73783
• 发表时间: 2021-12-01
• 期刊: eLife
• 影响因子: 7.7
• 作者: Schneider-Mizell CM;Bodor AL;Collman F;Brittain D;Bleckert A;Dorkenwald S;Turner NL;Macrina T;Lee K;Lu R;Wu J;Zhuang J;Nandi A;Hu B;Buchanan J;Takeno MM;Torres R;Mahalingam G;Bumbarger DJ;Li Y;Chartrand T;Kemnitz N;Silversmith WM;Ih D;Zung J;Zlateski A;Tartavull I;Popovych S;Wong W;Castro M;Jordan CS;Froudarakis E;Becker L;Suckow S;Reimer J;Tolias AS;Anastassiou CA;Seung HS;Reid RC;Costa NMD
• 通讯作者: Costa NMD

CAVE: Connectome Annotation Versioning Engine.

CAVE：连接体注释版本控制引擎。

• DOI: 10.1101/2023.07.26.550598
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Dorkenwald,Sven;Schneider-Mizell,CaseyM;Brittain,Derrick;Halageri,Akhilesh;Jordan,Chris;Kemnitz,Nico;Castro,ManualA;Silversmith,William;Maitin-Shephard,Jeremy;Troidl,Jakob;Pfister,Hanspeter;Gillet,Valentin;Xenes,Daniel;Bae,JA
• 通讯作者: Bae,JA