OpenTutorials#20 | neuromaps: a toolbox for comparing brain maps

文摘   2024-09-02 12:00   江苏  

OpenTutorials是OpenScience组织的在线教学与交流活动,本活动旨在促进交流一线研究中的实践技巧与经验。在本活动中,由国内外的研究者,尤其是青年研究者,分享自己在研究用到的实用技巧与经验。这些技巧可能是各种工具包的使用、编程技能、统计方法等各种内容。分享语言以中文为主,分享人偏好英文时,将使用英文。欢迎大家推荐分享人或者自荐作为分享人。





分享信息

题目



neuromaps: a toolbox for comparing brain maps


摘要



The growing amount of high-resolution reference brain maps has outpaced our ability to effectively compare and integrate them with experimentally generated maps. We present neuromaps, an open-source toolbox designed to streamline access, transformation, and analysis of brain annotations. Neuromaps offers a curated library of over 80 brain maps across diverse modalities including microstructure, function, electrophysiology, and receptor distributions. It implements robust transformations between major coordinate systems (MNI152, fsaverage, fsLR, and CIVET) and incorporates spatial null models for statistically rigorous assessment of map-to-map similarities. This standardized framework enables systematic workflows for comprehensive structural and functional annotation enrichment analysis of the human brain. By addressing the challenge of comparing data in disparate coordinate systems, neuromaps facilitates discovery across neuroscientific disciplines. As of August 2024, the toolbox has garnered over 200 stars and 50 forks on GitHub, with over 20000 downloads in the past 6 months.



报告语言




英文,中文


分享人



刘桢琦Zhen-Qi Liu

PhD student, Montreal Neurological Institute & McGill University



Zhen-Qi Liu is a 5th year PhD student at the Montreal Neurological Institute and McGill University, working under the supervision of Dr. Bratislav Misic. His research focuses on network neuroscience, connectomics, and structure-function relationship in the brain. Zhen-Qi's work aims to unravel how structure supports and constrains function at the macroscale. He is also an active open-source contributor, maintaining several packages from the Network Neuroscience Lab, including neuromaps and netneurotools, which facilitate advanced neuroimaging analysis and network modeling.



主持人



Qing Wang

Shanghai Mental Health Center,School of Medicine, Shanghai Jiao Tong University




时间



北京时间[GMT+8] 2024年9月21日(周六) 9:00 pm~10:30 pm

欧洲中部时间[CET] 2024年9月21(周六) 3:00 pm~4:30 pm

美国东部时间[EDT] 2024年9月21(周六) 9:00 am~10:30 am
美国西部时间[PST] 2024年9月21(周六) 6:00 am~7:30 am

zoom信息



Zoom meeting link: https://us06web.zoom.us/j/
Zoom meeting ID:  86304049478

References



Paper: https://www.nature.com/articles/s41592-022-01625-w
Toolbox:
https://github.com/netneurolab/neuromaps
Documentation:
https://netneurolab.github.io/neuromaps/
Network Neuroscience Lab:
https://netneurolab.github.io/



其他



本报告可将录屏公开至B站





组织团队(按名字首字母倒序排列)
COSN 学术策划小组
张晗(博士), A*STAR, Singapore
张磊(博士), University of Birmingham, UK
楊毓芳(博士), Freie Universität Berlin, Germany
杨金骉(博士), MPI Psycholinguistics, the Netherlands
徐婷(博士), Child Mind Institute, USA
肖钦予, University of Vienna, Austria
王鑫迪(博士), 待业
王庆(博士), 上海精神卫生中心
鲁彬(博士), 中科院心理所
刘泉影(博士), 南方科技大学
金淑娴(博士), University of Sussex, UK
金海洋(博士), 浙江理工大学
胡传鹏(博士), 南京师范大学
耿海洋(博士), 天桥脑科学研究院
葛鉴桥 (博士), 北京大学
高梦宇(博士), 北京师范大学
陈志毅(博士), 第三军医大学
陈妍秀(博士), 中科院心理所
陈骥(博士), 浙江大学
曹淼(博士), 北京大学

neurochat团队
张文昊(UT Southwestern Medical Center, USA)
张洳源(上海交通大学)
张磊(University of Birmingham, UK)
应浩江(苏州大学)
徐婷(Child Mind Institute, USA)
王鑫迪(待业) 
滕相斌(香港中文大学) 
鲁彬(中国科学院心理研究所)
孔祥祯(浙江大学)
胡传鹏(南京师范大学)
邸新(New Jersey Institute of Technology, USA)



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Chinese Open Science Network, a network for Transparent, Open, & Reproducible Science.开放科学中文社区,传播透明、开放和可重复的基础研究理念和实践。
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