Marie-Hélène Bourget, Lee Kamentsky, Satrajit S. Ghosh, Giacomo Mazzamuto, Alberto Lazari, Christopher J. Markiewicz, Robert Oostenveld, Guiomar Niso, Yaroslav O. Halchenko, Ilona Lipp, Sylvain Takerkart, Paule-Joanne Toussaint, Ali R. Khan, Gustav Nilsonne, Filippo Maria Castelli and Julien Cohen-Adad
Article (2022)
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Abstract
The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.
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| Department: |
Department of Electrical Engineering Institut de génie biomédical |
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| Research Center: | NeuroPoly - Laboratoire de Recherche en Neuroimagerie |
| Funders: | Canada Research Chair in Quantitative Magnetic Resonance Imaging, Canadian Institute of Health Research, Canada Foundation for Innovation, Fonds de Recherche du Québec - Santé et Technology, GRSNG / NSERC, Canada First Research Excellence Fund (IVADO and TransMedTech), Courtois NeuroMod Project, Quebec BioImaging Network, INSPIRED, Mila-Tech Transfer Funding Program, Canada First Research Excellence Fund/Apogée, US Brain Initiative, National Institutes of Health, Wellcome Trust - Wellcome Centre for Integrative Neuroimaging, French Agence Nationale de la Recherche, National Insitute of Health - General Hospital Corporation Center |
| Grant number: | 950-230815, CIHR FDN-143263, 32454, 34824, 322736, RGPIN-2019-07244, 5886, 35450, R24MH117295, P41EB019936, 203139/Z/16/Z, 5R24MH117179, ANR 9-DATA-0021-01, U01MH117023 |
| PolyPublie URL: | https://publications.polymtl.ca/51165/ |
| Journal Title: | Frontiers in Neuroscience (vol. 16) |
| Publisher: | Frontiers Media |
| DOI: | 10.3389/fnins.2022.871228 |
| Official URL: | https://doi.org/10.3389/fnins.2022.871228 |
| Date Deposited: | 18 Apr 2023 14:58 |
| Last Modified: | 08 Jan 2026 00:33 |
| Cite in APA 7: | Bourget, M.-H., Kamentsky, L., Ghosh, S. S., Mazzamuto, G., Lazari, A., Markiewicz, C. J., Oostenveld, R., Niso, G., Halchenko, Y. O., Lipp, I., Takerkart, S., Toussaint, P.-J., Khan, A. R., Nilsonne, G., Castelli, F. M., & Cohen-Adad, J. (2022). Microscopy-BIDS: an extension to the brain imaging data structure for microscopy data. Frontiers in Neuroscience, 16, 8 pages. https://doi.org/10.3389/fnins.2022.871228 |
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