Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
Bourget MH, Kamentsky L, Ghosh SS, Mazzamuto G, Lazari A, Markiewicz CJ, Oostenveld R, Niso G, Halchenko YO, Lipp I, Takerkart S, Toussaint PJ, Khan AR, Nilsonne G, Castelli FM, BIDS Maintainers, Cohen-Adad J
Identifiers and access
- DOI
- 10.3389/fnins.2022.871228
- PubMed
- 35516811
- PMC
- PMC9063519
Key findings
Microscopy-BIDS extends the Brain Imaging Data Structure to 2D/3D, ex/in vivo, micro-CT, optical, and electron microscopy data, providing comprehensible hardware, acquisition, and sample metadata definitions to support multi-modal, multi-scale imaging harmonisation.
Abstract
Source: pubmed
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.
Topics
- reproducibility-tooling
- open-data-standards
Lab authors
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