AUTHOR=Bourget Marie-Hélène , Kamentsky Lee , Ghosh Satrajit S. , Mazzamuto Giacomo , Lazari Alberto , Markiewicz Christopher J. , Oostenveld Robert , Niso Guiomar , Halchenko Yaroslav O. , Lipp Ilona , Takerkart Sylvain , Toussaint Paule-Joanne , Khan Ali R. , Nilsonne Gustav , Castelli Filippo Maria ,  The BIDS Maintainers , Cohen-Adad Julien , Appelhoff Stefan , Blair Ross , Earl Eric , Feingold Franklin , Galassi Anthony , Gau Rémi , Markiewicz Christopher J. , Salo Taylor 

TITLE=Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

JOURNAL=Frontiers in Neuroscience

VOLUME=16

YEAR=2022

URL=https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228

DOI=10.3389/fnins.2022.871228

ISSN=1662-453X

ABSTRACT=<p>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, <italic>ex</italic>/<italic>in vivo</italic>, 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.</p>