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

Year: 2022

Authors: Bourget MH., Kamentsky L., Ghosh S., Mazzamuto G., Lazari A., Markiewicz CJ., Oostenveld R., Niso G., Halchenko YO., Lipp I., Takerkart S., Toussaint PJ., Khan AR., Nilsonne G., Castelli FM., Cohen-Adad J.

Autors Affiliation: NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada; Kwanghun Chung Lab, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, United States; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, United States; National Research Council, National Institute of Optics, Sesto Fiorentino, Italy; European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy; Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, Oxford, United Kingdom; Department of Psychology, Stanford University, Stanford, CA, United States; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands; NatMEG, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States; Department of Psychological and Brain Sciences, Center for Open Neuroscience, Dartmouth College, Hanover, NH, United States; Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Institut de Neurosciences de la Timone, CNRS-Aix Marseille Université, Marseille, France; Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada; Robarts Research Institute, University of Western Ontario, London, ON, Canada; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Swedish National Data Service, Gothenburg University, Gothenburg, Sweden; Mila – Quebec AI Institute, Montreal, QC, Canada; Functional Neuroimaging Unit, Centre de Recherche de l’Institut Universitaire de Montréal (CRIUGM), Université de Montréal, Montreal, QC, Canada;

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.


Volume: 16      Pages from: -  to:

KeyWords: data sharing, data structure, microscopy, open science, specification, standardization
DOI: 10.3389/fnins.2022.871228