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  Microscopy-BIDS: An extension to the brain imaging data structure for microscopy data

Bourget, M.-H., Kamentsky, L., Ghosh, S. S., Mazzamuto, G., Lazari, A., Markiewicz, C. J., et al. (2022). Microscopy-BIDS: An extension to the brain imaging data structure for microscopy data. Frontiers in Neuroscience, 16: 871228. doi:10.3389/fnins.2022.871228.

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Bourget, Marie-Hélène1, Author
Kamentsky, Lee2, Author
Ghosh, Satrajit S.3, 4, Author
Mazzamuto, Giacomo5, 6, Author
Lazari, Alberto7, Author
Markiewicz, Christopher J.8, Author
Oostenveld, Robert9, 10, Author
Niso, Guiomar11, Author
Halchenko, Yaroslav O.12, Author
Lipp, Ilona13, Author           
Takerkart, Sylvain14, Author
Toussaint, Paule-Joanne15, Author
Khan, Ali R.16, Author
Nilsonne, Gustav17, 18, Author
Castelli, Filippo Maria6, Author
Cohen-Adad, Julien1, 19, 20, Author
1NeuroPoly Lab, Institute of Biomedical Engineering, École Polytechnique de Montréal, QC, Canada, ou_persistent22              
2Kwanghun Chung Lab, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA, ou_persistent22              
3McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA, ou_persistent22              
4Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA, ou_persistent22              
5National Institute of Optics, Sesto Fiorentino, Italy, ou_persistent22              
6European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy, ou_persistent22              
7Nuffield Department Clinical Neurosciences, FMRIB Centre, University of Oxford, United Kingdom, ou_persistent22              
8Department of Psychology, Stanford University, CA, USA, ou_persistent22              
9Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands, ou_persistent22              
10NatMEG, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden, ou_persistent22              
11Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA, ou_persistent22              
12Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA, ou_persistent22              
13Department Neurophysics (Weiskopf), MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_2205649              
14Institut des Neurosciences de la Timone, Aix-Marseille Université, France, ou_persistent22              
15Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada, ou_persistent22              
16Robarts Research Institute, University of Western Ontario, London, ON, Canada, ou_persistent22              
17Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden, ou_persistent22              
18Swedish National Data Service, University of Gothenburg, Sweden, ou_persistent22              
19Mila – Quebec Artificial Intelligence Institute, Montréal, QC, Canada, ou_persistent22              
20Unité de neuroimagerie fonctionnelle, Centre de recherche de l'Institut universitaire de gériatrie de Montréal, QC, Canada, ou_persistent22              


Free keywords: Data sharing; Data structure; Microscopy; Open science; Specification; Standardization
 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.


Language(s): eng - English
 Dates: 2022-02-072022-03-012022-04-19
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.3389/fnins.2022.871228
Other: eCollection 2022
PMID: 35516811
PMC: PMC9063519
 Degree: -



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Project information

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Project name : -
Grant ID : 950-230815
Funding program : -
Funding organization : Canada Research Chair in Quantitative Magnetic Resonance Imaging
Project name : -
Grant ID : CIHR FDN-143263
Funding program : -
Funding organization : Canadian Institute of Health Research
Project name : -
Grant ID : 32454, 34824
Funding program : -
Funding organization : Canada Foundation for Innovation
Project name : -
Grant ID : 322736
Funding program : -
Funding organization : Fonds de Recherche du Québec–Santé
Project name : -
Grant ID : RGPIN-2019-07244
Funding program : -
Funding organization : Natural Sciences and Engineering Research Council of Canada
Project name : -
Grant ID : 5886, 35450
Funding program : -
Funding organization : Quebec BioImaging Network
Project name : -
Grant ID : R24MH117295, 5R24MH117179
Funding program : -
Funding organization : US BRAIN Initiative
Project name : -
Grant ID : P41EB019936
Funding program : -
Funding organization : National Institutes of Health
Project name : -
Grant ID : 203139/Z/16/Z
Funding program : -
Funding organization : Wellcome Trust
Project name : -
Grant ID : ANR 19-DATA-0021-01
Funding program : -
Funding organization : French Agence Nationale de la Recherche
Project name : -
Grant ID : U01MH117023
Funding program : -
Funding organization : General Hospital Corporation Center of the National Institutes of Health

Source 1

Title: Frontiers in Neuroscience
  Other : Front Neurosci
Source Genre: Journal
Publ. Info: Lausanne, Switzerland : Frontiers Research Foundation
Pages: - Volume / Issue: 16 Sequence Number: 871228 Start / End Page: - Identifier: ISSN: 1662-4548
ISSN: 1662-453X
CoNE: https://pure.mpg.de/cone/journals/resource/1662-4548