Frontiers in Neuroscience (Apr 2022)
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
- Marie-Hélène Bourget,
- Lee Kamentsky,
- Satrajit S. Ghosh,
- Satrajit S. Ghosh,
- Giacomo Mazzamuto,
- Giacomo Mazzamuto,
- Alberto Lazari,
- Christopher J. Markiewicz,
- Robert Oostenveld,
- Robert Oostenveld,
- Guiomar Niso,
- Yaroslav O. Halchenko,
- Ilona Lipp,
- Sylvain Takerkart,
- Paule-Joanne Toussaint,
- Ali R. Khan,
- Gustav Nilsonne,
- Gustav Nilsonne,
- Filippo Maria Castelli,
- The BIDS Maintainers,
- Julien Cohen-Adad,
- Julien Cohen-Adad,
- Julien Cohen-Adad,
- Stefan Appelhoff,
- Ross Blair,
- Eric Earl,
- Franklin Feingold,
- Anthony Galassi,
- Rémi Gau,
- Christopher J. Markiewicz,
- Taylor Salo
Affiliations
- Marie-Hélène Bourget
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
- Lee Kamentsky
- Kwanghun Chung Lab, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, United States
- Satrajit S. Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Satrajit S. Ghosh
- Department of Otolaryngology–Head and Neck Surgery, Harvard Medical School, Boston, MA, United States
- Giacomo Mazzamuto
- National Research Council, National Institute of Optics, Sesto Fiorentino, Italy
- Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy
- Alberto Lazari
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, Oxford, United Kingdom
- Christopher J. Markiewicz
- Department of Psychology, Stanford University, Stanford, CA, United States
- Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- Robert Oostenveld
- 0NatMEG, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Guiomar Niso
- 1Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States
- Yaroslav O. Halchenko
- 2Department of Psychological and Brain Sciences, Center for Open Neuroscience, Dartmouth College, Hanover, NH, United States
- Ilona Lipp
- 3Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Sylvain Takerkart
- 4Institut de Neurosciences de la Timone, CNRS–Aix Marseille Université, Marseille, France
- Paule-Joanne Toussaint
- 5Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
- Ali R. Khan
- 6Robarts Research Institute, University of Western Ontario, London, ON, Canada
- Gustav Nilsonne
- 7Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Gustav Nilsonne
- 8Swedish National Data Service, Gothenburg University, Gothenburg, Sweden
- Filippo Maria Castelli
- European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy
- The BIDS Maintainers
- Julien Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
- Julien Cohen-Adad
- 9Mila – Quebec AI Institute, Montreal, QC, Canada
- Julien Cohen-Adad
- 0Functional Neuroimaging Unit, Centre de Recherche de l’Institut Universitaire de Montréal (CRIUGM), Université de Montréal, Montreal, QC, Canada
- Stefan Appelhoff
- Ross Blair
- Eric Earl
- Franklin Feingold
- Anthony Galassi
- Rémi Gau
- Christopher J. Markiewicz
- Taylor Salo
- DOI
- https://doi.org/10.3389/fnins.2022.871228
- Journal volume & issue
-
Vol. 16
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.
Keywords
