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Updated: Sep 24, 2025

Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

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Published on: October 8, 2013

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

Marie-Hélène Bourget¹, Lee Kamentsky², Satrajit S Ghosh^3,4

¹NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada.

Frontiers in Neuroscience

|May 6, 2022

Summary

This summary is machine-generated.

A new extension called Microscopy-BIDS standardizes microscopy imaging data organization and sharing. This Brain Imaging Data Structure extension supports diverse microscopy methods and metadata for better data harmonization.

Keywords:

data sharing data structure microscopy open science specification standardization

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Published on: August 1, 2022

Area of Science:

Neuroscience
Microscopy
Data Science

Background:

The Brain Imaging Data Structure (BIDS) is a standard for neuroimaging data organization.
BIDS has successfully expanded to various neuroimaging modalities beyond MRI.

Purpose of the Study:

To introduce an extension of the Brain Imaging Data Structure (BIDS) specifically for microscopy imaging data.
To facilitate standardized organization, sharing, and archiving of microscopy datasets.

Main Methods:

Developed a BIDS extension tailored for microscopy data.
Included support for various microscopy techniques (2D/3D, ex/in vivo, micro-CT, optical, electron microscopy).
Defined metadata for hardware, acquisition, and sample properties.

Main Results:

Presented Microscopy-BIDS, an extension for microscopy imaging data.
Provided example datasets to demonstrate the application of Microscopy-BIDS.
Established comprehensive metadata definitions for microscopy.

Conclusions:

Microscopy-BIDS enhances data harmonization across different microscopy modalities.
This extension supports multi-modal and multi-scale imaging research, including quantitative MRI applications.
Facilitates reproducible research and data sharing in microscopy.