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

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.

A practical guide to bioimaging research data management in core facilities

“…Examples are the ISA framework, including tools, data model and serialisation for (meta)data, 82,83 or BIDS for Microscopy. 42 Version control software (e.g., Git, Gitlab, DataLad) might be an option for computer-affine users. 84 File naming conventions with tokens can be discussed in project consultations.…”

“…However, users can learn from core facility staff about community‐established guidelines. Highlighted examples are the Recommended Metadata for Biological Images (REMBI), 37 the NBO tiered guidelines 38 and recommendations for certain fields and modalities like MITI for multiplexed tissue imaging, 39 MIHCSME for high‐content screening, 40 3D‐MMS for 3D volume microscopy 41 or the Brain Imaging Data Structure (BIDS) 42 . Tools are available to support metadata annotation 43–45 .…”

“…Where a bioimaging RDM platform is lacking, core facility staff can help users to adopt community‐approved data structuring in file systems. Examples are the ISA framework, including tools, data model and serialisation for (meta)data, 82,83 or BIDS for Microscopy 42 . Version control software (e.g., Git, Gitlab, DataLad) might be an option for computer‐affine users 84 .…”

High-speed light-sheet microscopy imaging and data post-processing using custom hardware and software solutions

“…The published datasets are a downscaled version of the acquired data (voxel size ≈ 3.5 µm isotropic, after the affine transformation described at the end of section 3), and are available for download from the DANDI † repository 5 where they are formatted according to the BIDS ‡ specification. 6…”

OME-Zarr: a cloud-optimized bioimaging file format with international community support

“…Thus, DANDI allows data to be operated on in the cloud using standardized methods and computational servers near the data. It enforces the organized structure of the Brain Imaging Data Structure (BIDS) and its microscopy extensions (Bourget et al 2022), with the latest specification 35 allowing such data to be stored in the OME-Zarr format. DANDI uses standardized metadata (JSON, JSON-LD), data organization (BIDS, or BIDS-like subset), and data storage formats (e.g., OME-Zarr) that allow the metadata to be queried before data access, and data to be accessed partially and at different resolutions.…”