Bioimaging

Bioimaging data in open science is organised around a small set of open file format standards, a network of specialist archives, and coordinated national and European infrastructure for instrument access and platform governance.

Standards and quality

OME File Formats (OME-TIFF and OME-Zarr) are the open standards for storing and sharing biological microscopy image data, produced by the OME consortium and implemented through the OMERO image management platform. REMBI provides the metadata standard governing what information must accompany image deposits. QUAREP-LiMi is the quality assessment and reproducibility initiative for light microscopy, developing ISO-aligned measurement protocols for instrument calibration and reporting.

Data archives

IDR (Image Data Resource, EMBL-EBI) curates reference image datasets from published studies and is the primary destination for open-access publication-linked microscopy data. BioImage Archive (EMBL-EBI) serves as the broad-intake archive for all biological image data deposited under open access mandates. EMPIAR (EMBL-EBI) is the dedicated archive for raw electron microscopy image data, accepting cryo-EM datasets with no volume limit. NeuroMorpho.Org is the primary open repository for digitally reconstructed neuron and glia morphologies in SWC format.

Infrastructure and initiatives

National microscopy platforms are federated through France BioImaging (the French national node) and its European counterpart Euro-BioImaging, which provides open access to imaging technologies across 41 nodes in 18 countries. GT-GeDeM coordinates FAIR data management practices for microscopy platforms in France. BIII (BioImage Informatics Index) is the ELIXIR-affiliated community registry for bioimaging software tools, workflows, and training materials. foundingGIDE is a funded international project coordinated by Euro-BioImaging, launched in 2024, to lay the foundations for a Global Image Data Ecosystem connecting biological and biomedical image data resources across Europe, Australia, and Japan.

For the computational model repositories that store morphological reconstructions derived from bioimaging, see Reproducibility.