IDR — Image Data Resource

Overview

The Image Data Resource (IDR) is a public repository for reference image datasets from published scientific studies, hosted at EMBL-EBI and operated jointly with the University of Dundee OME team. It is the primary open-access archive for biological microscopy and biomedical imaging data associated with peer-reviewed publications. IDR focuses on curated reference datasets that support reproducibility and reanalysis of published findings, rather than raw data submissions. All datasets are FAIR-compliant and linked to their source publications, with structured metadata following REMBI and OME File Formats standards.

Scope and Content

IDR hosts imaging datasets across a wide range of biological modalities. Light microscopy is well represented, including fluorescence, confocal, super-resolution, and high-content screening data. Electron microscopy modalities (TEM, SEM, and correlative CLEM) are also covered, as are medical imaging datasets from clinical radiology and pathology, high-content phenotypic screens with associated compound libraries, and spatial transcriptomics and multiplexed imaging.

Technical Infrastructure

IDR runs on OME’s OMERO platform. It provides programmatic access via OMERO Python, Java, and R APIs, as well as web-based image browsing and annotation. Datasets can be analysed remotely via integration with Jupyter notebooks, without downloading the underlying files. Metadata is stored in OME File Formats (OME-TIFF and OME-Zarr) for interoperability, and DOIs are assigned through the EMBL-EBI data submission system.

Relationship to BioImage Archive

BioImage Archive and IDR are complementary EMBL-EBI services that serve different purposes within the open bioimaging ecosystem. IDR is a curated repository of reference datasets from published studies, built on OMERO and providing rich metadata, programmatic access, and tools for remote reanalysis. BioImage Archive is a broader submission repository for all biological image data submitted to meet open access mandates.

Connections

• Operated by: EMBL (EMBL-EBI) / University of Dundee OME
• Built on: OMERO
• Metadata standard: REMBI
• Curated counterpart: BioImage Archive (broader image submission)

Resources

• https://idr.openmicroscopy.org
• https://idr.openmicroscopy.org/about/
• https://doi.org/10.1038/nmeth.4326 (Williams et al. 2017, IDR primary publication)