Biological and Biomedical Sciences

About

EuroBioImaging is an EU ESFRI Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences. It provides access to a broad range of state-of-the-art technologies in biological and biomedical imaging for life scientists. In addition, it offers image data support and training for users and providers. It consists of 29 geographically distributed Node Candidates (specialised imaging facilities) and 36 imaging technologies are offered. The BioImage Archive, as managed at EMBL-EBI, stores and distributes biological images that are useful to life-science researchers. It provides data archiving services to the broader bioimaging database community. The Archive was launched in July 2019, and currently is a collection of resources:

  • EMPIAR for electron microscopy data,
  • Cell-IDR and Tissue-IDR (Image Data Resource) for high quality, curated light microscopy data on cellular and tissue level respectively,
  • BioStudies database that is a generic resource able to accept any other imaging datasets that do not fit into EMPIAR, Cell-IDR, or Tissue-IDR.

With content including marine microscopy data, the resource integrates imaging data with molecular and phenotype data from, e.g., ELIXIR data resources. It includes information on experimental protocols and outputs: parameters, analyses and variations observed in cells and features under different experimental variables/parameters. All data is available at the portal. All software for building and running the archive and reading metadata is open source and available on GitHub.

Type & number of data sets

The BioImage Archive contains the following number of data sets as of November 2019: EMPIAR (265 datasets), BioStudies (434 datasets), Cell-IDR (57 datasets) and Tissue-IDR (17) datasets. See https://idr.openmicroscopy.org/about/studies.html for IDR data summary. These 4 separate databases hav with different metadata and data models, and different search and access API’s. Content is only partly marine related. Blue-Cloud should focus on images and databases relevant for the marine domain.

Figure 1: Homepage of BioImage Archive with access to EMPIAR, Cell-IDR, Tissue-IDR, and BioStudies

EMPIAR provides image data in the formats in which they are uploaded; it is recommended to use common formats in the field including MRC, MRCS, TIFF, DM4, IMAGIC, SPIDER, MRC FEI and RAW FEI. IDR accepts and allows downloading data in formats readable by Bio-Formats library. BioStudies accepts and distributes data in any format; it is recommended to use imaging formats readable by the Bio-Formats library.

Core Services

The BioImage Archive has discovery for each of its database modules EMPIAR, Cell-IDR and Tissue-IDR, and BioStudies.

Index of BioImage Archive datasets in EMPIAR and BioStudies (currently does not include Cell-IDR or Tissue-IDR):

Figure 2: Example of image at EMPIAR


Blue-Cloud partners involved