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OMERO is a server dedicated to image data management. Built-in with Bioformats , it supports a large collection of proprietary microscopy file formats. It is a cooperative setting that enables users to share images and experimental context, represented as (biological) metadata within their research groups.

OMERO server @ CAi (as of 01/01/2024):

  • Installed on a Virtual Machine of the ZIM
  • ~70 monthly users
  • 16.5 TB of data
  • Available plugins from the webclient (https://omero-cai.hhu.de):
    • OMERO.iviewer (browse image planes)
    • OMERO.figure (create publication ready figures)
    • OMERO.tagsearch (filter & find tagged data)
    • OMERO.autotag (tag images from filenames)
    • OMERO.parade (plot data points from attached tables of data)
    • OMERO.gallery (gallery of image thumbnails)
    • OMERO.fpbioimage (3D viewer)

The OMERO server can also be accessed directly within dedicated tools, for example:

  • Fiji plugin OMERO + macro language extension
  • QuPath
  • napari
  • Python scripts