Bringing the power of ImageJ to the OMERO platform

Alison Walter, UW-Madison LOCI & Morgridge Institute for Research


Bi-directional software bridge between ImageJ and OMERO

  • Upload and download:
    • Images
    • ROIs
    • Tables
  • Run ImageJ scripts from OMERO
  • Work with OMERO data from within ImageJ


  • N-dimensional data structures
  • Modular design
  • Extensible
  • Backwards compatibility with ImageJ 1.x
  • New:
    • Tables
    • ROIs
Want to know more about ImageJ2?
Check out the ImageJ2 paper!


  • Equivalent shapes for OMERO and ImageJ 1.x
  • N-dimensional
  • Combine-able (while preserving provenance)

On To The Demos »

From OMERO: ImageJ-Ops

From OMERO: ImageJ 1.x

From ImageJ: Updating ROIs


In ImageJ:

  • Enable OMERO 5.4 update site

In OMERO (Admins only!):

  • Install Fiji as a library in OMERO
  • Enable OMERO 5.4 update site
  • Generate scripts
For detailed installation instructions see the ImageJ-OMERO Github repository:



  • LOCI: Kevin Eliceiri, Curtis Rueden

  • KNIME: Gabriel Einsdorf

  • MPI-CBG: Tobias Pietszch

  • OME Team