Easing batch image processing from OMERO: a new toolbox for ImageJ

F1000Res. 2022 Apr 5:11:392. doi: 10.12688/f1000research.110385.2. eCollection 2022.


The Open Microscopy Environment Remote Objects (OMERO) is an open-source image manager used by many biologists to store, organize, view, and share microscopy images, while the open-source software ImageJ/Fiji is a very popular program used to analyse them. However, there is a lack of an easy-to-use generic tool to run a workflow on a batch of images without having to download them to local computers, and to automatically organize the results in OMERO. To offer this functionality, we have built (i) a library in Java: "Simple OMERO Client", to communicate with an OMERO database from Java software, (ii) an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and (iii) a new set of Macro Functions, "OMERO Macro extensions", dedicated to interact with OMERO in macro-programming. The latter is intended for developers, with additional possibilities using tag criteria, while the "Batch OMERO plugin" is more geared towards non-IT scientists and has a very easy to use interface. Each tool is illustrated with a use case.

Keywords: Automation; Fiji; Image Analysis; Image processing; ImageJ; Java; Microscopy; OMERO.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual
  • Humans
  • Image Processing, Computer-Assisted* / methods
  • Microscopy
  • Software*
  • Workflow

Grants and funding

The Université Côte d'Azur and EMBRC-France OMERO Database deployment was financially supported by the "Complexity and diversity of living systems" Academie of Excellence established within the framework of the UCAJEDI IdEx program. This work has been supported by the French government, through the UCAJEDI Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-15-IDEX-01. The work of PP and SD was supported by CNRS, INSERM, Université Clermont Auvergne (UCA), 16-IDEX-0001 CAP 20-25 challenge 1, and the COST-Action INDEPTH (CA16212), the work of RV was supported by Pack Ambition Recherche project Noyau-HD from the Region Auvergne Rhone Alpes.