Easing batch image processing from OMERO: a new toolbox for ImageJ [version 1; peer review: 2 approved]

Abstract

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 three tools in Java language: “Simple OMERO Client”, a library to communicate with an OMERO database from Java softwares ; an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and “OMERO Macro extensions“, a dedicated vocabulary 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. Both tools are illustrated with a use case.

Keywords

• OMERO
• Fiji
• ImageJ
• Java
• Image Analysis
• Image processing
• eng