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

Clicks: 106
ID: 276978
2022
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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 (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.
Reference Key
pouchin2022easingf1000research Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Pouchin, P.
Journal F1000Research
Year 2022
DOI
10.12688/f1000research.110385.1
URL
Keywords Keywords not found

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