![]() The organisation, browsing and searching of images is eased by multiple cataloguing tools, as data can be annotated with tags, comments, key-value pairs, tables, and supplementary files. Over 150 proprietary microscopy image formats are supported. OMERO is a complete platform designed for managing (organizing, editing, analysing and sharing) images online through standalone clients (OMERO.insight) and dedicated web interfaces, including a viewer for full multi-dimensional image display, a figure editor, analysis with internal scripts and an integrated data mining tool. ![]() In this ecosystem, the Open Microscopy Environment (OME) Remote Objects (OMERO), 11 and ImageJ/Fiji 12 – 14 benefit from a high level of historical implementation in the microscopy landscape involving a large community of users and developers. While some of these programs are focused essentially on the analysis of images and others on their management, the global trend for image analysis in the machine and deep learning era is to use complementary software or platforms integrating a combination of these tools. Over the last decade many tools emerged which are in constant development: software platforms (QuPath, 1 Cell Profiler, 2 Icy, 3 KNIME, 4 napari 5), browser-based and collaborative frameworks (ImJoy, 6 BIAFLOWS, 7 TissUUmaps 8), and image databases (BisQUE, 9 Cytomine 10). Photonic microscopes and associated areas of expertise in image analysis are often available in cellular imaging facilities which tend to propose unified tools to manage images and associated projects. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Ĭell biology research is a big provider of multidimensional image data through the use of multimodal microscopy approaches to decipher cellular processes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 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. ![]() ![]() 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. Grant information: 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. Each tool is illustrated with a use case. 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. 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. 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. 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.
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