Easing batch image processing from OMERO: ...
Document type :
Article dans une revue scientifique: Article original
PMID :
Title :
Easing batch image processing from OMERO: a new toolbox for ImageJ
Author(s) :
Pouchin, Pierre [Auteur]
Génétique, Reproduction et Développement [GReD]
Zoghlami, Rayan [Auteur]
Institut de pharmacologie moléculaire et cellulaire [IPMC]
Valarcher, Rémi [Auteur]
Génétique, Reproduction et Développement [GReD]
Delannoy, Maxence [Auteur]
Polytech Nice-Sophia
Carvalho, Manon [Auteur]
Polytech Nice-Sophia
Belle, Clémence [Auteur]
Polytech Nice-Sophia
Mongy, Marc [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Desset, Sophie [Auteur]
Génétique, Reproduction et Développement [GReD]
Brau, Frédéric [Auteur]
Institut de pharmacologie moléculaire et cellulaire [IPMC]
Génétique, Reproduction et Développement [GReD]
Zoghlami, Rayan [Auteur]
Institut de pharmacologie moléculaire et cellulaire [IPMC]
Valarcher, Rémi [Auteur]
Génétique, Reproduction et Développement [GReD]
Delannoy, Maxence [Auteur]
Polytech Nice-Sophia
Carvalho, Manon [Auteur]
Polytech Nice-Sophia
Belle, Clémence [Auteur]
Polytech Nice-Sophia
Mongy, Marc [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Desset, Sophie [Auteur]
Génétique, Reproduction et Développement [GReD]
Brau, Frédéric [Auteur]
Institut de pharmacologie moléculaire et cellulaire [IPMC]
Journal title :
F1000Research
Pages :
392
Publisher :
Faculty of 1000
Publication date :
2022
ISSN :
2046-1402
English keyword(s) :
Automation
Fiji
Image Analysis
Image processing
ImageJ
Java
Microscopy
OMERO
Fiji
Image Analysis
Image processing
ImageJ
Java
Microscopy
OMERO
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
English abstract : [en]
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 ...
Show more >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.Show less >
Show more >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.Show less >
Language :
Anglais
Peer reviewed article :
Oui
Audience :
Internationale
Popular science :
Non
Source :
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- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9171289/pdf
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- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9171289/pdf
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- Access the document
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