❗ NOTE: This repository is out of sync, lagging far behind the developement branch in WebProtégé. Until the sync between WebProtégé and Git is established, the development and releases will happen there. See NCBO BioPortal or https://edamontology.org/EDAM-bioimaging.owl for the latest release. ❗
Poster: EDAM Bioimaging 2024 (older, citable poster is at 
An ontology of imaging and related techniques and technologies, image processing and analysis, image data and formats, within bio- and other sciences.
EDAM Bioimaging is an extension to the EDAM ontology (http://edamontology.org), dedicated to imaging and (bio)image informatics, AI/ML, mass spectrometry, and cytometry. It has been developed by an open, global community of contributors, including consortia and projects such as NEUBIAS/GloBIAS, COMULIS, ELIXIR, Euro-BioImaging, vEM, QUAREP-LiMi, foundingGIDE, EOSC OSCARS, and more, within bio- and other sciences.
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Last released version at the NCBO BioPortal
Always the latest version:
- In OWL format from http://edamontology.org/EDAM-bioimaging.owl
This is an open community project (transparent and participatory), and thus contributions are very welcome!
The most accessible way of contributing is writing comments with suggestions or needs for clarification, and starting discussion threads. Multiple channels are avaialable:
Preferred:
- Add comments to the live development version of EDAM-bioimaging at WebProtégé. Free registration at WebProtégé is required. Select a concept and "Start new thread" in the "Comments" widget|window (not "Comments" tab, stay in the "Classes" tab). Contribute to already open threads ibid or in the "Comments" tab.
Other options:
- Submit or comment on an issue at GitHub
- Add a proposal or comment to EDAM Bioimaging at the NCBO BioPortal
- to a selected concept in the "Classes" tab by clicking the small "Notes" tab on the right (still within the big "Classes" tab)
- on the general level in the "Notes" tab. You can include new concept proposals here.
If you want to contribute in person, please join or organise a hackathon. Get in touch via WebProtégé, GitHub, or drmatuskalas@duck.com for planning. Sucessful example hackathons for editing EDAM Bioimaging were the NEUBIAS Taggathons.
The content of EDAM Bioimaging is developed collaboratively at http://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes. Everyone can post comments with suggestions, and reply to other comments (see above). Onboarded editors can edit.
(Download BibTeX)
Before a full article is published, please cite the following when refering to EDAM Bioimaging in a scholarly publication:
- Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A. Kirschmann, Anatole Chessel, Leandro Scholz, Fabienne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, and Perrine Paul-Gilloteaux. We are welcoming new contributors! (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000Research, 9(ELIXIR): 162. Poster.
Open Access
The "mainline" EDAM ontology can be cited by:
- Melissa Black, Lucie Lamothe, Hager Eldakroury, Mads Kierkegaard, Ankita Priya, Anne Machinda, Uttam Singh Khanduja, Drashti Patoliya, Rashika Rathi, Tawah Peggy Che Nico, Gloria Umutesi, Claudia Blankenburg, Anita Op, Precious Chieke, Omodolapo Babatunde, Steve Laurie, Steffen Neumann, Veit Schwämmle, Ivan Kuzmin, Chris Hunter, Jonathan Karr, Jon Ison, Alban Gaignard, Bryan Brancotte, Hervé Ménager, Matúš Kalaš (2022). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. F1000Research, 11(ISCB Comm J): 1. Poster.
Open access
