CORDIS provides links to public deliverables and publications of HORIZON projects.
Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .
Deliverables
The mandatory DEC.
Model evaluation platform (opens in new window)The web-based service allows model developers whose models are registered in the BioImage Model Zoo to apply them to BioImage Archive reference data, together with model scoring and associated leaderboards.
All project management procedures are established and the Executive Board is assembled
Risk Management Plan (opens in new window)A plan on how to monitor and manage risks exists and is made accessible.
Documentation on BioEngine application development (accessible from the AI4LIFE website) (opens in new window)The documentation on the BioEngine application development is targeted toward contributors/developers who want to create new services that are then available for all users of AI4LIFE.
Annotation standards and software, libraries and reference examples (opens in new window)A public release through GitHub or a similar source code hosting site of the format description together with software to use and convert the formats and links to reference examples hosted in the BIA
Report on AI4LIFE workshops, hackathons and communication activities, with other LS RIs (opens in new window)A full account on all workshops, workshop participations, teaching events, hackathons, outreach events, etc. conducted during the project.
First stable BioImage Zoo Model format + software tools, libraries and reference examples. (opens in new window)Public release of the format specification for the BMZ model format together with example code and links to reference examples in the BMZ
Assessment report of the end-user experience (opens in new window)Report describing: 1) the established communication channels with the users and the developers and giving figures in their usage; 2) the end-user feedback and rating of each DL model in the BioImage Model Zoo. The information can be used to improve the website (WP2); 3) the new BioImage Model Zoo members and the links built to connect consumer software with other open-source software that contributes to the AI flow in BioImage Analysis.
Documentation and training material report (opens in new window)Report summarizing the documentation and training material developed to guide: 1) developers on uploading and documenting the shared DL models and tools; 2) end-users through the selection and adoption of new models or new image processing applications.
Release resource and data sharing standards (accessible from the AI4LIFE website) (opens in new window)Our formats to store, access, share and use data and AI models have value beyond AI4LIFE. We will make them fully open, available for others to use.This will help other projects and SMEs to built other useful resources and guarantee compatibility between initiatives that would otherwise be separated by incompatible formats.
Report on FAIR guidelines followed in the consortium. (opens in new window)A full account of all guidelines the consortium has worked out and implemented during AI4LIFE.
Report on all Public Challenge activities (annually updated and published on the AI4LIFE website, also available as PDF) (opens in new window)The report will contain all analysis problems selected to be cast in a public challenge, a full description of the open and secret data used to perform the challenge, and a ranking of all participating/submitted methods including links to the models that are now available in the BMZ.
Data Management Plan (opens in new window)The data management plan will be worked out and made accessible.
BIA infrastructure and deposition pipeline for versioned reference annotations. (opens in new window)A well documented web-based deposition system allowing users to submit reference annotations for BIA datasets, search for those annotations and retrieve them through both the website and an API.
Terms of service for the BMZ website and infrastructure (opens in new window)Terms of service for the BioImage Model Zoo will be worked out and made publicly available.
Report on all Open Call activities (annually updated and published on the AI4LIFE website, also available as PDF) (opens in new window)The report will contain all applicants, protocol of selection committee meetings, selected projects, the specifications worked out with all selected partners, a summary of all collaborative activities, and an overview of al achieved results and created/deployed models/methods.
Policy Brief (opens in new window)Policy brief highlighting key findings, recommendations, and policy implications of the AI4Life project.
Strategy for dissemination of information within the consortium (opens in new window)Dissemination strategy within the consortium is established and agreed upon
Human-in-the-loop interfaces enable users to interact with data and/or results interactively and (when applicable) iteratively in order to improve results/ labels/ annotations.
Cloud infrastructure (accessible from the AI4LIFE website) (opens in new window)The cloud infrastructure is set up as described in Task 22
Notebooks and algorithms repository (accessible from the AI4LIFE website) (opens in new window)Notebooks to trainexecute models and supporting functionality eg for data handling will be available via a searchable repository on the AI4LIFE website Users can browse and launch them enabling them to apply any available method to their own data
User-friendly versions of zero-code tools (opens in new window)Release of novel versions of the zero-code community partners tools (i.e., deepImageJ, ZeroCostDL4Mic) supporting user-friendly connection with the BioImage Model Zool toassure its deployment by end-users. The software will be accessed through the BoImage.IO web page.
Deployment of the container system of (accessible from the AI4LIFE website) (opens in new window)The container system will allow contributors and developers to conveniently deploy their contributed methods and models.
Deployment kit for user institutions to replicate the cloud infrastructure (accessible from the AI4LIFE website) (opens in new window)The deployment kit will enable users and/or institutions to install the AI4LIFE cloud infrastructure of D2.1 on their own HPC hardware (“on premise”). This is particularly helpful if users work on sensitive data that can’t leave their own servers.
Terms of service (opens in new window)Release of terms of service for users and contributors
Publications
Author(s):
Robinson-Lehtinen, Rachel; Dörr, Dorothea
Published in:
2023
Publisher:
Zenodo
DOI:
10.5281/ZENODO.7786436
Author(s):
Ouyang, Wei; Russell, Craig
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.11085173
Author(s):
Jug, Florian; Serrano-Solano, Beatriz
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.13618545
Author(s):
Hartley, Matthew; Zulueta Coarasa, Teresa
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14938271
Author(s):
Fuster-Barcelo, Caterina
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14169720
Author(s):
Martins, Nuno Pimpão; Kalaidzidis, Yannis; Zerial, Marino; Jug, Florian
Published in:
2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 2023
Publisher:
2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)
DOI:
10.48550/ARXIV.2308.08365
Author(s):
Fuster-Barceló, Caterina; Muñoz-Barrutia, Arrate
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.17247923
Author(s):
Hartley, Matthew; Zulueta Coarasa, Teresa
Published in:
2023
DOI:
10.5281/zenodo.8296393
Author(s):
Workshop participants
Published in:
zenodo.org, 2023
Publisher:
Zenodo
DOI:
10.5281/zenodo.7681686
Author(s):
Henriques, Ricardo
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.10948859
Author(s):
Seifi, Mehdi; Jug, Florian; Galinova, Vera; Serrano-Solano, Beatriz; Deschamps, Joran
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.17247985
Author(s):
Caterina Fuster-Barceló,
Published in:
Focal Plane, 2023
Publisher:
FocalPlane
Author(s):
Ouyang, Wei; Hård, Joanna
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14169805
Author(s):
Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Published in:
bioRxiv.org, 2023
Publisher:
bioRxiv
DOI:
10.1101/2023.08.13.553080V1
Author(s):
Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Published in:
2023
Publisher:
Zenodo
DOI:
10.5281/ZENODO.10212906
Author(s):
Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Published in:
arxiv.org, 2023
Publisher:
Arxiv
DOI:
10.48550/ARXIV.2303.03793
Author(s):
Carlos Garcia-Lopez-de-Haro, Caterina Fuster-Barcelo, Curtis T. Rueden, Jonathan Heras, Vladimir Ulman, Daniel Franco-Barranco, Adrian Ines, Kevin W. Eliceiri, Jean-Christophe Olivo-Marin, Jean-Yves Tinevez, Daniel Sage, Arrate Muñoz-Barrutia
Published in:
2025
Publisher:
arXiv
DOI:
10.48550/ARXIV.2506.02783
Author(s):
Serrano-Solano, Beatriz
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14938360
Author(s):
Serrano-Solano, Beatriz
Published in:
2023
DOI:
10.5281/zenodo.7785759
Author(s):
Fuster-Barceló, Caterina
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14938584
Author(s):
Beuttenmüller, Fynn; Kreshuk, Anna; Ferreira, Mariana; Gómez de Mariscal, Estibaliz
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.17247946
Author(s):
Kreshuk, Anna; Hartley, Matthew
Published in:
No journal title, 2023
Publisher:
Zenodo
DOI:
10.5281/zenodo.7785654
Author(s):
Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Published in:
2023
Publisher:
Zenodo
DOI:
10.5281/ZENODO.7785511
Author(s):
Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Published in:
2023
DOI:
10.5281/zenodo.7987775
Author(s):
Wei Ouyang; Fynn Beuttenmueller; Estibaliz Gómez-de-Mariscal; Constantin Pape; Tom Burke; Carlos Garcia-López-de-Haro; Craig Russell; Lucía Moya-Sans; Cristina de-la-Torre-Gutiérrez; Deborah Schmidt; Dominik Kutra; Maksim Novikov; Martin Weigert; Uwe Schmidt; Peter Bankhead; Guillaume Jacquemet; Daniel Sage; Ricardo Henriques; Arrate Muñoz-Barrutia; Emma Lundberg; Florian Jug; Anna Kreshuk
Published in:
bioRxiv -, 2022
DOI:
10.1101/2022.06.07.495102
Author(s):
Mechtel, Nils; Ouyang, Wei
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14169758
Author(s):
Galinova, Vera; Jug, Florian
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.17248028
Author(s):
Hartley, Matthew
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.10948400
Author(s):
Dörr, Dorothea; Mathur, Aastha; Serrano-Solano, Beatriz; Jug, Florian; Kreshuk, Anna
Published in:
2025
Publisher:
Zenodo
DOI:
10.5281/ZENODO.17251575
Author(s):
Ouyang, Wei
Published in:
2024
Publisher:
Zenodo
DOI:
10.5281/ZENODO.14169672
Author(s):
Robinson-Lehtinen, Rachel
Published in:
AI4LIFE, Issue 1.1, 2023
Publisher:
Zenodo
DOI:
10.5281/zenodo.7786366
Author(s):
Ouyang, Wei
Published in:
Zenodo, 2023
Publisher:
Zenodo
DOI:
10.5281/ZENODO.8380089
Author(s):
Robinson-Lehtinen, Rachel
Published in:
AI4Life, Issue D1.2, 2023
Publisher:
Zenodo
DOI:
10.5281/zenodo.7785849
Author(s):
Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Published in:
Journal of Cell Science, Issue 137, 2024, ISSN 0021-9533
Publisher:
The Company of Biologists
DOI:
10.1242/JCS.261545
Author(s):
Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Cameron Shand, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones
Published in:
Nature Methods, Issue 22, 2025, ISSN 1548-7091
Publisher:
Springer Science and Business Media LLC
DOI:
10.1038/S41592-025-02794-0
Author(s):
Teresa Zulueta-Coarasa, Florian Jug, Aastha Mathur, Josh Moore, Arrate Muñoz-Barrutia, Liviu Anita, Kolawole Babalola, Peter Bankhead, Perrine Gilloteaux, Nodar Gogoberidze, Martin L. Jones, Gerard J. Kleywegt, Paul Korir, Anna Kreshuk, Aybüke Küpcü Yoldaş, Luca Marconato, Kedar Narayan, Nils Norlin, Bugra Oezdemir, Jessica L. Riesterer, Craig Russell, Norman Rzepka, Ugis Sarkans, Beatriz Serrano-Solano, Christian Tischer, Virginie Uhlmann, Vladimír Ulman, Matthew Hartley
Published in:
Nature Methods, 2025, ISSN 1548-7091
Publisher:
Springer Science and Business Media LLC
DOI:
10.48550/ARXIV.2311.10443
Author(s):
Damian Dalle Nogare; Matthew Hartley; Joran Deschamps; Jan Ellenberg; Florian Jug
Published in:
Nature Methods, 2023, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/S41592-023-01929-5
Author(s):
Mehdi Seifi; Damian Dalle Nogare; Juan Manuel Battagliotti; Vera Galinova; Ananya Kedige Rao; Pierre-Henri Jouneau; Anwai Archit; Fynn Beuttenmueller; Dorothea Dörr; Mariana G. Ferreira; Caterina Fuster-Barceló; Vera Galinova; Carlos García-López-de-Haro; Estibaliz Gómez-de-Mariscal; Matthew Hartley; Ricardo Henriques; Iván Hidalgo-Cenalmor; Florian Jug; Anna Kreshuk; Emma Lundberg; Nils Mechtel; Arrate Muñoz-Barrutia; Wei Ouyang; Constantin Pape; Craig T. Russell; Mehdi Seifi; Beatriz Serrano-Solano; Tomaz Vieira; Teresa Zulueta-Coarasa; Constantin Pape; Johan Decelle; Florian Jug; Joran Deschamps
Published in:
npj Imaging, 2025, ISSN 2948-197X
Publisher:
Nature Publishing Group US
DOI:
10.1038/S44303-025-00089-9
Author(s):
Christoph Spahn; Stuart Middlemiss; Estibaliz Gómez-de-Mariscal; Ricardo Henriques; Helge B. Bode; Séamus Holden; Mike Heilemann
Published in:
Nature Communications, 2025, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.1038/S41467-025-58723-4
Author(s):
Ouyang, Wei; Hartley, Matthew
Published in:
zenodo.org, 2023
Publisher:
Zenodo
DOI:
10.5281/zenodo.8296448
Author(s):
Luke Sorensen, Adam Humenick, Sabrina S. B. Poon, Myat Noe Han, Narges S. Mahdavian, Matthew C. Rowe, Ryan Hamnett, Estibaliz Gómez-de-Mariscal, Peter H. Neckel, Ayame Saito, Keith Mutunduwe, Christie Glennan, Robert Haase, Rachel M. McQuade, Jaime P. P. Foong, Simon J. H. Brookes, Julia A. Kaltschmidt, Arrate Muñoz-Barrutia, Sebastian K. King, Nicholas A. Veldhuis, Simona E. Carbone, Daniel P. Poole, Pradeep Rajasekhar
Published in:
Journal of Cell Science, Issue 137, 2024, ISSN 0021-9533
Publisher:
The Company of Biologists
DOI:
10.1242/JCS.261950
Author(s):
Iván Hidalgo-Cenalmor; Joanna W. Pylvänäinen; Mariana G. Ferreira; Craig T. Russell; Alon Saguy; Ignacio Arganda-Carreras; Yoav Shechtman; Arrate Muñoz-Barrutia; Beatriz Serrano-Solano; Caterina Fuster Barcelo; Constantin Pape; Emma Lundberg; Florian Jug; Joran Deschamps; Mariana G. Ferreira; Matthew Hartley; Mehdi Seifi; Teresa Zulueta-Coarasa; Vera Galinova; Wei Ouyang; Guillaume Jacquemet; Ricardo Henriques; Estibaliz Gómez-de-Mariscal
Published in:
Nature Methods, 2024, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1101/2023.11.19.567606
Author(s):
Joanna W. Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Published in:
Current Opinion in Cell Biology, Issue 85, 2025, ISSN 0955-0674
Publisher:
Elsevier BV
DOI:
10.1016/J.CEB.2023.102271
Author(s):
Christopher Schmied; Michael S. Nelson; Sergiy Avilov; Gert-Jan Bakker; Cristina Bertocchi; Johanna Bischof; Ulrike Boehm; Jan Brocher; Mariana T. Carvalho; Catalin Chiritescu; Jana Christopher; Beth
Published in:
Nature Methods, 2023, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.48550/ARXIV.2302.07005
Author(s):
Bruno M. Saraiva; Inês Cunha; António D. Brito; Gautier Follain; Raquel Portela; Robert Haase; Pedro M. Pereira; Guillaume Jacquemet; Ricardo Henriques
Published in:
Nature Methods, 2025, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/S41592-024-02562-6
Author(s):
Daniel Franco-Barranco; Jesús A. Andrés-San Román; Ivan Hidalgo-Cenalmor; Lenka Backová; Aitor González-Marfil; Clément Caporal; Anatole Chessel; Pedro Gómez-Gálvez; Luis M. Escudero; Donglai Wei; Arrate Muñoz-Barrutia; Ignacio Arganda-Carreras
Published in:
Nature Methods, 2024, ISSN 1548-7105
Publisher:
Nature Publishing Group US
DOI:
10.1101/2024.02.03.576026
Author(s):
Dominik Kylies; Hannah S. Heil; Arturo G. Vesga; Mario Del Rosario; Maria Schwerk; Malte Kuehl; Milagros N. Wong; Victor G. Puelles; Ricardo Henriques
Published in:
Nature Protocols, 2025, ISSN 1750-2799
Publisher:
Nature Protocols
DOI:
10.1038/S41596-025-01178-0
Author(s):
Beth A. Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Klara Jambor, Martin L. Jones, Florian Jug, Anna H. Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G. Martins, Sara McArdle, Kota Miura, Arrate Muñoz-Barrutia, Laura C. Murphy, Michael S. Nelson, Simon F. Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna W. Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin W. Eliceiri
Published in:
Journal of Cell Science, Issue 137, 2024, ISSN 0021-9533
Publisher:
The Company of Biologists
DOI:
10.1242/JCS.262322
Author(s):
Ananya Kedige Rao, Daniel Yee, Fabien Chevalier, Charlotte LeKieffre, Marie Pavie, Marine Olivetta, Omaya Dudin, Benoit Gallet, Elisabeth Hehenberger, Mehdi Seifi, Florian Jug, Joran Deschamps, Ting-Di Wu, Rebecca Gast, Pierre-Henri Jouneau, Johan Decelle
Published in:
Current Biology, Issue 35, 2025, ISSN 0960-9822
Publisher:
Elsevier BV
DOI:
10.1016/J.CUB.2025.03.076
Author(s):
Afonso Mendes; Bruno M. Saraiva; Guillaume Jacquemet; João I. Mamede; Christophe Leterrier; Ricardo Henriques
Published in:
Nature Communications, 2024, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.21203/RS.3.RS-5182329/V1
Author(s):
Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Published in:
Journal of Microscopy, Issue 295, 2024, ISSN 0022-2720
Publisher:
Wiley
DOI:
10.1111/JMI.13282
Author(s):
Caterina Fuster-Barceló; Carlos García López de Haro; Estibaliz Gómez-de-Mariscal; Wei Ouyang; Jean-Christophe Olivo-Marin; Daniel Sage; Arrate Muñoz-Barrutia
Published in:
Biological Imaging, 2024, ISSN 2633-903X
Publisher:
Cambridge University Press
DOI:
10.1017/S2633903X24000114
Author(s):
Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez‐de‐Mariscal, Iván Hidalgo‐Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman
Published in:
Small Methods, Issue 9, 2025, ISSN 2366-9608
Publisher:
Wiley
DOI:
10.1101/2023.07.06.548004
Author(s):
Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Published in:
Histochemistry and Cell Biology, 2023, ISSN 1432-119X
Publisher:
Histochemistry and Cell Biology
DOI:
10.5281/ZENODO.7788899
Author(s):
García López de Haro, Carlos; Dallongeville, Stéphane; Musset, Thomas; Gómez-De-Mariscal, Estibaliz; Sage, Daniel; Ouyang, Wei; Muñoz-Barrutia, Arrate; Tinevez, Jean-Yves; Olivo-Marin, Jean-Christophe
Published in:
Nature Methods, 2024, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.48550/ARXIV.2306.04796
Author(s):
Craig T Russell, Jean-Marie Burel , Awais Athar , Simon Li , Ugis Sarkans , Jason Swedlow , Alvis Brazma , Matthew Hartley , Virginie Uhlmann
Published in:
Bioinformatics, 2025, ISSN 1367-4811
Publisher:
Oxford University Press
DOI:
10.1093/BIOINFORMATICS/BTAF412
Author(s):
Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Published in:
Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Publisher:
Frontiers
DOI:
10.3389/fbinf.2023.1233748
Author(s):
Gómez-De-Mariscal, Estibaliz; Grobe, Hanna; Pylvänäinen, Joanna; Xénard, Laura; Henriques, Ricardo; Tinevez, Jean-Yves; Jacquemet, Guillaume
Published in:
PLOS Biology, 2024, ISSN 1545-7885
Publisher:
PLOS
DOI:
10.1371/JOURNAL.PBIO.3002740
Author(s):
Lei, Wanlu; Fuster-Barceló, Caterina; Reder, Gabriel; Muñoz-Barrutia, Arrate; Ouyang, Wei
Published in:
Nature Methods, 2024, ISSN 1548-7105
Publisher:
Nature Publishing Group US
DOI:
10.5281/ZENODO.10967840
Author(s):
Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug
Published in:
2023
Publisher:
ICCV'23
DOI:
10.48550/ARXIV.2211.12872
Author(s):
Ashesh Ashesh, Florian Jug
Published in:
2024
Publisher:
ECCV'24
DOI:
10.48550/ARXIV.2403.11854
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