Artificial Intelligence for Image Data Analysis in the Life Sciences

Informations projet

AI4LIFE

N° de convention de subvention: 101057970

DOI

10.3030/101057970

Projet clôturé

Date de signature de la CE 31 Mai 2022

Date de début 1 Septembre 2022

Date de fin 31 Août 2025

Financé au titre de

• Research infrastructures

Coût total

€ 4 141 167,53

Contribution de l’UE

€ 4 141 166,00

Coordonné par

EURO-BIOIMAGING ERIC
Finland

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Websites, patent fillings, videos etc. (2)

Plan for dissemination and exploitation including communication activities

The mandatory DEC.

Model evaluation platform

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.

Documents, reports (17)

Report on establishment of project management procedures and executive group

All project management procedures are established and the Executive Board is assembled

Risk Management Plan

A plan on how to monitor and manage risks exists and is made accessible.

Documentation on BioEngine application development (accessible from the AI4LIFE website)

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

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

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.

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

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

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)

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.

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)

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

The data management plan will be worked out and made accessible.

BIA infrastructure and deposition pipeline for versioned reference annotations.

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

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)

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

Policy brief highlighting key findings, recommendations, and policy implications of the AI4Life project.

Strategy for dissemination of information within the consortium

Dissemination strategy within the consortium is established and agreed upon

Other (7)

Release of human-in-the-loop interfaces (accessible from the AI4LIFE website).

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)

The cloud infrastructure is set up as described in Task 22

Notebooks and algorithms repository (accessible from the AI4LIFE website)

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

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)

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)

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

Release of terms of service for users and contributors

Publications

Other (33)

AI4Life Deliverable D1.3 - Risk Management Plan

Auteurs: Robinson-Lehtinen, Rachel; Dörr, Dorothea
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.7786436

AI4Life Deliverable D2.2 - Deployment kit for user institutions to replicate the cloud infrastructure (accessible from the AI4Life website)

Auteurs: Ouyang, Wei; Russell, Craig
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.11085173

AI4Life Deliverable D7.3 - Report on FAIR guidelines followed in the consortium

Auteurs: Jug, Florian; Serrano-Solano, Beatriz
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.13618545

AI4Life Deliverable D5.4 - Model evaluation platform

Auteurs: Hartley, Matthew; Zulueta Coarasa, Teresa
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14938271

AI4Life Deliverable D3.2 - User-friendly versions of zero-code tools

Auteurs: Fuster-Barcelo, Caterina
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14169720

DeepContrast: Deep Tissue Contrast Enhancement using Synthetic Data Degradations and OOD Model Predictions

Auteurs: Martins, Nuno Pimpão; Kalaidzidis, Yannis; Zerial, Marino; Jug, Florian
Publié dans: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 2023
Éditeur: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)
DOI: 10.48550/ARXIV.2308.08365

AI4Life Deliverable D3.4 - Assessment report of the end-user experience

Auteurs: Fuster-Barceló, Caterina; Muñoz-Barrutia, Arrate
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.17247923

AI4Life Deliverable D5.1 - Annotation standards and software, libraries and reference examples

Auteurs: Hartley, Matthew; Zulueta Coarasa, Teresa
Publié dans: 2023
DOI: 10.5281/zenodo.8296393

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Auteurs: Workshop participants
Publié dans: zenodo.org, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7681686

AI4Life Deliverable D4.2 - Deployment of a container system (accessible from the AI4Life website)

Auteurs: Henriques, Ricardo
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.10948859

AI4Life Deliverable D6.1 - Report on all Open Call activities

Auteurs: Seifi, Mehdi; Jug, Florian; Galinova, Vera; Serrano-Solano, Beatriz; Deschamps, Joran
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.17247985

Outcomes of the Hackathon on Web and Cloud Infrastructure for AI-Powered BioImage Analysis

Auteurs: Caterina Fuster-Barceló,
Publié dans: Focal Plane, 2023
Éditeur: FocalPlane

AI4Life Deliverable D2.3 - Terms of service for the BMZ website and infrastructure

Auteurs: Ouyang, Wei; Hård, Joanna
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14169805

NanoPyx: super-fast bioimage analysis powered by adaptive machine learning

Auteurs: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Publié dans: bioRxiv.org, 2023
Éditeur: bioRxiv
DOI: 10.1101/2023.08.13.553080V1

AI4Life - Policy Brief I

Auteurs: Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.10212906

Roadmap on Deep Learning for Microscopy

Auteurs: Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Publié dans: arxiv.org, 2023
Éditeur: Arxiv
DOI: 10.48550/ARXIV.2303.03793

SAMJ: Fast image annotation on ImageJ/Fiji via Segment Anything Model

Auteurs: 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
Publié dans: 2025
Éditeur: arXiv
DOI: 10.48550/ARXIV.2506.02783

AI4Life Deliverable D7.2 - Report on AI4Life workshops, hackathons and communication activities with other LS RIs

Auteurs: Serrano-Solano, Beatriz
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14938360

AI4Life Deliverable D7.1 - Plan for dissemination and exploitation including communication activities

Auteurs: Serrano-Solano, Beatriz
Publié dans: 2023
DOI: 10.5281/zenodo.7785759

AI4Life Deliverable D3.3 - Documentation and Training Material Report

Auteurs: Fuster-Barceló, Caterina
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14938584

AI4Life Deliverable D4.4 - Release resource and data sharing standards (accessible from the AI4Life website)

Auteurs: Beuttenmüller, Fynn; Kreshuk, Anna; Ferreira, Mariana; Gómez de Mariscal, Estibaliz
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.17247946

AI4Life Deliverable D1.4 - Data Management Plan

Auteurs: Kreshuk, Anna; Hartley, Matthew
Publié dans: No journal title, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Auteurs: Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.7785511

AI4Life Deliverable D4.1 - Notebooks and algorithms repository (accessible from the AI4Life website)

Auteurs: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Publié dans: 2023
DOI: 10.5281/zenodo.7987775

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis

Auteurs: 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
Publié dans: bioRxiv -, 2022
DOI: 10.1101/2022.06.07.495102

AI4Life Deliverable D4.3 - Release of human-in-the-loop interfaces (accessible from the AI4Life website)

Auteurs: Mechtel, Nils; Ouyang, Wei
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14169758

AI4Life Deliverable D6.2 - Report on all Public Challenge activities

Auteurs: Galinova, Vera; Jug, Florian
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.17248028

AI4Life Deliverable D5.2 - BioImage Archive infrastructure and deposition pipeline for versioned reference annotations

Auteurs: Hartley, Matthew
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.10948400

AI4Life - Policy Brief II

Auteurs: Dörr, Dorothea; Mathur, Aastha; Serrano-Solano, Beatriz; Jug, Florian; Kreshuk, Anna
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.17251575

AI4Life Deliverable D2.4 - Documentation on BioEngine application development (accessible from the AI4Life website)

Auteurs: Ouyang, Wei
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14169672

AI4Life Deliverable D1.1 - Report on the establishment of the project management procedures and the executive group

Auteurs: Robinson-Lehtinen, Rachel
Publié dans: AI4LIFE, Numéro 1.1, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7786366

AI4Life Deliverable D2.1 - Cloud infrastructure (accessible from the AI4Life website)

Auteurs: Ouyang, Wei
Publié dans: Zenodo, 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.8380089

AI4Life Deliverable D1.2 - Strategy for dissemination of information within the consortium

Auteurs: Robinson-Lehtinen, Rachel
Publié dans: AI4Life, Numéro D1.2, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785849

Peer reviewed articles (26)

Harnessing artificial intelligence to reduce phototoxicity in live imaging

Auteurs: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Publié dans: Journal of Cell Science, Numéro 137, 2024, ISSN 0021-9533
Éditeur: The Company of Biologists
DOI: 10.1242/JCS.261545

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy

Auteurs: Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Cameron Shand, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones
Publié dans: Nature Methods, Numéro 22, 2025, ISSN 1548-7091
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S41592-025-02794-0

MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

Auteurs: 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
Publié dans: Nature Methods, 2025, ISSN 1548-7091
Éditeur: Springer Science and Business Media LLC
DOI: 10.48550/ARXIV.2311.10443

Nature Methods

Auteurs: Damian Dalle Nogare; Matthew Hartley; Joran Deschamps; Jan Ellenberg; Florian Jug
Publié dans: Nature Methods, 2023, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/S41592-023-01929-5

FeatureForest: the power of foundation models, the usability of random forests

Auteurs: 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
Publié dans: npj Imaging, 2025, ISSN 2948-197X
Éditeur: Nature Publishing Group US
DOI: 10.1038/S44303-025-00089-9

Nature Communications

Auteurs: Christoph Spahn; Stuart Middlemiss; Estibaliz Gómez-de-Mariscal; Ricardo Henriques; Helge B. Bode; Séamus Holden; Mike Heilemann
Publié dans: Nature Communications, 2025, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/S41467-025-58723-4

AI4Life Deliverable D5.3 - First stable BioImage Zoo Model format, software tools, libraries and reference examples

Auteurs: Ouyang, Wei; Hartley, Matthew
Publié dans: zenodo.org, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8296448

Gut Analysis Toolbox – automating quantitative analysis of enteric neurons

Auteurs: 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
Publié dans: Journal of Cell Science, Numéro 137, 2024, ISSN 0021-9533
Éditeur: The Company of Biologists
DOI: 10.1242/JCS.261950

Nature Methods

Auteurs: 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
Publié dans: Nature Methods, 2024, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1101/2023.11.19.567606

Live-cell imaging in the deep learning era

Auteurs: Joanna W. Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Publié dans: Current Opinion in Cell Biology, Numéro 85, 2025, ISSN 0955-0674
Éditeur: Elsevier BV
DOI: 10.1016/J.CEB.2023.102271

Nature Methods

Auteurs: 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
Publié dans: Nature Methods, 2023, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.48550/ARXIV.2302.07005

Nature Methods

Auteurs: Bruno M. Saraiva; Inês Cunha; António D. Brito; Gautier Follain; Raquel Portela; Robert Haase; Pedro M. Pereira; Guillaume Jacquemet; Ricardo Henriques
Publié dans: Nature Methods, 2025, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/S41592-024-02562-6

BiaPy: accessible deep learning on bioimages

Auteurs: 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
Publié dans: Nature Methods, 2024, ISSN 1548-7105
Éditeur: Nature Publishing Group US
DOI: 10.1101/2024.02.03.576026

Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues

Auteurs: Dominik Kylies; Hannah S. Heil; Arturo G. Vesga; Mario Del Rosario; Maria Schwerk; Malte Kuehl; Milagros N. Wong; Victor G. Puelles; Ricardo Henriques
Publié dans: Nature Protocols, 2025, ISSN 1750-2799
Éditeur: Nature Protocols
DOI: 10.1038/S41596-025-01178-0

The crucial role of bioimage analysts in scientific research and publication

Auteurs: 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
Publié dans: Journal of Cell Science, Numéro 137, 2024, ISSN 0021-9533
Éditeur: The Company of Biologists
DOI: 10.1242/JCS.262322

Hijacking and integration of algal plastids and mitochondria in a polar planktonic host

Auteurs: 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
Publié dans: Current Biology, Numéro 35, 2025, ISSN 0960-9822
Éditeur: Elsevier BV
DOI: 10.1016/J.CUB.2025.03.076

Nature Communications

Auteurs: Afonso Mendes; Bruno M. Saraiva; Guillaume Jacquemet; João I. Mamede; Christophe Leterrier; Ricardo Henriques
Publié dans: Nature Communications, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.21203/RS.3.RS-5182329/V1

The rise of data‐driven microscopy powered by machine learning

Auteurs: Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Publié dans: Journal of Microscopy, Numéro 295, 2024, ISSN 0022-2720
Éditeur: Wiley
DOI: 10.1111/JMI.13282

Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ

Auteurs: Caterina Fuster-Barceló; Carlos García López de Haro; Estibaliz Gómez-de-Mariscal; Wei Ouyang; Jean-Christophe Olivo-Marin; Daniel Sage; Arrate Muñoz-Barrutia
Publié dans: Biological Imaging, 2024, ISSN 2633-903X
Éditeur: Cambridge University Press
DOI: 10.1017/S2633903X24000114

This Microtubule Does Not Exist: Super‐Resolution Microscopy Image Generation by a Diffusion Model

Auteurs: Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez‐de‐Mariscal, Iván Hidalgo‐Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman
Publié dans: Small Methods, Numéro 9, 2025, ISSN 2366-9608
Éditeur: Wiley
DOI: 10.1101/2023.07.06.548004

Building a FAIR image data ecosystem for microscopy communities

Auteurs: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publié dans: Histochemistry and Cell Biology, 2023, ISSN 1432-119X
Éditeur: Histochemistry and Cell Biology
DOI: 10.5281/ZENODO.7788899

Nature Methods

Auteurs: 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
Publié dans: Nature Methods, 2024, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.48550/ARXIV.2306.04796

bia-binder: a web-native cloud compute service for the bioimage analysis community

Auteurs: Craig T Russell, Jean-Marie Burel , Awais Athar , Simon Li , Ugis Sarkans , Jason Swedlow , Alvis Brazma , Matthew Hartley , Virginie Uhlmann
Publié dans: Bioinformatics, 2025, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/BIOINFORMATICS/BTAF412

Moving beyond the desktop: prospects for practical bioimage analysis via the web

Auteurs: Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Publié dans: Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Éditeur: Frontiers
DOI: 10.3389/fbinf.2023.1233748

CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data

Auteurs: Gómez-De-Mariscal, Estibaliz; Grobe, Hanna; Pylvänäinen, Joanna; Xénard, Laura; Henriques, Ricardo; Tinevez, Jean-Yves; Jacquemet, Guillaume
Publié dans: PLOS Biology, 2024, ISSN 1545-7885
Éditeur: PLOS
DOI: 10.1371/JOURNAL.PBIO.3002740

BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging

Auteurs: Lei, Wanlu; Fuster-Barceló, Caterina; Reder, Gabriel; Muñoz-Barrutia, Arrate; Ouyang, Wei
Publié dans: Nature Methods, 2024, ISSN 1548-7105
Éditeur: Nature Publishing Group US
DOI: 10.5281/ZENODO.10967840

Conference proceedings (2)

µSplit: efficient image decomposition for microscopy data

Auteurs: Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug
Publié dans: 2023
Éditeur: ICCV'23
DOI: 10.48550/ARXIV.2211.12872

denoiSplit: A Method for Joint Microscopy Image Splitting and Unsupervised Denoising

Auteurs: Ashesh Ashesh, Florian Jug
Publié dans: 2024
Éditeur: ECCV'24
DOI: 10.48550/ARXIV.2403.11854