Artificial Intelligence for Image Data Analysis in the Life Sciences

Projektinformationen

AI4LIFE

ID Finanzhilfevereinbarung: 101057970

DOI

10.3030/101057970

Projekt abgeschlossen

EK-Unterschriftsdatum 31 Mai 2022

Startdatum 1 September 2022

Enddatum 31 August 2025

Finanziert unter

• Research infrastructures

Gesamtkosten

€ 4 141 167,53

EU-Beitrag

€ 4 141 166,00

Koordiniert durch

EURO-BIOIMAGING ERIC
Finland

CORDIS bietet Links zu öffentlichen Ergebnissen und Veröffentlichungen von HORIZONT-Projekten.

Links zu Ergebnissen und Veröffentlichungen von RP7-Projekten sowie Links zu einigen Typen spezifischer Ergebnisse wie Datensätzen und Software werden dynamisch von OpenAIRE abgerufen.

Leistungen

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

Veröffentlichungen

Other (33)

AI4Life Deliverable D1.3 - Risk Management Plan

Autoren: Robinson-Lehtinen, Rachel; Dörr, Dorothea
Veröffentlicht in: 2023
Herausgeber: 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)

Autoren: Ouyang, Wei; Russell, Craig
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.11085173

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

Autoren: Jug, Florian; Serrano-Solano, Beatriz
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.13618545

AI4Life Deliverable D5.4 - Model evaluation platform

Autoren: Hartley, Matthew; Zulueta Coarasa, Teresa
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14938271

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

Autoren: Fuster-Barcelo, Caterina
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14169720

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

Autoren: Martins, Nuno Pimpão; Kalaidzidis, Yannis; Zerial, Marino; Jug, Florian
Veröffentlicht in: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 2023
Herausgeber: 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

Autoren: Fuster-Barceló, Caterina; Muñoz-Barrutia, Arrate
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.17247923

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

Autoren: Hartley, Matthew; Zulueta Coarasa, Teresa
Veröffentlicht in: 2023
DOI: 10.5281/zenodo.8296393

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Autoren: Workshop participants
Veröffentlicht in: zenodo.org, 2023
Herausgeber: Zenodo
DOI: 10.5281/zenodo.7681686

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

Autoren: Henriques, Ricardo
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.10948859

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

Autoren: Seifi, Mehdi; Jug, Florian; Galinova, Vera; Serrano-Solano, Beatriz; Deschamps, Joran
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.17247985

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

Autoren: Caterina Fuster-Barceló,
Veröffentlicht in: Focal Plane, 2023
Herausgeber: FocalPlane

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

Autoren: Ouyang, Wei; Hård, Joanna
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14169805

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

Autoren: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Veröffentlicht in: bioRxiv.org, 2023
Herausgeber: bioRxiv
DOI: 10.1101/2023.08.13.553080V1

AI4Life - Policy Brief I

Autoren: Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Veröffentlicht in: 2023
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.10212906

Roadmap on Deep Learning for Microscopy

Autoren: Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Veröffentlicht in: arxiv.org, 2023
Herausgeber: Arxiv
DOI: 10.48550/ARXIV.2303.03793

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

Autoren: 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
Veröffentlicht in: 2025
Herausgeber: arXiv
DOI: 10.48550/ARXIV.2506.02783

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

Autoren: Serrano-Solano, Beatriz
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14938360

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

Autoren: Serrano-Solano, Beatriz
Veröffentlicht in: 2023
DOI: 10.5281/zenodo.7785759

AI4Life Deliverable D3.3 - Documentation and Training Material Report

Autoren: Fuster-Barceló, Caterina
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14938584

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

Autoren: Beuttenmüller, Fynn; Kreshuk, Anna; Ferreira, Mariana; Gómez de Mariscal, Estibaliz
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.17247946

AI4Life Deliverable D1.4 - Data Management Plan

Autoren: Kreshuk, Anna; Hartley, Matthew
Veröffentlicht in: No journal title, 2023
Herausgeber: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Autoren: Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Veröffentlicht in: 2023
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.7785511

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

Autoren: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Veröffentlicht in: 2023
DOI: 10.5281/zenodo.7987775

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

Autoren: 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
Veröffentlicht in: 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)

Autoren: Mechtel, Nils; Ouyang, Wei
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14169758

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

Autoren: Galinova, Vera; Jug, Florian
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.17248028

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

Autoren: Hartley, Matthew
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.10948400

AI4Life - Policy Brief II

Autoren: Dörr, Dorothea; Mathur, Aastha; Serrano-Solano, Beatriz; Jug, Florian; Kreshuk, Anna
Veröffentlicht in: 2025
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.17251575

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

Autoren: Ouyang, Wei
Veröffentlicht in: 2024
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.14169672

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

Autoren: Robinson-Lehtinen, Rachel
Veröffentlicht in: AI4LIFE, Ausgabe 1.1, 2023
Herausgeber: Zenodo
DOI: 10.5281/zenodo.7786366

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

Autoren: Ouyang, Wei
Veröffentlicht in: Zenodo, 2023
Herausgeber: Zenodo
DOI: 10.5281/ZENODO.8380089

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

Autoren: Robinson-Lehtinen, Rachel
Veröffentlicht in: AI4Life, Ausgabe D1.2, 2023
Herausgeber: Zenodo
DOI: 10.5281/zenodo.7785849

Peer reviewed articles (26)

Harnessing artificial intelligence to reduce phototoxicity in live imaging

Autoren: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Veröffentlicht in: Journal of Cell Science, Ausgabe 137, 2024, ISSN 0021-9533
Herausgeber: 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

Autoren: Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Cameron Shand, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones
Veröffentlicht in: Nature Methods, Ausgabe 22, 2025, ISSN 1548-7091
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Methods, 2025, ISSN 1548-7091
Herausgeber: Springer Science and Business Media LLC
DOI: 10.48550/ARXIV.2311.10443

Nature Methods

Autoren: Damian Dalle Nogare; Matthew Hartley; Joran Deschamps; Jan Ellenberg; Florian Jug
Veröffentlicht in: Nature Methods, 2023, ISSN 1548-7091
Herausgeber: Nature Publishing Group
DOI: 10.1038/S41592-023-01929-5

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

Autoren: 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
Veröffentlicht in: npj Imaging, 2025, ISSN 2948-197X
Herausgeber: Nature Publishing Group US
DOI: 10.1038/S44303-025-00089-9

Nature Communications

Autoren: Christoph Spahn; Stuart Middlemiss; Estibaliz Gómez-de-Mariscal; Ricardo Henriques; Helge B. Bode; Séamus Holden; Mike Heilemann
Veröffentlicht in: Nature Communications, 2025, ISSN 2041-1723
Herausgeber: 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

Autoren: Ouyang, Wei; Hartley, Matthew
Veröffentlicht in: zenodo.org, 2023
Herausgeber: Zenodo
DOI: 10.5281/zenodo.8296448

Gut Analysis Toolbox – automating quantitative analysis of enteric neurons

Autoren: 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
Veröffentlicht in: Journal of Cell Science, Ausgabe 137, 2024, ISSN 0021-9533
Herausgeber: The Company of Biologists
DOI: 10.1242/JCS.261950

Nature Methods

Autoren: 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
Veröffentlicht in: Nature Methods, 2024, ISSN 1548-7091
Herausgeber: Nature Publishing Group
DOI: 10.1101/2023.11.19.567606

Live-cell imaging in the deep learning era

Autoren: Joanna W. Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Veröffentlicht in: Current Opinion in Cell Biology, Ausgabe 85, 2025, ISSN 0955-0674
Herausgeber: Elsevier BV
DOI: 10.1016/J.CEB.2023.102271

Nature Methods

Autoren: 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
Veröffentlicht in: Nature Methods, 2023, ISSN 1548-7091
Herausgeber: Nature Publishing Group
DOI: 10.48550/ARXIV.2302.07005

Nature Methods

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

BiaPy: accessible deep learning on bioimages

Autoren: 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
Veröffentlicht in: Nature Methods, 2024, ISSN 1548-7105
Herausgeber: Nature Publishing Group US
DOI: 10.1101/2024.02.03.576026

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

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

The crucial role of bioimage analysts in scientific research and publication

Autoren: 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
Veröffentlicht in: Journal of Cell Science, Ausgabe 137, 2024, ISSN 0021-9533
Herausgeber: The Company of Biologists
DOI: 10.1242/JCS.262322

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

Autoren: 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
Veröffentlicht in: Current Biology, Ausgabe 35, 2025, ISSN 0960-9822
Herausgeber: Elsevier BV
DOI: 10.1016/J.CUB.2025.03.076

Nature Communications

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

The rise of data‐driven microscopy powered by machine learning

Autoren: Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Veröffentlicht in: Journal of Microscopy, Ausgabe 295, 2024, ISSN 0022-2720
Herausgeber: Wiley
DOI: 10.1111/JMI.13282

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

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

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

Autoren: Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez‐de‐Mariscal, Iván Hidalgo‐Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman
Veröffentlicht in: Small Methods, Ausgabe 9, 2025, ISSN 2366-9608
Herausgeber: Wiley
DOI: 10.1101/2023.07.06.548004

Building a FAIR image data ecosystem for microscopy communities

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

Nature Methods

Autoren: 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
Veröffentlicht in: Nature Methods, 2024, ISSN 1548-7091
Herausgeber: Nature Publishing Group
DOI: 10.48550/ARXIV.2306.04796

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

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

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

Autoren: Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Veröffentlicht in: Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Herausgeber: Frontiers
DOI: 10.3389/fbinf.2023.1233748

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

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

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

Autoren: Lei, Wanlu; Fuster-Barceló, Caterina; Reder, Gabriel; Muñoz-Barrutia, Arrate; Ouyang, Wei
Veröffentlicht in: Nature Methods, 2024, ISSN 1548-7105
Herausgeber: Nature Publishing Group US
DOI: 10.5281/ZENODO.10967840

Conference proceedings (2)

µSplit: efficient image decomposition for microscopy data

Autoren: Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug
Veröffentlicht in: 2023
Herausgeber: ICCV'23
DOI: 10.48550/ARXIV.2211.12872

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

Autoren: Ashesh Ashesh, Florian Jug
Veröffentlicht in: 2024
Herausgeber: ECCV'24
DOI: 10.48550/ARXIV.2403.11854