Artificial Intelligence for Image Data Analysis in the Life Sciences

Información del proyecto

AI4LIFE

Identificador del acuerdo de subvención: 101057970

DOI

10.3030/101057970

Proyecto cerrado

Fecha de la firma de la CE 31 Mayo 2022

Fecha de inicio 1 Septiembre 2022

Fecha de finalización 31 Agosto 2025

Financiado con arreglo a

• Research infrastructures

Coste total

€ 4 141 167,53

Aportación de la UE

€ 4 141 166,00

Coordinado por

EURO-BIOIMAGING ERIC
Finland

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Documents, reports (5)

Report on establishment of project management procedures and executive group

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

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

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

Data Management Plan

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

Strategy for dissemination of information within the consortium

Dissemination strategy within the consortium is established and agreed upon

Other (3)

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

Terms of service

Release of terms of service for users and contributors

Publicaciones

Other (42)

AI4Life Deliverable D1.3 - Risk Management Plan

Autores: Robinson-Lehtinen, Rachel; Dörr, Dorothea
Publicado en: 2023
Editor: 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)

Autores: Ouyang, Wei; Russell, Craig
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.11085173

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

Autores: Jug, Florian; Serrano-Solano, Beatriz
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13618545

AI4Life Deliverable D5.4 - Model evaluation platform

Autores: Hartley, Matthew; Zulueta Coarasa, Teresa
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.14938271

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

Autores: Fuster-Barcelo, Caterina
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.14169720

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

Autores: Martins, Nuno Pimpão; Kalaidzidis, Yannis; Zerial, Marino; Jug, Florian
Publicado en: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 2023
Editor: 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

Autores: Fuster-Barceló, Caterina; Muñoz-Barrutia, Arrate
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.17247923

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

Autores: Hartley, Matthew; Zulueta Coarasa, Teresa
Publicado en: 2023
DOI: 10.5281/zenodo.8296393

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Autores: Workshop participants
Publicado en: zenodo.org, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7681686

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

Autores: Henriques, Ricardo
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.10948859

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

Autores: Serrano-Solano, Beatriz
Publicado en: No journal title, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7785759

AI4Life - Policy Brief

Autores: Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Publicado en: 2023
Editor: ZENODO
DOI: 10.5281/ZENODO.10212907

AI4Life Deliverable D1.3 - Risk Management Plan

Autores: Robinson-Lehtinen, Rachel
Publicado en: 2023
DOI: 10.5281/zenodo.7786437

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

Autores: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.7987775

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

Autores: Seifi, Mehdi; Jug, Florian; Galinova, Vera; Serrano-Solano, Beatriz; Deschamps, Joran
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.17247985

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

Autores: 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 Schm
Publicado en: bioRxiv.org, 2022
Editor: bioRxiv
DOI: 10.1101/2022.06.07.495102V1

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

Autores: Caterina Fuster-Barceló,
Publicado en: Focal Plane, 2023
Editor: FocalPlane

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

Autores: Ouyang, Wei; Hård, Joanna
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.14169805

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

Autores: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Publicado en: bioRxiv.org, 2023
Editor: bioRxiv
DOI: 10.1101/2023.08.13.553080V1

AI4Life - Policy Brief I

Autores: Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.10212906

Roadmap on Deep Learning for Microscopy

Autores: Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Publicado en: arxiv.org, 2023
Editor: Arxiv
DOI: 10.48550/ARXIV.2303.03793

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

Autores: 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
Publicado en: 2025
Editor: arXiv
DOI: 10.48550/ARXIV.2506.02783

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

Autores: Serrano-Solano, Beatriz
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.14938360

AI4Life Deliverable D1.3 - Risk Management Plan

Autores: Robinson-Lehtinen, Rachel; Dörr, Dorothea
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.17251441

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

Autores: Serrano-Solano, Beatriz
Publicado en: 2023
DOI: 10.5281/zenodo.7785759

AI4Life Deliverable D3.3 - Documentation and Training Material Report

Autores: Fuster-Barceló, Caterina
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.14938584

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

Autores: Beuttenmüller, Fynn; Kreshuk, Anna; Ferreira, Mariana; Gómez de Mariscal, Estibaliz
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.17247946

AI4Life Deliverable D1.4 - Data Management Plan

Autores: Kreshuk, Anna; Hartley, Matthew
Publicado en: No journal title, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Autores: Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.7785511

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

Autores: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Publicado en: 2023
DOI: 10.5281/zenodo.7987775

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

Autores: 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
Publicado en: 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)

Autores: Mechtel, Nils; Ouyang, Wei
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.14169758

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

Autores: Galinova, Vera; Jug, Florian
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.17248028

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

Autores: Hartley, Matthew
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.10948400

AI4Life Deliverable D1.3 - Risk Management Plan

Autores: Robinson-Lehtinen, Rachel
Publicado en: AI4LIFE, Edición 1.3, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7786437

AI4Life - Policy Brief II

Autores: Dörr, Dorothea; Mathur, Aastha; Serrano-Solano, Beatriz; Jug, Florian; Kreshuk, Anna
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.17251575

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

Autores: Ouyang, Wei
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.14169672

Community-developed checklists for publishing images and image analysis

Autores: Schmied, Christopher; Nelson, Michael; Avilov, Sergiy; Bakker, Gert-Jan; Bertocchi, Cristina; Bischof, Johanna; Boehm, Ulrike; Brocher, Jan; Carvalho, Mariana; Chiritescu, Catalin; Christopher, Jana; Cimini, Beth; Conde-Sousa, Eduardo; Ebner, Michael; Ecker, Rupert; Eliceiri, Kevin; Fernandez-Rodriguez, Julia; Gaudreault, Nathalie; Gelman, Laurent; Grunwald, David; Gu, Tingting; Halidi, Nadia; Hammer, Mathias; Hartley, Matthew; Held, Marie; Jug, Florian; Kapoor, Varun; Koksoy, Ayse Aslihan; Lacoste, Judith; Dévédec, Sylvia Le; Guyader, Sylvie Le; Liu, Penghuan; Martins, Gabriel; Mathur, Aastha; Miura, Kota; Llopis, Paula Montero; Nitschke, Roland; North, Alison; Parslow, Adam; Payne-Dwyer, Alex; Plantard, Laure; Rizwan, Ali; Schroth-Diez, Britta; Schütz, Lucas; Scott, Ryan T.; Seitz, Arne; Selchow, Olaf; Sharma, Ved; Spitaler, Martin; Srinivasan, Sathya; De Castillia, Caterina Strambio; Taatjes, Douglas; Tischer, Christian; Jambor, Helena Klara
Publicado en: 2023
Editor: Arxiv
DOI: 10.48550/ARXIV.2302.07005

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Autores: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Publicado en: arxiv.org, 2024
Editor: Arxiv
DOI: 10.1242/jcs.261545

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

Autores: Robinson-Lehtinen, Rachel
Publicado en: AI4LIFE, Edición 1.1, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7786366

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

Autores: Ouyang, Wei
Publicado en: Zenodo, 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.8380089

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

Autores: Robinson-Lehtinen, Rachel
Publicado en: AI4Life, Edición D1.2, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7785849

Peer reviewed articles (34)

Harnessing artificial intelligence to reduce phototoxicity in live imaging

Autores: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Publicado en: Journal of Cell Science, Edición 137, 2024, ISSN 0021-9533
Editor: 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

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

Building a FAIR image data ecosystem for microscopy communities

Autores: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publicado en: Histochem Cell Biol, 2023, ISSN 0948-6143
Editor: Springer Verlag
DOI: 10.1007/s00418-023-02203-7

Journal of Cell Science

Autores: Estibaliz Gómez-de-Mariscal; Mario Del Rosario; Joanna W. Pylvänäinen; Guillaume Jacquemet; Ricardo Henriques
Publicado en: Journal of Cell Science, 2024, ISSN 0021-9533
Editor: Journal of Cell Science
DOI: 10.48550/ARXIV.2308.04387

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

Autores: 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
Publicado en: Nature Methods, 2025, ISSN 1548-7091
Editor: Springer Science and Business Media LLC
DOI: 10.48550/ARXIV.2311.10443

Nature Methods

Autores: Damian Dalle Nogare; Matthew Hartley; Joran Deschamps; Jan Ellenberg; Florian Jug
Publicado en: Nature Methods, 2023, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/S41592-023-01929-5

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

Autores: 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
Publicado en: npj Imaging, 2025, ISSN 2948-197X
Editor: Nature Publishing Group US
DOI: 10.1038/S44303-025-00089-9

Nature Communications

Autores: Christoph Spahn; Stuart Middlemiss; Estibaliz Gómez-de-Mariscal; Ricardo Henriques; Helge B. Bode; Séamus Holden; Mike Heilemann
Publicado en: Nature Communications, 2025, ISSN 2041-1723
Editor: 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

Autores: Ouyang, Wei; Hartley, Matthew
Publicado en: zenodo.org, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8296448

Gut Analysis Toolbox – automating quantitative analysis of enteric neurons

Autores: 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
Publicado en: Journal of Cell Science, Edición 137, 2024, ISSN 0021-9533
Editor: The Company of Biologists
DOI: 10.1242/JCS.261950

Nature Methods

Autores: 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
Publicado en: Nature Methods, 2024, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1101/2023.11.19.567606

Journal of Cell Science

Autores: 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
Publicado en: Journal of Cell Science, 2024, ISSN 0021-9533
Editor: The Company of Biologists Ltd.
DOI: 10.1242/JCS.261950

Enabling global image data sharing in the life sciences

Autores: Peter Bajcsy, Sreenivas Bhattiprolu, Katy Börner, Beth A. Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Isabel Kemmer, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason R. Swedlow, Adam Taylor, Antje Keppler
Publicado en: Nature Methods, Edición 22, 2025, ISSN 1548-7091
Editor: Springer Science and Business Media LLC
DOI: 10.48550/ARXIV.2401.13023

Live-cell imaging in the deep learning era

Autores: Joanna W. Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Publicado en: Current Opinion in Cell Biology, Edición 85, 2025, ISSN 0955-0674
Editor: Elsevier BV
DOI: 10.1016/J.CEB.2023.102271

Nature Methods

Autores: 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
Publicado en: Nature Methods, 2023, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.48550/ARXIV.2302.07005

Nature Methods

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

BiaPy: accessible deep learning on bioimages

Autores: 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
Publicado en: Nature Methods, 2024, ISSN 1548-7105
Editor: Nature Publishing Group US
DOI: 10.1101/2024.02.03.576026

Journal of Cell Science

Autores: Cimini, Beth; Bankhead, Peter; d'Antuono, Rocco; Fazeli, Elnaz; Fernandez-Rodriguez, Julia; Fuster-Barceló, Caterina; Haase, Robert; Jambor, Helena Klara; Jones, Martin; Jug, Florian; Klemm, Anna; Kreshuk, Anna; Marcotti, Stefania; Martins, Gabriel; Mcardle, Sara; Miura, Kota; Muñoz-Barrutia, Arrate; Murphy, Laura; Nelson, Michael; Nørrelykke, Simon; Paul-Gilloteaux, Perrine; Pengo, Thomas; Pylvänäinen, Joanna; Pytowski, Lior; Ravera, Arianna; Reinke, Annika; Rekik, Yousr; Strambio-De-Castillia, Caterina; Thédié, Daniel; Uhlmann, Virginie; Umney, Oliver; Wiggins, Laura; Eliceiri, Kevin
Publicado en: Journal of Cell Science, 2024, ISSN 0021-9533
Editor: The Company of Biologists Ltd.
DOI: 10.1242/JCS.262322

AI4Life Deliverable D5.1 - Annotation Standards

Autores: Hartley, Matthew; Zulueta-Coarasa, Teresa
Publicado en: zenodo.org, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8296393

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

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

The crucial role of bioimage analysts in scientific research and publication

Autores: 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
Publicado en: Journal of Cell Science, Edición 137, 2024, ISSN 0021-9533
Editor: The Company of Biologists
DOI: 10.1242/JCS.262322

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

Autores: 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
Publicado en: Current Biology, Edición 35, 2025, ISSN 0960-9822
Editor: Elsevier BV
DOI: 10.1016/J.CUB.2025.03.076

Nature Communications

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

The rise of data‐driven microscopy powered by machine learning

Autores: Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Publicado en: Journal of Microscopy, Edición 295, 2024, ISSN 0022-2720
Editor: Wiley
DOI: 10.1111/JMI.13282

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

Autores: Ouyang, Wei
Publicado en: Zenodo, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8380089

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

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

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

Autores: Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez‐de‐Mariscal, Iván Hidalgo‐Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman
Publicado en: Small Methods, Edición 9, 2025, ISSN 2366-9608
Editor: Wiley
DOI: 10.1101/2023.07.06.548004

Building a FAIR image data ecosystem for microscopy communities

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

Nature Methods

Autores: 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
Publicado en: Nature Methods, 2024, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.48550/ARXIV.2306.04796

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

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

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

Autores: Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Publicado en: Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Editor: Frontiers
DOI: 10.3389/fbinf.2023.1233748

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

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

JDLL: A library to run Deep Learning models on Java bioimage informatics platforms

Autores: Carlos Garcia Lopez de Haro, Stephane Dallongeville, Thomas Musset, Estibaliz Gomez de Mariscal, Daniel Sage, Wei Ouyang, Arrate Munoz-Barrutia, Jean-Yves Tinevez, Jean-Christophe Olivo-Marin
Publicado en: arxiv.org, 2023
Editor: Arxiv
DOI: 10.48550/arXiv.2306.04796

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

Autores: Lei, Wanlu; Fuster-Barceló, Caterina; Reder, Gabriel; Muñoz-Barrutia, Arrate; Ouyang, Wei
Publicado en: Nature Methods, 2024, ISSN 1548-7105
Editor: Nature Publishing Group US
DOI: 10.5281/ZENODO.10967840

Conference proceedings (2)

µSplit: efficient image decomposition for microscopy data

Autores: Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug
Publicado en: 2023
Editor: ICCV'23
DOI: 10.48550/ARXIV.2211.12872

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

Autores: Ashesh Ashesh, Florian Jug
Publicado en: 2024
Editor: ECCV'24
DOI: 10.48550/ARXIV.2403.11854