Artificial Intelligence for Image Data Analysis in the Life Sciences

Deliverables

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

Risk Management Plan

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

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

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

Plan for dissemination and exploitation including communication activities

The mandatory DEC

Publications

Harnessing artificial intelligence to reduce phototoxicity in live imaging

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

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

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

Building a FAIR image data ecosystem for microscopy communities

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: Histochem Cell Biol, 2023, ISSN 0948-6143
Publisher: Springer Verlag
DOI: 10.1007/s00418-023-02203-7

Journal of Cell Science

Author(s): Estibaliz Gómez-de-Mariscal; Mario Del Rosario; Joanna W. Pylvänäinen; Guillaume Jacquemet; Ricardo Henriques
Published in: Journal of Cell Science, 2024, ISSN 0021-9533
Publisher: 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

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

Nature Methods

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

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

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

Nature Communications

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

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

Author(s): Ouyang, Wei; Hartley, Matthew
Published in: zenodo.org, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8296448

Gut Analysis Toolbox – automating quantitative analysis of enteric neurons

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

Nature Methods

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

Journal of Cell Science

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, 2024, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/JCS.261950

Enabling global image data sharing in the life sciences

Author(s): 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
Published in: Nature Methods, Issue 22, 2025, ISSN 1548-7091
Publisher: Springer Science and Business Media LLC
DOI: 10.48550/ARXIV.2401.13023

Live-cell imaging in the deep learning era

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

Nature Methods

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 A. Cimini; Eduardo Conde-Sousa; Michael Ebner; Rupert Ecker; Kevin Eliceiri; Julia Fernandez-Rodriguez; Nathalie Gaudreault; Laurent Gelman; David Grunwald; Tingting Gu; Nadia Halidi; Mathias Hammer; Matthew Hartley; Marie Held; Florian Jug; Varun Kapoor; Ayse Aslihan Koksoy; Judith Lacoste; Sylvia Le Dévédec; Sylvie Le Guyader; Penghuan Liu; Gabriel G. Martins; Aastha Mathur; Kota Miura; Paula Montero Llopis; Roland Nitschke; Alison North; Adam C. Parslow; Alex Payne-Dwyer; Laure Plantard; Rizwan Ali; Britta Schroth-Diez; Lucas Schütz; Ryan T. Scott; Arne Seitz; Olaf Selchow; Ved P. Sharma; Martin Spitaler; Sathya Srinivasan; Caterina Strambio-De-Castillia; Douglas Taatjes; Christian Tischer; Helena Klara Jambor
Published in: Nature Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.5281/ZENODO.7956563

Nature Methods

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

BiaPy: accessible deep learning on bioimages

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

Journal of Cell Science

Author(s): 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
Published in: Journal of Cell Science, 2024, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/JCS.262322

AI4Life Deliverable D5.1 - Annotation Standards

Author(s): Hartley, Matthew; Zulueta-Coarasa, Teresa
Published in: zenodo.org, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8296393

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

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

The crucial role of bioimage analysts in scientific research and publication

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

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

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

Nature Communications

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

The rise of data‐driven microscopy powered by machine learning

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

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

Author(s): Ouyang, Wei
Published in: Zenodo, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8380089

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

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

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

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

Building a FAIR image data ecosystem for microscopy communities

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

Nature Methods

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

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

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

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

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

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

Author(s): 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
Published in: arxiv.org, 2023
Publisher: Arxiv
DOI: 10.48550/arXiv.2306.04796

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

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

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

Author(s): Ouyang, Wei; Russell, Craig
Published in: 2024
DOI: 10.5281/ZENODO.11085173

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

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

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

Author(s): Hartley, Matthew; Zulueta Coarasa, Teresa
Published in: 2023
DOI: 10.5281/zenodo.8296393

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Author(s): Workshop participants
Published in: zenodo.org, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7681686

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

Author(s): Henriques, Ricardo
Published in: 2024
DOI: 10.5281/ZENODO.10948859

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

Author(s): Serrano-Solano, Beatriz
Published in: No journal title, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7785759

AI4Life - Policy Brief

Author(s): Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Published in: 2023
Publisher: ZENODO
DOI: 10.5281/ZENODO.10212907

AI4Life Deliverable D1.3 - Risk Management Plan

Author(s): Robinson-Lehtinen, Rachel
Published in: 2023
DOI: 10.5281/zenodo.7786437

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

Author(s): Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.7987775

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

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 Schm
Published in: bioRxiv.org, 2022
Publisher: bioRxiv
DOI: 10.1101/2022.06.07.495102V1

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

Author(s): Caterina Fuster-Barceló,
Published in: Focal Plane, 2023
Publisher: FocalPlane

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

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

Roadmap on Deep Learning for Microscopy

Author(s): Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Published in: arxiv.org, 2023
Publisher: Arxiv
DOI: 10.48550/ARXIV.2303.03793

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

Author(s): Serrano-Solano, Beatriz
Published in: 2023
DOI: 10.5281/zenodo.7785759

AI4Life Deliverable D1.4 - Data Management Plan

Author(s): Kreshuk, Anna; Hartley, Matthew
Published in: No journal title, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Author(s): Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.7785511

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

Author(s): Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Published in: 2023
DOI: 10.5281/zenodo.7987775

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

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

AI4Life Deliverable D1.3 - Risk Management Plan

Author(s): Robinson-Lehtinen, Rachel
Published in: AI4LIFE, Issue 1.3, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7786437

Community-developed checklists for publishing images and image analysis

Author(s): 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
Published in: 2023
Publisher: Arxiv
DOI: 10.48550/ARXIV.2302.07005

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Author(s): Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Published in: arxiv.org, 2024
Publisher: Arxiv
DOI: 10.1242/jcs.261545

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

Author(s): Robinson-Lehtinen, Rachel
Published in: AI4LIFE, Issue 1.1, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7786366

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

Author(s): Ouyang, Wei
Published in: Zenodo, 2023
DOI: 10.5281/ZENODO.8380089

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

Author(s): Robinson-Lehtinen, Rachel
Published in: AI4Life, Issue D1.2, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7785849

Deliverables

Publications

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