AI4Life - Policy Brief II
Dörr, Dorothea; Mathur, Aastha; Serrano-Solano, Beatriz; Jug, Florian; Kreshuk, Anna
AI4Life Deliverable D3.3 - Documentation and Training Material Report
Fuster-Barceló, Caterina
AI4Life Deliverable D3.4 - Assessment report of the end-user experience
Fuster-Barceló, Caterina; Muñoz-Barrutia, Arrate
AI4Life Deliverable D4.4 - Release resource and data sharing standards (accessible from the AI4Life website)
Beuttenmüller, Fynn; Kreshuk, Anna; Ferreira, Mariana; Gómez de Mariscal, Estibaliz
AI4Life Deliverable D5.4 - Model evaluation platform
Hartley, Matthew; Zulueta Coarasa, Teresa
AI4Life Deliverable D6.1 - Report on all Open Call activities
Seifi, Mehdi; Jug, Florian; Galinova, Vera; Serrano-Solano, Beatriz; Deschamps, Joran
AI4Life Deliverable D7.2 - Report on AI4Life workshops, hackathons and communication activities with other LS RIs
Serrano-Solano, Beatriz
bia-binder: a web-native cloud compute service for the bioimage analysis community
Craig T Russell, Jean-Marie Burel , Awais Athar , Simon Li , Ugis Sarkans , Jason Swedlow , Alvis Brazma , Matthew Hartley , Virginie Uhlmann
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy
Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Cameron Shand, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues
Nature Protocols· 2025DOI Dominik Kylies; Hannah S. Heil; Arturo G. Vesga; Mario Del Rosario; Maria Schwerk; Malte Kuehl; Milagros N. Wong; Victor G. Puelles; Ricardo Henriques
FeatureForest: the power of foundation models, the usability of random forests
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
Hijacking and integration of algal plastids and mitochondria in a polar planktonic host
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
Live-cell imaging in the deep learning era
Current Opinion in Cell Biology· 2025DOI Joanna W. Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
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
Nature Communications
Nature Communications· 2025DOI Christoph Spahn; Stuart Middlemiss; Estibaliz Gómez-de-Mariscal; Ricardo Henriques; Helge B. Bode; Séamus Holden; Mike Heilemann
Nature Methods
Bruno M. Saraiva; Inês Cunha; António D. Brito; Gautier Follain; Raquel Portela; Robert Haase; Pedro M. Pereira; Guillaume Jacquemet; Ricardo Henriques
SAMJ: Fast image annotation on ImageJ/Fiji via Segment Anything Model
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
This Microtubule Does Not Exist: Super‐Resolution Microscopy Image Generation by a Diffusion Model
Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez‐de‐Mariscal, Iván Hidalgo‐Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman
AI4Life Deliverable D2.2 - Deployment kit for user institutions to replicate the cloud infrastructure (accessible from the AI4Life website)
Ouyang, Wei; Russell, Craig
AI4Life Deliverable D2.3 - Terms of service for the BMZ website and infrastructure
Ouyang, Wei; Hård, Joanna
AI4Life Deliverable D2.4 - Documentation on BioEngine application development (accessible from the AI4Life website)
Ouyang, Wei
AI4Life Deliverable D3.2 - User-friendly versions of zero-code tools
Fuster-Barcelo, Caterina
AI4Life Deliverable D4.2 - Deployment of a container system (accessible from the AI4Life website)
Henriques, Ricardo
AI4Life Deliverable D4.3 - Release of human-in-the-loop interfaces (accessible from the AI4Life website)
Mechtel, Nils; Ouyang, Wei
AI4Life Deliverable D5.2 - BioImage Archive infrastructure and deposition pipeline for versioned reference annotations
Hartley, Matthew
AI4Life Deliverable D6.2 - Report on all Public Challenge activities
Galinova, Vera; Jug, Florian
AI4Life Deliverable D7.3 - Report on FAIR guidelines followed in the consortium
Jug, Florian; Serrano-Solano, Beatriz
BiaPy: accessible deep learning on bioimages
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
BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging
Lei, Wanlu; Fuster-Barceló, Caterina; Reder, Gabriel; Muñoz-Barrutia, Arrate; Ouyang, Wei
Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
Biological Imaging· 2024DOI Caterina Fuster-Barceló; Carlos García López de Haro; Estibaliz Gómez-de-Mariscal; Wei Ouyang; Jean-Christophe Olivo-Marin; Daniel Sage; Arrate Muñoz-Barrutia
CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data
Gómez-De-Mariscal, Estibaliz; Grobe, Hanna; Pylvänäinen, Joanna; Xénard, Laura; Henriques, Ricardo; Tinevez, Jean-Yves; Jacquemet, Guillaume
denoiSplit: A Method for Joint Microscopy Image Splitting and Unsupervised Denoising
Ashesh Ashesh, Florian Jug
Gut Analysis Toolbox – automating quantitative analysis of enteric neurons
Journal of Cell Science· 2024DOI 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
Harnessing artificial intelligence to reduce phototoxicity in live imaging
Journal of Cell Science· 2024DOI Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Nature Communications
Nature Communications· 2024DOI Afonso Mendes; Bruno M. Saraiva; Guillaume Jacquemet; João I. Mamede; Christophe Leterrier; Ricardo Henriques
Nature Methods
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
Nature Methods
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
The crucial role of bioimage analysts in scientific research and publication
Journal of Cell Science· 2024DOI 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
The rise of data‐driven microscopy powered by machine learning
Journal of Microscopy· 2024DOI Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
AI4Life - Policy Brief I
Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations
Workshop participants
AI4Life Deliverable D1.1 - Report on the establishment of the project management procedures and the executive group
Robinson-Lehtinen, Rachel
AI4Life Deliverable D1.2 - Strategy for dissemination of information within the consortium
Robinson-Lehtinen, Rachel
AI4Life Deliverable D1.3 - Risk Management Plan
Robinson-Lehtinen, Rachel; Dörr, Dorothea
AI4Life Deliverable D1.4 - Data Management Plan
No journal title· 2023DOI Kreshuk, Anna; Hartley, Matthew
AI4Life Deliverable D2.1 - Cloud infrastructure (accessible from the AI4Life website)
Ouyang, Wei
AI4Life Deliverable D3.1 - Terms of Service
Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
AI4Life Deliverable D4.1 - Notebooks and algorithms repository (accessible from the AI4Life website)
Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
AI4Life Deliverable D5.1 - Annotation standards and software, libraries and reference examples
Hartley, Matthew; Zulueta Coarasa, Teresa
AI4Life Deliverable D5.3 - First stable BioImage Zoo Model format, software tools, libraries and reference examples
Ouyang, Wei; Hartley, Matthew
AI4Life Deliverable D7.1 - Plan for dissemination and exploitation including communication activities
Serrano-Solano, Beatriz
Building a FAIR image data ecosystem for microscopy communities
Histochemistry and Cell Biology· 2023DOI Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
DeepContrast: Deep Tissue Contrast Enhancement using Synthetic Data Degradations and OOD Model Predictions
2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)· 2023DOI Martins, Nuno Pimpão; Kalaidzidis, Yannis; Zerial, Marino; Jug, Florian
Moving beyond the desktop: prospects for practical bioimage analysis via the web
Frontiers in Bioinformatics· 2023DOI Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
NanoPyx: super-fast bioimage analysis powered by adaptive machine learning
Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Nature Methods
Damian Dalle Nogare; Matthew Hartley; Joran Deschamps; Jan Ellenberg; Florian Jug
Nature Methods
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
Outcomes of the Hackathon on Web and Cloud Infrastructure for AI-Powered BioImage Analysis
Focal Plane· 2023
Caterina Fuster-Barceló,
Roadmap on Deep Learning for Microscopy
Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
µSplit: efficient image decomposition for microscopy data
Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug
BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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