Artificial Intelligence for Image Data Analysis in the Life Sciences

Project Information

AI4LIFE

Grant agreement ID: 101057970

DOI

10.3030/101057970

Project closed

EC signature date 31 May 2022

Start date 1 September 2022

End date 31 August 2025

Funded under

• Research infrastructures

Total cost

€ 4 141 167,53

EU contribution

€ 4 141 166,00

Coordinated by

EURO-BIOIMAGING ERIC
Finland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (6)

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

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

Websites, patent fillings, videos etc. (1)

Plan for dissemination and exploitation including communication activities

The mandatory DEC

Publications

Peer reviewed articles (6)

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

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

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

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

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

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

Other (20)

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 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 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