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 (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

Publicaciones

Other (23)

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
DOI: 10.5281/ZENODO.11085173

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
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

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

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

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

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 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 D1.3 - Risk Management Plan

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

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
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 (8)

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

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

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 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
Publicado en: Nature Methods, 2023, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.5281/ZENODO.7956563

AI4Life Deliverable D5.1 - Annotation Standards

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

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

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

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