Artificial Intelligence for Image Data Analysis in the Life Sciences

Informacje na temat projektu

AI4LIFE

Identyfikator umowy o grant: 101057970

DOI

10.3030/101057970

Projekt został zamknięty

Data podpisania przez KE 31 Maja 2022

Data rozpoczęcia 1 Września 2022

Data zakończenia 31 Sierpnia 2025

Finansowanie w ramach

• Research infrastructures

Koszt całkowity

€ 4 141 167,53

Wkład UE

€ 4 141 166,00

Koordynowany przez

EURO-BIOIMAGING ERIC
Finland

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

Publikacje

Other (23)

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

Autorzy: Ouyang, Wei; Russell, Craig
Opublikowane w: 2024
DOI: 10.5281/ZENODO.11085173

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

Autorzy: Hartley, Matthew; Zulueta Coarasa, Teresa
Opublikowane w: 2023
DOI: 10.5281/zenodo.8296393

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Autorzy: Workshop participants
Opublikowane w: zenodo.org, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7681686

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

Autorzy: Henriques, Ricardo
Opublikowane w: 2024
DOI: 10.5281/ZENODO.10948859

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

Autorzy: Serrano-Solano, Beatriz
Opublikowane w: No journal title, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7785759

AI4Life - Policy Brief

Autorzy: Mathur, Aastha; Kreshuk, Anna; Jug, Florian; Serrano-Solano, Beatriz; Dörr, Dorothea
Opublikowane w: 2023
Wydawca: ZENODO
DOI: 10.5281/ZENODO.10212907

AI4Life Deliverable D1.3 - Risk Management Plan

Autorzy: Robinson-Lehtinen, Rachel
Opublikowane w: 2023
DOI: 10.5281/zenodo.7786437

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

Autorzy: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/ZENODO.7987775

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

Autorzy: 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
Opublikowane w: bioRxiv.org, 2022
Wydawca: bioRxiv
DOI: 10.1101/2022.06.07.495102V1

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

Autorzy: Caterina Fuster-Barceló,
Opublikowane w: Focal Plane, 2023
Wydawca: FocalPlane

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

Autorzy: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Opublikowane w: bioRxiv.org, 2023
Wydawca: bioRxiv
DOI: 10.1101/2023.08.13.553080V1

Roadmap on Deep Learning for Microscopy

Autorzy: Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Opublikowane w: arxiv.org, 2023
Wydawca: Arxiv
DOI: 10.48550/ARXIV.2303.03793

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

Autorzy: Serrano-Solano, Beatriz
Opublikowane w: 2023
DOI: 10.5281/zenodo.7785759

AI4Life Deliverable D1.4 - Data Management Plan

Autorzy: Kreshuk, Anna; Hartley, Matthew
Opublikowane w: No journal title, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Autorzy: Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/ZENODO.7785511

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

Autorzy: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Opublikowane w: 2023
DOI: 10.5281/zenodo.7987775

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

Autorzy: 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
Opublikowane w: bioRxiv -, 2022
DOI: 10.1101/2022.06.07.495102

AI4Life Deliverable D1.3 - Risk Management Plan

Autorzy: Robinson-Lehtinen, Rachel
Opublikowane w: AI4LIFE, Numer 1.3, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7786437

Community-developed checklists for publishing images and image analysis

Autorzy: 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
Opublikowane w: 2023
Wydawca: Arxiv
DOI: 10.48550/ARXIV.2302.07005

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Autorzy: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Opublikowane w: arxiv.org, 2024
Wydawca: Arxiv
DOI: 10.1242/jcs.261545

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

Autorzy: Robinson-Lehtinen, Rachel
Opublikowane w: AI4LIFE, Numer 1.1, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7786366

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

Autorzy: Ouyang, Wei
Opublikowane w: Zenodo, 2023
DOI: 10.5281/ZENODO.8380089

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

Autorzy: Robinson-Lehtinen, Rachel
Opublikowane w: AI4Life, Numer D1.2, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7785849

Peer reviewed articles (8)

Building a FAIR image data ecosystem for microscopy communities

Autorzy: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Opublikowane w: Histochem Cell Biol, 2023, ISSN 0948-6143
Wydawca: 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

Autorzy: Ouyang, Wei; Hartley, Matthew
Opublikowane w: zenodo.org, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8296448

Nature Methods

Autorzy: 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
Opublikowane w: Nature Methods, 2023, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.5281/ZENODO.7956563

AI4Life Deliverable D5.1 - Annotation Standards

Autorzy: Hartley, Matthew; Zulueta-Coarasa, Teresa
Opublikowane w: zenodo.org, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8296393

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

Autorzy: Ouyang, Wei
Opublikowane w: Zenodo, 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8380089

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

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

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

Autorzy: Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Opublikowane w: Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Wydawca: Frontiers
DOI: 10.3389/fbinf.2023.1233748

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

Autorzy: 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
Opublikowane w: arxiv.org, 2023
Wydawca: Arxiv
DOI: 10.48550/arXiv.2306.04796