Artificial Intelligence for Image Data Analysis in the Life Sciences

Livrables

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

Building a FAIR image data ecosystem for microscopy communities

Auteurs: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7788899

AI4Life & BioImage Archive FAIR AI Workshop - Summary of recommendations

Auteurs: Workshop participants
Publié dans: zenodo.org, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7681686

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

Auteurs: Serrano-Solano, Beatriz
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785759

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

Auteurs: Henriques, Ricardo; Gómez de Mariscal, Estibaliz; Hidalgo, Iván
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7987775

AI4Life Deliverable D1.4 - Data Management Plan

Auteurs: Kreshuk, Anna; Hartley, Matthew
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785654

AI4Life Deliverable D3.1 - Terms of Service

Auteurs: Fuster Barcelo, Caterina; Muñoz-Barrutia, Arrate
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785511

AI4Life Deliverable D1.3 - Risk Management Plan

Auteurs: Robinson-Lehtinen, Rachel
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7786437

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

Auteurs: Robinson-Lehtinen, Rachel
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7786366

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

Auteurs: Robinson-Lehtinen, Rachel
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7785849

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

Auteurs: Ouyang, Wei; Hartley, Matthew
Publié dans: zenodo.org, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8296448

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

Auteurs: 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
Publié dans: bioRxiv.org, 2022
Éditeur: bioRxiv
DOI: 10.1101/2022.06.07.495102v1

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

Auteurs: Caterina Fuster-Barceló,
Publié dans: Focal Plane, 2023
Éditeur: FocalPlane

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

Auteurs: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Publié dans: bioRxiv.org, 2023
Éditeur: bioRxiv
DOI: 10.1101/2023.08.13.553080

Roadmap on Deep Learning for Microscopy

Auteurs: Giovanni Volpe, Carolina Wählby, Lei Tian, et al.
Publié dans: arxiv.org, 2023
Éditeur: Arxiv
DOI: 10.48550/arXiv.2303.03793

AI4Life Deliverable D5.1 - Annotation Standards

Auteurs: Hartley, Matthew; Zulueta-Coarasa, Teresa
Publié dans: zenodo.org, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8296393

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

Auteurs: Ouyang, Wei
Publié dans: Zenodo, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8380089

Community-developed checklists for publishing images and image analysis

Auteurs: 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
Publié dans: CORNELL UNIVERSITY, 2023
Éditeur: Arxiv
DOI: 10.48550/arXiv.2302.07005

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

Auteurs: Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini
Publié dans: Frontiers in Bioinformatics, 2023, ISSN 2673-7647
Éditeur: Frontiers
DOI: 10.3389/fbinf.2023.1233748

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Auteurs: Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Publié dans: arxiv.org, 2023
Éditeur: Arxiv
DOI: 10.48550/arXiv.2308.04387

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

Auteurs: 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
Publié dans: arxiv.org, 2023
Éditeur: Arxiv
DOI: 10.48550/arXiv.2306.04796

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