Artificial Intelligence for Image Data Analysis in the Life Sciences

Rezultaty

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

Publikacje

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: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7788899

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

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

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

AI4Life Deliverable D1.4 - Data Management Plan

Autorzy: Kreshuk, Anna; Hartley, Matthew
Opublikowane w: 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 D1.3 - Risk Management Plan

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

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

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

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

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

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

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: 10.1101/2023.08.13.553080

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 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

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: CORNELL UNIVERSITY, 2023
Wydawca: Arxiv
DOI: 10.48550/arXiv.2302.07005

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

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, 2023
Wydawca: Arxiv
DOI: 10.48550/arXiv.2308.04387

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

Rezultaty

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