Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community

no code implementations • 18 Dec 2023 • Chong Zhang, Alban Gaignard, Matus Kalas, Florian Levet, Felipe Delestro, Joakim Lindblad, Natasa Sladoje, Laure Plantard, Alain Latour, Robert Haase, Gabriel Martins, Paula Sampaio, Leandro Scholz, NEUBIAS taggers, Sébastien Tosi, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux

Software tools (> 1300), image databases for benchmarking (>20) and training materials (>70) for bio image analysis are referenced and curated following standards constructed by the community and then reaching a broader audience.

Benchmarking

Towards deep learning-powered IVF: A large public benchmark for morphokinetic parameter prediction

no code implementations • 1 Mar 2022 • Tristan Gomez, Magalie Feyeux, Nicolas Normand, Laurent David, Perrine Paul-Gilloteaux, Thomas Fréour, Harold Mouchère

An important limitation to the development of Artificial Intelligence (AI)-based solutions for In Vitro Fertilization (IVF) is the absence of a public reference benchmark to train and evaluate deep learning (DL) models.

Parameter Prediction

A registration error estimation framework for correlative imaging

1 code implementation • 10 Mar 2021 • Guillaume Potier, Frédéric Lavancier, Stephan Kunne, Perrine Paul-Gilloteaux

Correlative imaging workflows are now widely used in bioimaging and aims to image the same sample using at least two different and complementary imaging modalities.

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

no code implementations • 21 Jan 2021 • Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M Brown, Aurelien Dauphin, Ian M Dobbie, John E Eriksson, Orestis Faklaris, Julia Fernandez-Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J North, Tobias M Rasse, Ute Resch-Genger, Lucas C Schuetz, Arne Seitz, Caterina Strambio-De-Castillia, Jason R Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert-Jan Bakker, Rodrigo R Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch, Juergen Breitlow, Lisa A Cameron, Joe Chalfoun, James J Chambers, Chieh-Li Chen, Eduardo Conde-Sousa, Alexander D Corbett, Fabrice P Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A Holst, Michelle S Itano, Claudia B Jaffe, Helena K Jambor, Stuart C Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Marco Marcello, Gabriel G Martins, Daniel J Metcalf, Claire A Mitchell, Joshua Moore, Tobias Mueller, Michael S Nelson, Stephen Ogg, Shuichi Onami, Alexandra L Palmer, Perrine Paul-Gilloteaux, Jaime A Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth-Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D Wilms, Graham D Wright, Roland Nitschke

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed.

Cross-modal registration using point clouds and graph-matching in the context of correlative microscopies

1 code implementation • 1 Dec 2020 • Stephan Kunne, Guillaume Potier, Jean Mérot, Perrine Paul-Gilloteaux

Correlative microscopy aims at combining two or more modalities to gain more information than the one provided by one modality on the same biological structure.

Graph Matching