Notice
Les outils machine/deep learning open source pour plateforme de microscopie
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Descriptif
Présentation Bertrand Vernay
UMR7104 IGBMC, Institut de génétiques et de biologie moléculaire et cellulaire
Université de Strasbourg Illkirch
Thème
Documentation
lien utiles
1- Machine learning
Machine learning for bio-image analysis Robert Haase 08a Machine Learning for Pixel and Object Classification https://www.youtube.com/watch?v=dstjhCPBDOY&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U&index=19
Robert Haase 08b Machine Learning for Pixel Classification in Fiji https://www.youtube.com/watch?v=TfS7ncUaOq4&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U&index=20
Robert Haase 08c Machine Learning for Pixel and Object Classification in ilastik https://www.youtube.com/watch?v=35ykpzsUDRE&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U&index=21
Trainable Weka Segmentation (https://imagej.net/Trainable_Weka_Segmentation)
ilastik (https://www.ilastik.org/)
Webinaire #1: ilastik beyond pixel classification - [NEUBIASAcademy@Home] Webinar https://www.youtube.com/watch?v=_ValtSLeAr0&t=0s
QuPath (https://qupath.github.io/)
Webinaire #1: Quantitative Pathology & BioImage Analysis: QuPath - [NEUBIASAcademy@Home]
Webinar https://www.youtube.com/watch?v=4An5n6Y_rRI&t=0s
2- deep learning
StarDist ( https://github.com/stardist/stardist )
Introduction to nuclei segmentation with StarDist - [NEUBIASAcademy@Home] Webinar https://www.youtube.com/watch?v=Amn_eHRGX5M
CellPose ( https://www.cellpose.org/ )
Webinaire #1: Cellpose: a generalist algorithm for cellular segmentation https://www.youtube.com/watch?v=7y9d4VIKiS8
Webinaire #2: Using Deep Learning for Cellular Segmentation by Carsen Stringer https://www.youtube.com/watch?v=4ZZjr6SFBV8
DeepImageJ ( https://deepimagej.github.io/deepimagej/about.html )
Webinaire #1: Intro to Machine Learning-DeepLearning-DeepimageJ - [NEUBIASAcademy@Home]
Webinar https://www.youtube.com/watch?v=0vTbsO8Vnuo
ZerocostDL4Mic ( https://github.com/HenriquesLab/ZeroCostDL4Mic )
Webinaire #1: Romain Laine - ZeroCostDL4Mic: state-of-the-art deep learning for microscopy, made hassle-free https://www.youtube.com/watch?v=JxzflpmjMm4 Webinaire #2: I2K 2020 tutorial: Deep learning assisted image analysis using ZeroCostDL4Mic https://www.youtube.com/watch?v=A7yyAhT12mQ
3- Outils d'annotation
Labkit ( https://imagej.net/Labkit )
labelImg ( https://github.com/tzutalin/labelImg )
itk-SNAP ( http://www.itksnap.org/pmwiki/pmwiki.php )
makesense.ai ( https://www.makesense.ai/ )
discussion sur les outils d'annotation sur le forum image.sc https://forum.image.sc/t/comparaison-of-some-tools-for-3d-dense-ground-truth-annotations/38918
4 - Dépôts de données
NEUBIAS Zenodo https://zenodo.org/communities/neubias/?page=1&size=20 Bioimage Model Zoo ( https://bioimage.io/#/ )
Image Data Resource( https://idr.openmicroscopy.org/ ) https://bioimage.io/#/
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