It includes SepaNet, adapted from U-Net to separate structures that were co-stained in the same color channel, allowing to reduce experimentally the number of necessary channels

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

For day 5 of #neubiaspasteur2025 we learned to crash our GPU memory with @strigaud.bsky.social . And also to do efficient image analysis on GPU with #clesperanto

Followed by a very interesting presentation from Stephan Fisher on the Bioinformatics analysis part of the spatial omics pipeline, and a great improvised session of retraining Cellpose in QuPath using SAM annotation by Thierry Pecot

Second day with Ilastik (@ilastik-team.bsky.social) covered by @MinhSonPhan, with @strigaud.bsky.social and @jytinevez.bsky.social as helpers. How to easily train a pixel classifier to segment focal adhesions..

Happy International Women & Girls in Science Day 2025 #WomenInScience #womeninSTEM

Minor bug corrected in DeXtrusion🎊 : There was an issue to export ROI to Fiji with recent version of roifile. It is now hopefully fixed, please update DeXtrusion to 0.0.8 (gitlab.pasteur.fr/gletort/dext...) !

Nice focalplane post by @AlexisVillars on how and why we developped DeXtrusion😍 and how to use it : focalplane.biologists.com/2023/10/06/b...