A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales elifesciences.org/articles/107...

Quatre années plus tard Des copains, des souvenirs Et un doctorat 🍾🎓

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

Congratulations @alicegros.bsky.social @jules-vanaret.bsky.social & @dunsingvalentin.bsky.social for this huge team effort! Gastruloids morphogenesis is so fascinating and now we can explore and travel through them in 3D & at cell resolution day and night 🤩

So excited to share my 1st paper !!🌞 Co-authored with @jules-vanaret.bsky.social @dunsingvalentin.bsky.social, we developped an integrated pipeline for imaging, segmenting and analysing cell-scale patterns in gene expression + tissue properties in complex 3D tissues elifesciences.org/reviewed-pre...