Check out our latest preprint in which we re-investigate the role of differential proliferation in embryonic axial extension! biorxiv.org/content/10.110…

Hello there ! I am now part of Julie Batut’s team at CBI (Toulouse) as a postdoctoral researcher to work on olfactive cells tracking in zebra fish embryos on 3D spinning disk microscope images ! Stay tuned 😎 cbi-toulouse.fr/fr/equipe-batut

A long-awaited new feature in our #BioImageAnalysis software #CellACDC is finally out! You can now easily export to video directly from the GUI. Select your preferences (contours, timestamp, scale bar etc.), click on Export, sit back and enjoy the process 😎

I'm glad to announce that our paper dedicated to the classification of segmentation ROIs based on CNN has been accepted in Scientific Reports 🥳 nature.com/articles/s4159…

A simple example of what Svetlana can actually achieve !

A kind reminder 😇

So happy to see how far napari has gone! The repo was created with Juan Nunez-Iglesias on the Caltrain on the way to the Computer History Museum Museum. Fast forward 6 (!) years and napari is an essential tool for bioimaging and the Python Science ecosystem. Thanks to a thriving

If you're not already following Christopher Hamblin, you definitely should! 😉 I'm super proud of this work, and there's more on the way. In case you're curious, Chris created these images without diffusion—just pure gradient ascent on a classifier. A true magician 🐇

I implemented an oldie-but-goodie for Jupyter Notebooks: Interactive plotting and clustering with segmented images side-by-side; new in #stackview 0.7.11: "clusterplot", inspired by the napari-clusters-plotter 🔬💻🤩 github.com/haesleinhuepf/…

Researchers at IMACTIV-3D and Les Maths à Toulouse aim to streamline the classification of #histopathology segmentation results by minimizing the amount of manual annotation. 🖊️ Learn about the plugin they've created to address this issue in Scientific Reports: go.nature.com/3VCYnKE

Our Napari plugin Svetlana (napari-hub.org/plugins/napari…) for classifying ROIs in segmentation masks has improved. Try it! 1) The unbalance between classes is now managed better. 2) An interactive loss plotting is available in the GUI. 3) An automatic check-for-updates.

Our new paper EDF RIM

🚀 Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Just open your browser and dive into terabytes of developmental biology data. We used it to build the virtual embryozoo.org of

Find out more about InstanSeg from Thibaut himself at his Virtual I2K tutorial next week! Register at i2kconference.org/virtual.html

I just uploaded my slides for the webinar about #BioImageAnalysis Code Generation at #I2K2024 - #openaccess. See you in an hour! 🔬🖥️🤖🔓 zenodo.org/records/140010…

Amazing, Stephane Rigaud is demonstrating multi-GPU support🎉 using #pyclesperanto(without _prototype) for #BioImageAnalysis at #I2K2024(virtual)!🔬🖥️🚀 The notebook is available online #openaccess github.com/StRigaud/clesp…

Last year, we found that diffusion models are nearly bridging the gap between human and machine (diversity vs. recognizability) for drawing arxiv.org/pdf/2301.11722. This year, we’re exploring which inductive bias best captures human-like creativity in VAE latents 🎨

SAMCell: Generalized Label-Free Biological Cell Segmentation with Segment Anything Alexandra Dunnum VandeLoo, Nathan J. Malta, Emilio Aponte, Caitlin van Zyl, Danfei Xu and Craig Forest doi.org/10.1101/2025.0…

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. nature.com/articles/s4159…

Thrilled to share MyoFuse, an AI-based workflow for automated skeletal muscle cell fusion quantification! 🥳 This is a collaboration with Benjamin Lair and Cedric Moro (I2MC-Toulouse), improving the Fusion Index (FI) measurement. Preprint: biorxiv.org/content/10.110…