#Sketchpose is out in @MELBAJournal ! Go read it if you are interested in training cell segmentation models using few partial annotations😀 melba-journal.org/papers/202…

Thrilled to share MyoFuse, an AI-based workflow for automated skeletal muscle cell fusion quantification! 🥳 This is a collaboration with @Benjamin_Lair_ and @CedricMoro_I2MC (@I2mcT), improving the Fusion Index (FI) measurement. Preprint: biorxiv.org/content/10.1101/…

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/s41592-0…

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/10.1101/2025.02.06.6…

Researchers at @Imactiv3D and @maths_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 @SciReports: go.nature.com/3VCYnKE

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

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 🎨

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

I just uploaded my slides for the webinar about #BioImageAnalysis Code Generation at #I2K2024 - #openaccess. See you in an hour! 🔬🖥️🤖🔓 zenodo.org/records/14001044

🚀 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 tracked embryonic development datasets 🐭🪰🪱🪲🐠, but you can also use it for your own data! 🔬 Preprint: biorxiv.org/content/10.1101/… Repository: github.com/royerlab/inTRACKt… This project was spear-headed by @TeunHuijben, together with engineers Andrew Sweet and @aganders3 from @cziscience @czbbiohub #CZBiohubSF #devbio #tracking #web #visualization 🧵1/n

Our new paper EDF RIM

Our Napari plugin Svetlana (napari-hub.org/plugins/napar…) 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.

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/sta…

If you're not already following @Christophe21664, 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 🐇

So happy to see how far @napari_imaging has gone! The repo was created with @jnuneziglesias on the Caltrain on the way to the @ComputerHistory Museum. Fast forward 6 (!) years and napari is an essential tool for bioimaging and the Python Science ecosystem. Thanks to a thriving and tireless community! Congrats to all contributors, past and present! #SoProud

A kind reminder 😇

A simple example of what Svetlana can actually achieve !

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/s41598-0…

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 😎

Hello there ! I am now part of @batut_julie’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-ba…