Chicken balancing for #3DThursday!🐔 These utricle hair cells sense gravity & straight-line motion. We segmented them with #CellposeSAM in #syGlass.

🥼: Stefan Heller Group
🏛️: Stanford @stanfordmedicine.bsky.social
🎬: syGlass.io v2.4.0, out now!

#Neuroanatomy #Microscopy #3DVisualization #SciComm

Automated Segmentation by Cellpose-SAM using syGlass for #3DThursday! This took about 30 minutes to run on one of the gaming laptops. Crazy.

🔬: Synchrotron #MicroCT
🥼: Keith Cheng, MD, PhD, @pennstateuniv.bsky.social
📝: #CellposeSAM www.biorxiv.org/content/10.1...
🥽: syGlass.io v2.4.0 -- out soon!

2 wks left to apply to join #BoBiAC2026! This course will teach you how to use Python to segment fluorescence images w/tools like @ilastik-team.bsky.social & CellposeSAM, & even how to measure cell features, neighborhood relationships, & colocalization. No coding experience needed! bobiac.github.io

Apply to join #BoBiAC2026 this summer! You'll learn how to use Python to segment fluorescence images w/tools like @ilastik-team.bsky.social & CellposeSAM, & even learn how to measure cell features, neighborhood relationships, & colocalization. No coding experience needed! More info: bobiac.github.io

Even with the really good microsam/cellposesam generalist models, annotating specialist labels and retraining is always better.

Having difficulties segmenting your 3D🔬 datasets ? You can try the CellposeSAM plugin🧑‍💻directly in MorphoNet in one click ! No python required 😌

We fine-tuned a set of models (Omnipose, CellposeSAM, microSAM, and Cellpose3) for segmentation of fluorescent membranes in rod-shaped bacteria 🦠. However, light diffraction was negativley influencing the segmentation results in crowded cells 💡, so how could we tackle this? 🤔

CellposeSAM: superhuman generalization for cellular segmentation
HHMI's Janelia Research Campus
youtu.be/qciLV2NPoi0?...

We would like to thank Vanessa Barone & al. for the data provided ! Read the paper here: doi.org/10.1242/dev....
CellposeSAM paper: www.biorxiv.org/content/10.1...