Neurons segmentation

[PMLLancao]

Hello.
I tried the online version of Cellpose with some hippocampal neurons in culture at 3DIV.
I wanted to see if CEllpose can segment the neurites and axon and if the program can count automatically the number of extension per cell. This feature would be a great advantage compared to other free sources since most of the detection of neurites or axon requires manual tracking.

Cellpose could detect cell body ( I did not have a nuclei stain) relatively well, but not the rest of the cell extension.
Maybe is not the main purpose of CEllpose to detect neurons but it would be a great tool.
To quantify the number of neurites and length or even fluorescence intensity in those structures.

Thanks for this great tool.
Regards

[marius10p]

Sorry, the pretrained Cellpose is specifically for cell body segmentation. You could imagine retraining it on a large dataset of neurites, but there is too much crossing between segments and Cellpose doesn't handle overlaps.

[zyazdani-92]

Hello,
I intend to use the new version of Cellpose (Cellpose 2.0) to train and build a model to segment all neurons' dendrites and axons, then I faced these comments here!
Even with the new version, would overlap in connections even with some training data (manual segmentation image) cause problems for Cellpose?

[noamza]

Hello, I intend to use the new version of Cellpose (Cellpose 2.0) to train and build a model to segment all neurons' dendrites and axons, then I faced these comments here! Even with the new version, would overlap in connections even with some training data (manual segmentation image) cause problems for Cellpose?

I am interested in this as well