Issues with segmentation #8

broper89 · 2023-07-06T07:22:42Z

Hi,
Thanks so much for making this program, its very useful!

I'm having issues with the segmentation of my blood vessels. Basically, I have images blood vessels in subcutaneous mouse tumours using intravital imaging and Quantum dot vessel tracker. I have greyscale TIF stacks of the blood vessel shape. However, no matter what parameters I change, I keep getting extensions off the main blood vessels that are artifacts. I believe this is to do with the pruning/length limit/diameter scale parameters, but I cant seem to improve it. Could you please advise about what I should do? Please note, I'm a wet lab scientist so have little experience with coding/programming. I've attached some images of what I mean. I'm using Version 1.1.0 (I cant seem to be able to download 1.1.1). I've also tried on napari, but I couldn't work out how to change the segmentation parameters on that program.

I've attached the original file I'm trialling the program on as a zip file, a screenshot of the settings I'm using on VesselExpress, as well as screenshots of the binary and skeleton output (highlighting the pruning issue). I've also attached the data generated.. If you have any advice on how to improve the segmentation, that would be greatly appreciated.

Thanks,
Brooke Pereira