Low contrast blood vessel segment in a 3d stack

Hi, I am new in here. Could anyone help to recommend a plugin or software to segment blood vessels? I tried some plugins before but they did not take into account of the large variation of the blood vessel diameter (5 um to 100 um) in a 3D stack. Also usually it requires good contrast. Thanks!

@liangy10

I haven’t done a lot of this type of analysis myself… but just searching here on the forum - people seem to have used:

  1. 3D Image Suite (you can access it by activating the update sites of both 3D ImageJ Suite and ImageScience)

  2. Simple Neurite Tracer (here is how to access it: https://imagej.net/Simple_Neurite_Tracer#Installation)

Perhaps you can share an original image here with us (or via link to file sharing site) - and let us know exactly what you wish to do for your analysis… That might help us help you better.

Thanks! i will give tools a try and may get back here with more specific questions. Kevin

1 Like