Hello, I am trying to trace vessels from brain slices. I am trying to use the MOST plugin and get apparently good skeletonisation and accurate tracing of my vessels. However, I find two issues-

1. the diameter of the nodes don't seem to match the diameter of the vessel. I would like it to calculate it based on the XY signal as my Z resolution is approximately 5 times lower than my XY resolution.

2. the trace doesn't seem to run down the middle of the vessels. Instead it appears to sit on a plane above. This worries me because then I can't be sure that the 3D reconstruction is accurate enough.

In contrast, if I run APP2 then I can get an accurate XY vessel diameter and the reconstruction to run down the middle of the vessel, but because it was designed for cells, vessels that are not connected do not get traced...

Is there anything in the settings that I can do to fix this? I have to admit, I am a bit baffled with the settings and so have left most of them at default....

Should I be running Ultratracer instead? If so, will this be available for MacOSX soon?

Thank you

Lorena

For your questions:
1. You can try "neuron_utilities" --> "neuron_radius" plugin to re-estimate radius after you get the tracing result.
2. You can run "image_filters" --> "Grayscale_Image_Distance_Transform" plugin to pre-process the imagr, and then run MOST tracing.

You don't have to run ultratracer if the image size is not large. Instead, you can try "neuTube" or "Vaa3D-FarSight_snake_tracing" tracing plugins.