Removing object edge brightness in CT image

Hi there,

I am trying to segment out the individual components this rock (see images below, components to segment circled in red). I have a CT stack and am using imagej, however even after playing around with the threshold and contrast I just cant get around this bright edge effect on the surface of the object. Usually I use Dragonfly to segment data but am stuck on this sample and went to imajej to try and edit the images themselves.

I wonder is there some sort of plugin that deals with this?

Mongolian2_37.397um_Export0927.tiff (1.9 MB)
Mongolian2_37.397um_Export0927.tif (456.3 KB)

Hello Sarah,
Welcome to the Forum.
I suggest you make an exact copy of your stack, then use Edit > invert the copy followed by Process > Image Calculator and do a difference of the two, that will give you a wider intensity range. Then attempt the Threshold again.


A possible solution would involve:

  1. Non-local means filter to reduce noise
  2. A local threshold to segment your features

Hope that helps.