I’ve gave it a try and the workflow we described above works quite well, except that certain operations takes minutes to complete. They can be automated, though, so if you have to run this analysis on many images then you don’t need to click and wait, just start the script and you get all the results at the end.
Workflow:
- Go to Segment editor module, add segment
- Threshold effect: Apply (to add all bright areas to the segment)
- Margin effect: margin size = 3.0mm, operation = shrink, Apply 2 times (maybe 3x, to separate blobs)
- Island effect: Split islands to segments, minimum size = 30 voxels (it takes a few minutes, creates a separate segment from each blob)
- Threshold effect: Use for masking (to make sure segments will remain inside bright areas)
- Grow from seeds effect: seed locality = 1.0, click Initialize, then Apply (takes 10-20 minutes, we’ll have to investigate why, we should be able to fix it so that it completes within 1-2 minutes)
- If you need to remove clipped segments at the boundary: this can be automated with some Python scripting but you can do it manually, too: select Paint effect, enable “Color smudge”, then for each segment: click on the segment in the image (this will select the segment), then click Remove to delete the segment
- Compute statistics using Segment Statistics module
