I am trying to segment nuclei within the Arabidopsis shoot apical meristem to quantify their volume following the section “3D segmentation” from the MGX manual, and I am having some problems. In particular, after using “ITK Watershed Auto Seeded” with different values (level) only a few nuclei are segmented and show weird shapes that not correspond to the actual nuclei.
Is there any possibility of manual 3D segmentation? As there is for 2D segmentation… Or should I play with other tools (which ones) before using “ITK Watershed Auto Seeded”?
Just in case, I write the sequence of tools that I am using:
- Brighten darken (2.0)
- Gaussian blur (x,y,z sigma = 0.7)
- Binarize stack (threshold 10,000)
- Hand-correct stack using Pixel Editor tool
- ITK Watershed Auto Seeded (level values tried = 500-1500)
Thank you very much in advance.