I was wondering if VMTK can segment OCT .dcm images. I’ve used VMTK before for MRI/CT dicoms, but when I try it for the OCT file, I get no output. The PypePad executes, but stops after a while.
OCT images are typically much lower quality than CT and MRI, so it is not surprising if automatic segmentation fails, but you can try to apply some processing that makes them more similar to CT: convert RGB images to grayscale, apply noise filtering, vessel enhancement, etc. If you post a few example images then we might have more specific suggestions.
If automatic segmentation fails then you can always segment your image manually, using Segment Editor module in 3D Slicer.
What kind to semi-automatic segmentation plugins ImageJ’s Segmentation Editor has? I’ve checked what is in Fiji->Plugins->Segmentation Editor and found this thing: