Dear.
I am Emanuele Martini a Biomedical Engineer who works in a Reserach Center in Milan as Software Developer for image analysis.
I use daily imaging and programming skills to solve tasks similar to the one proposed by you.
I think that we can use C# or also other program languages/image analysis software as Jython, Matlab or Fiji.
If you are interested, please contact me.
Thank you for your attention,
kind regards
Emanuele Martini