I have been working on a jython script in Fiji to measure the size and shape of soft latex particles embedded in vitreous ice and imaged by cryoTEM. I have my example script and exemplar image in a github repository.
I am trying to redirect the overlay from the binary image to the processed (background subtracted to compensate for fluctuations in ice thickness.) The code does not redirect the overlays… This is my largest concern at the moment. I am hoping a few other pairs of eyes will discover what I missed.
I had tried to perform a watershed separation on my binary image (code not included here) but the result had fine lines separating the particles. if someone sees a good way to do this, I would appreciate pointers.