I am working on carbonate crystal structures in bivalve shells and have alot of SEM images of polished and etched thick sections. I am trying to measure crystal sizes and shapes and for that reason am trying to segment individual crystals.
My typical image looks like this:
I am working alot on improving image quality / preparating technique to segment the crystals via etching before taking the pictures. Nontheless, I need to produce first data with what I have and am looking for a routine to get the best result.
With Trainable Weka Segmentation or also with Automatic thresholding I can achieve a reasonable result like this:
The crystals are seperated quite well, however there are a lot of artificial “bridges” where the contrast wasn’t high enough to segment individual crystals. I’ve circled some of them in this picture:
So my Question is how can I “interpolate” the lost elements of segmentation? I understand that watershed is suited quite well for this. However I still fail to apply it as it heavily over-segments other areas of the picture. Is what I am trying to achieve not possible? Will I need to put more effort in sample preparation / image acquisition for this to work at all? Is my segmentation method faulty?