We plan to create photographs of small particles using a microscope. These small elements tend to be convex and they are not supposed to touch each other. The background can be a little bit noisy, but there should be a large contrast between the background and the elements (we aim to create pictures like the example). I would like to extract all the individual elements, crop them and save as individual pictures. I need a tool, that is able to solve this problem also in cases where the border between an element and the background is less defined.
After I extracted all the photographs I run a Matlab script on each picture.
Operating system: preferably Linux, but Windows is also ok.
I prefer the selection to be as automatic as possible (to be able to run the algorithm on hundreds of pictures).