The colors are added in, of course, with it being an electron microscope image. Another picture:
this post was submitted on 14 Jan 2025
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When I segmented 3D MRI and CT scan images before I used the contrast borders for help a lot. There were some algorithms for finding edges that you could tune by setting search radiuses and thresholds. There was also an option of growing an area by a certain amount of pixels outward, and then threshholding the result back down to only the brighter parts, that kind of thing. You had to be a little clever about how you'd combine it. And ultimately, sometimes I just had to add and subtract a few points manually.
Segmenting is more assigning areas to distinct objects (separating bones from the rest in my case), but you could totally use it as a basis for coloring, so I assume the process is similar here.