Hello, it’d be nice if you could give me a hand with the following problem:
I have a lot of brightfield images of arrays of square wells (micro-well arrays) that contain cells. Now I need to figure out the area, perimeter and ellipsoid of the area that the cells are taking up within the micro-well array. The problem is that the particle analyser can’t tell content of the micro-well and the micro-well edge apart, so I can only actually get the micro-wells from the analyser.
How do I get rid off the wells? I’ve tried trained Weka segmentation which seems to work somewhat, because it seems to understand better that the edges or the micro-wells are background. Unfortunately it takes a really long time, and while it’s alright-ish for the micro-well edges, I can’t get it to work well enough on the contents of the wells.
I’m just posting in the hopes I missed something very obvious, so any help would be appreciated. I can post an example if that helps