At a research lab, we currently have students manually count the number of cells after a tissue sample is sliced and observed under microscope.
The problem here is that the cells are well inter-connected, even after turning the image in grayscale. Tried to apply a manually specified binary threshold (because wasn’t able to get OTSU to find an optical threshold value), and attempted to apply watershed to the image, followed by finding contours. But so far no dice. Does anyone have a suggestion as to how to best automate this cell counting process?
Problem 1: Cells are pretty next to each other, closely
Problem 2: Difficulty in finding optimal threshold value for binary separation
Problem 3: Cells are not circular in shape, thus, Huges circles aren’t working well here
Problem 4: Cells are of no particular size. Some are big…are are small… in irregular shapes.
Appreciate any feedbacks and comments!