It sounds like a quite straightforward question, however I find it's actually something very difficult to quantify. The problem is that cells have different thickness, and so when you take the images of them, at different section, you have different number of vesicles.
Some suggest that you can set a threshold where you take image at a particular depth into the cell, let say 5um into the cell of every cell you image. However, the problem with this method is that cells have different thickness, so 5um into one cell can be different from 5um into the other cell, so it's still not very comparable.
Another suggested way is to take a z-stack of those imaged cells but this will take too long and quantifying z-stack images is a nightmare.
Has anybody encountered this problem before? How would you go about to solve this?
Thank you very much
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