Hi, I have images taken with a fluorescent microscope of cfos labelled with GFP. The tif file of the image comes in B&W and I'm trying to automatically count cfos cells with ImageJ. What I do is: open the image, invert (such that my cfos cells are dark against a lighter contrast) adjust contrast, subtract background, adjust threshold and then I go onto particle anaysis to define the size of the dots I want to consider. However every time I try to do this, ImageJ can't find 'big dots', i.e. nucleus of cells, but instead counts every single little dot within the nucleus...so I end up with a much bigger number of cfos labelled nuclei than what I should, simply because it's not considering nuclei as wholes but it's counting every little dot within the nucleus (which however is just background). How can I adjust for this? see images below

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