If you have microscopy images it's pretty easy in ImageJ (bonus: free).
Just open the image, set a Threshold that highlights the objects you want to count (I find Otsu is a very good starting point), then use the Analyze Particles tool to count them. You can even narrow things down by setting brackets for particle area to be counted, in order to exclude junk or adjust the shape parameters to focus on round objects.
Depending on your images, you may need to play around a bit with the thresholding and maybe use a binary filter like watershed and erode, to break up clumps, but if you have just nuclei stained then it's really simple.
You can sanity check the counts by enabling Overlay Masks or Outlines which will show you on the image what is being counted.
I also use IHC Toolbox plugin to get the image with just DAB staining by simply selecting "H-DAB model" and then "color" on that plugin . Now, you have an image consisting of only brown stainings , nothing else. Then you can do the followings:
Image>Type>RGB Stack
Image>Adjust>Threshold ( Now, all brown stainings are in red)
Analyze>Analyze Particles
You should play with the parameters. For CD68, I used 30-infinity, 0-1, outlines. It worked well for my images. Finally, you have all the counting.
Hope this helps.
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