I think it is very similar to the problem of counting bacteria colonies. For the bacteria colonies counting, there are a lot of software for free, so you can use some of them, e.g., openCFU http://opencfu.sourceforge.net/
I'm sure it will works for the problem of cell counting too.
Now New Technique in this matter. like 5D system. developed by Dr... he is belongs from India in Amaravati. (Nagpur) Pl contact him. I don't know perfect but listen he live in USA.