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.
Counting blood cells is a standard procedure and does not require sophisticated assumption. I wonder whether you are performing some very special experiment in a 3D. But I doubt it as red blood cells donot grow in 3D but stays at the bottom of the slide. Then you may any protocol of cell counting (Neubauer chamber for instance). This is the first Google hit for Neubauer chamber, you may have a look