Is not much the software as the method you use, look for any software that integrates stereological procedures to it. As for an introductory approach to understand stereology I recommend:

Unbiased Stereology: Three-dimensional Measurement in Microsacopy. C.V. Howard and M.G. Reed.BIOS Scientific Publishers, Ltd. and Springer-Verlag, New York, 246 p, 1998.

Hi Sheraz,

For what you plan to do I would use a method called the optical fractionator or fractionator method. To do this you can use a software program called StereoInvestigator, made by a company called MBF. Using this program you can count 'live' on a system that is fitted with the software and some hardware (you need a motorised XY stage and a Z encoder) or you can use the software alone and count from image stacks offline. You can use tissue processed for light microscopy or fluorescence. The major drawback of this software is that it is expensive, so I would suggest asking around your department or university to see if you can get access to it. However, what you want to do is fairly simple so there maybe a cheaper alternative such as an ImageJ plugin or other software. The benefit of StereoInvestigator is that it is designed for unbiased counting so if you use another method you will have to take more care with your study design. Hope this helps. 

http://www.stereology.info/the-optical-fractionator/

Have you tried Image J? It's an open-source program available from NIH at http://imagej.nih.gov/ij/.

Hi! You may use ImageJ software, which is free and essentially performing as well as expensive commercial solutions. Following links on the website you will find multiple tool packages for different applications including automated cell counting. Certainly, documentation and support is better in commercial software. The same often applies to user-friendlyness. You will have to decide, whether this is worth several thousand dollars. I would suggest to download some free trial versions and compare them to the free imageJ as a basis for your decision.

Best, Just

There are some plugins for ImageJ that allow automatic cell counting and, best of all, they are free so might be worth trying out in your system. The ones I know of are:

http://wiki.imagej.net/Particle_Analysis

http://www.bioimage.ucsb.edu/automatic-nuclei-counter-plug-in-for-imagej

I'm not sure how well either package works. I used automated detection once in the Fiji distribution of ImageJ (

I have used New C.A.S.T from VisioPharm. It is very powerful, but you would use some training.

Hi! Thanks for the suggestions. They were useful. I dint know ImageJ could be used for unbiased counting as well! I have that software. I actually used it for measuring immunoreactivity of dopaminergic fibers in the striatum.

Thank you Miguel! I will read your paper.