Hi Tabinda, CellProfiler works great! You should be able to put together a pipeline and do some automated cell counting after only an hour or two of getting to know the program. Plus, it is kind of fun, and very powerful software.

You should be able to use Fiji (imageJ) for doing these. I use the plugin called QuimP on Fiji ( you can get the QuimP guide online) and it works pretty good for me to do segmentation and analysis (to be precise it gives you area, fluorescence (both cortical and cytoplasmic), circularity, elongation analysis followed by a heat map too if you want to generate one.