Usually you decide on the algorithm first, then this forum will help you on the MATLAB coding. It sounds like perhaps you alreadyknow the algorithm you're planning to use since younamed it, yet you're asking us. Maybe you're just looking for us to validate your choice. Well, I have no idea,(especially without providing an image for us to look at). If you don't have an algorithm yet, you might search here :http://iris.usc.edu/Vision-Notes/bibliography/contents.html
OK, and what was your algorithm? Was it this: http://www.mathworks.com/products/demos/image/color_seg_k/ipexhistology.html or this: http://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/ or something else? Where is your code that you're having trouble with?