Startup Idea: 3D Cell Counting and Fluorescence Overlap Analysis Software

Startup idea to develop an advanced software solution that can automatically count cells within a 3D tissue slice and evaluate the overlap of fluorescence between multiple protein channels. The program should significantly reduce manual work and enhance the efficiency of cell analysis.

I am looking for a software that can automatically count cells for me within a 3d slice of tissue. The cells have been scanned for 3 different flourescing proteins. The cell counting program would need to asses total number of cells (from one of the fluorescent channels), then the number of cells in each other fluorescent group. Finally, it would need to be able to asses overlap of fluorescence between all three channels.

We have tried to create a program in Matlab. Right now it isn't sophisticated enough to perform the work automatically. This means we are doing a lot of point and clicking on cells (ie: mostly we are doing everything manually that is incredibly time consuming.