Startup Idea: Cell Counting Software for 3D Tissue Imaging

Startup idea to develop a sophisticated software that can automatically count and categorize cells in a 3d tissue slice based on the fluorescence from different proteins. The software should also be able to analyze overlap of fluorescence between all three channels, effectively reducing manual work.

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.