Arabidopsis Epidermis Help!

The lab I do research for is looking for a way to count cells and identify cell types of Arbidopsis epidermis. We take images using an optical profilometer and also with a conventional light microscope. This image attached is from using the optical profilometer.
Can anyone give me a few pointers as to where to start or any ideas on how to use CellProfiler 2.0 to identify the cells and then count them?
There are two types of cells we are interested in: Pavement Cells (the oddly shaped large ones), and Stomata (smaller and kind of look like mouths).
Any suggestions would be greatly appreciated!!

Perhaps the pipeline from this thread might be helpful? Stomata and pavement cell counting

I tooled around with the pipeline a bit but am still having trouble. It seems to count some of the pavement cells, but others it will divide.