CellProfiler for Tissue Microarray Immunohistochemistry

Recently used CellProfiler and examples worked fine
Using Mac( intel) OS X Leopard
I need help in using CellProfiler as quantitative image analysis tool for the cropped or copied tissue core images
Immunohistochemistry is diaminobenzidine -peroxidase -based ( usually brown but sometimes red or blue color)
See sample Tma image attached.
The attached image is a small set of Tma. I am using immunoperoxidase-based immunohistochemistry to determine the level of stained “protein” in each tissue core. I previously used an

ImageJ plugin TMA color decon but the output is all brown intensity and individual cell content of “protein” not determined. I like the multiple features available in CellProfiler. I also like the fact it is automated.
Hoping image is OK


Have you checked out the Example Tissue Neighbors pipeline, and the Wound Healing Assay? both explain how to quantify staining in tissue monolayers.