I have an idea that I would like to implement within a CellProfiler (CP) module and I was wondering if anybody could give me guidance, but first I will give you some background so you can understand the problem. Over the last few months I have been trying to develop a solid pipeline to identify foci within the nucleus of all types of cells. Although I have developed pipelines with settings that work well for some cell lines (ie human cancer cells that have bright foci and little background), these same settings do not work well with other cell lines [most notably mouse embryonic fibroblasts (MEFs) which have weaker foci signal and much more background]. Among other things MEFs need stricter thresholding correction values etc to account for all of the background. I have arranged the settings countless different ways and I cannot develop a single pipeline with middle ground powerful enough to use on different kinds of cells. I have come to this conclusion by comparing the object (foci) count CP gives for each nucleus versus a manual count repeated in triplicates and I find too much variability in the statistical results. I appreciate the per object analysis available within CP but from my experience it is still not precise enough for the needs of the laboratory I work for. So I went in a different direction and developed a thresholding method/program in Matlab and I am at the point where I want to implement and test it within CP. I’m a biologist and I am not a computer programmer, but I have familiarized myself by reading Python programming books and I can understand some code and the order that it follows. I downloaded the developer’s version and I am able to access the individual modules but I was wondering if you could give me advice to embed my code. What’s the best way to implement my idea and call Matab commands within Python? I would appreciate any help.