I would like to get a sense of how easliy existing pipelines could be adapted for the simple grid pattern analysis described.
We’re a large bulk water supplier and are keen to validate a widely used water quality assessment system (Colilert). The system quantifies Total Coliforms and *E.coli *in water samples. Without going into detail the system uses a grid of wells containing the test water sample (image couldn’t be attached as board quota was already full). Substrates in each well are hydrolized by the target organisms yeiding either a yellow (coliforms) or fluorescent (E.coli) metabolite. The manufacturer has not provided an automated system for reading the results and our experience is that some analyists may interpret weak positive reactions differently. I’d like to consider an “objective” approch to analyzing the intensity of each well and counting those that lie above a suitable threshold. While these requirements are rather simple, my lack of image analysis, Matlab and Cellprofiler experience may prevent ready progress. I’d appreciate help from anyone with Cellprofiler grid analysis experience who may be willing to take a look at some images from my lab and give me a sense of simplest way to use Cellprofiler for the purpose described above.