I am new to Cellprofiler and try to use it to analyze my multichannel fluorescence images of tumors. It seems that it is a very powerful software and I especially like the object-oriented approach (e.g., cell objects, blood vessel objects etc.). Thank you very much for developing this software and sharing it with everyone for free!
One aspect of my work involves the analysis of microvessel-related parameters in tumor tissue, so this was the topic for my first test pipelines.
After some trial and error I managed to get to the point were results started to look promising. E.g., I have an image from a brain tumor which was stained for CD34 to highlight the tumor microvessels. I wanted to extract some basic information from this image: microvessel density and intercapillary distances. Microvessel density was no problem. I also managed to define “microvascular domains” around each microvessel (using “IdentifySecondaryObjects” with the “Distance - N” strategy starting with the microvessel objects).
Using “MeasureObjectSizeShape” I then extracted some quantitative data from the microvascular domain objects. Unfortunately, some of the results were not what I expected (too low to be biologically plausible), especially the mean radius of the objects (from which the intercapillary distance can be derived).
So called a “SaveImage” procedure and exported the microvascular domain objects and then imported them into Image Pro Premier (Media Cybernetics) to double check the results. In IPP, I was able to find the exact same image objects with identical X and Y coordinates. The results of the area measurements were also identical in the CP and IPP output. However, in keeping with my reservations regarding the radius measurements in CP, these measurements were much higher in IPP (factor 3-4) and now much more in line with my expectations.
Does anyone have an explanation for these differences? I understand that it is most likely that there is something that I am doing wrong but I checked repeatedly and found no explanantion (especially since the area measurements turn out completely identical in CP and IPP, but the radius measurements don’t). Of course, I will gladly provide the pipeline and the image I am talking about.
Thank you very much in advance.
Arnulf Mayer, University Medical Center Mainz, Germany