I am relatively new and not yet very familiar with CellProfiler. At the moment, I try to identify nuclei and cell borders of cardiomyocytes and to measure intensities and area sizes afterwards. Identification and the gros of the measurements work fine, but I still have a little problem concerning a few measurements. Some of the output values are just NaN which, in my judgement, shouldn’t be.
I attached the pipeline I built and one of the cardiomyocyte images. I would be very glad if you had a quick look on it.
P.S.: One other question: Is it possible to change the outline colors in the EditObjectsManually module on my own? Currently, I work with heart cross sections stained in red (nuclei) and green (cell membranes). Sometimes, I find it quite difficult to distinguish if the object outlines are continuous or dashed. In other words, sometimes, it’s hard to determine if I already selected the objects or not. What I think of is just changing the outline color into white. I suppose it would be much more distinguishable. Is there any possibility to do that?
Auswertung_WGA_.cppipe (15.2 KB)
NRCM_Kernintensität_Zellgröße.cppipe (12.7 KB)