I am interested in writing a new cellprofiler module or expanding an existing one.
If you could point me which direction would be best/easiest, that would help a lot.
The goal is to make a radial distribution of nuclei in a colony: I expect to have a round spot, covered with cells. The nuclei are stained. I want to plot the intensity of the nuclei as a function of the distance from the center.
I am comfortable with numpy and was initially planning to write my own tool for this.
But this thread seems to show a way to do this using built-in methods.
How exactly is the intensity of a dot (a collapsed object) determined? I would like to use the median (or mean) intensity of an object.
The difference is that the center of a colony has to be determined by its shape (I guess we could use Identify Primary Objects for this).
What do you think would be the best way to make this radial distribution of nucleus intensity in a circular colony?