Radial distribution of nucleus intensity in colony

Hi there,

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?

I have found a workable solution in the meantime, although I don’t have any good pictures yet to test this. I will get back to you.

Just to inform anyone who wants to do the same: the best way I’ve found so far is to use the Identify Primary Objects module for both the colonies and the nuclei, then measure the intensity of the nuclei and export to spreadsheet: Colony position, Nuclei position, Nuclei Intensity.

Then run a python script to plot the radial distribution as averaged over the nuclei. This is not that meaningful yet, but comparing multiple channels of images may show that some fluorescence is located more at the edges of the colonies, compared to other colors, which are more intense in the nuclei in the center.

I can’t seem to attach .py files unfortunately.