Identify every object regardless size or shared space

I’ve found that something that makes CP hard to use is the capability to identify all your target cells, nuclei, objects…
And I think that this is because it seems to rule out a smaller structure when it finds a larger one that encloses the first.
Also one sometimes has to try a lot to find the appropriate function to identify the primary objects.
I was thinking…
Would it be very hard to make an automatic function that gives you the largest possible number of possible objects,and then, similar to the CPA classifier let it know what is positive and what is not to?

Thanks a lot in advance.


I see what you’re getting at (and can certainly understand the frustration of having to tune the settings of a pipeline for what seems like forever!) but what you’re suggesting is unfortunately not really possible, practically speaking.

The reason I say this is that the decision as to what counts as a “possible object” is one that the computer is not equipped to make. Each setting will give you a different set of objects, and the “largest number” of possible objects would be large indeed. Most likely no user wants to sit through and wade through all possible combinations of settings (and the objects they return) produced by the computer to find out which objects are “right.”

The choice of what is (or is not) an object of interest is, ultimately, a decision best made by the user. The trick is, knowing what settings and what modules best give the objects you want, for as many circumstances as possible. The example pipelines on the website are intended to help with this issue, and we will have more tutorials to assist novices users as they face this task.

If you are interested specifically in finding smaller structures within larger structures, I can suggest looking at the Example Speckles pipeline which detects DNA damage foci within the nucleus. This same approach can be used to identify sub-objects even when they are visible in the same florescence stain as the larger objects.

Hope this helps!