Decide to keep one nucleus only


#1

Hi,

I would like to choose between two nearby nuclei.
That is to say if the distance between two nuclei is less than 20 pixels, i decide to keep only one( it is not a fusion).Another example:If i have 4 nuclei with a distance less thant 20 pixels, i decide to keep only the nearest nucleus from the center. I don’t know if it is possible to do this within cellprofiler.so i need your help to tell me if i could do this and if there is an interesting function to do this.I tried to use different module but I didn’t manage to obtain what I want.
thanks for your help


#2

Hello,
I think I understand your question (although it is a bit harder to understand the biological goal without more explanation!)

I think most likely there is not currently a module in CellProfiler that can do precisely what you request. I think you are requesting this: if multiple nuclei are within a certain distance of each other, arbitrarily (randomly) choose a single one of them for further analysis in the pipeline, without merging/fusing them together. Did I rephrase your question properly?

You can do something perhaps similar: First, use MeasureObjectNeighbors to measure the distance between each nucleus and its nearest neighbors. You then have two options: (1) FilterObjects to remove the nuclei that are < 20 pixels from a neighbor [to throw out ALL of nuclei that are near each other - not exactly what you want, I think] or (2) When you export your data to Excel, you can perhaps write a macro to see which nuclei have a neighbor < 20 pixels away, and then randomly choose which ones to throw out from your numerical analysis.

I don’t think a module to do exactly what you are asking is likely to be a very commonly used feature, so we won’t be adding it to CellProfiler, but I hope this is somewhat helpful.

Let me know if we can help further!
Anne