Point pattern analysis


I was wondering if there is a way to get data from point pattern distribution inside a cell using CellProfiler. I am comparing the distribution of some vesicles inside the cell between control and knockdown cells. The vesicles in control cells group together forming a cluster. Well, kind of a cluster. It’s not a perfect cluster, and there are also vesicles in some other areas of the cell. The knockdown cells show distribution of vesicles all over the cell. I have created a pipeline where I can identify nuclei, cells and spots. I have even tried using the module “MeasureIObjectIntensityDistribution”, but it doesn’t work very well because not all the spots have the same intensity. Is it possible to use the Measure Object Distribution measuring number of particles instead of intensity? Is there a way to get some point pattern analysis per cell to check if there is more or less clustering?

Any advice or tip would be more than welcome.
Thanks a lot in advance.

Sounds like MeasureObjectNeighbors would be helpful? Though I don’t think there is a way to set it to respect the Parent-Children relationships from the Relate module.

Hello Dr. Carpenter,

Thank you very much for your advice. I have tried the MeasureObjectNeighbors module and it doesn’t give me what I need. So now I’m trying to do the analysis cell by cell using this Fiji plugin:


It is slower and I can not analyze as many cells as with CellProfiler, but it works.

Thanks a lot for your help.



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