I am trying to analyze the effect of a toxin in cell junction (stained with a B-catenin antibody). In order to do this, I created a CellProfiler pipeline that basically creates a threshold (ApplyThreshold module) of my B-catenin image following a MeasureImageAreaOccupied module. The output of this pipeline is AreaOccupied, Perimeter and TotalArea. The output data from this pipeline (area or perimeter of the fluorescence) is not correlating very well with my images. In fact, I would like to only quantify voided areas. How can I analyze voided areas in cellprofiler version 2.2.0 (can’t use further versions)? Do you have any suggestions on how to improve my analysis?
Also, I would like to know if I can integrate a matlab script into cellprofiler v.2.2.0.
Thank you for your help!