I am using cellprofiler to segment and measure intensities. I export the intensities in CSV and in database form for use with CellProfiler Analyst (uploaded images). I use the mean intensity values for two different channels to make a scatter plot. When I use the CSV and import the intensities into Matlab (red scatter) and create a scatter plot, it looks very different from what I see in Cellprofiler Analyst (blue scatter) using the same numbers. My question is, is CellProfiler Analyst doing any normalization or preprocessing of the mean intensities when making a scatter plot? If so, how do I turn off?
The reason is, I am trying to create gates in Analyst for a classifier. I want the cells in the extreme arms seen in the Matlab figure. However, they are lost when plotted in Analyst. Is there a workaround anyone knows about?