Plotting cellprofiler data from Spreadsheet

Usage & Issues
#1

I am new to cellprofiler. I have managed to use the speckle counting and translocation example pipelines to measure 1. No. of H2AX (Red channel) foci per nucleus, 2. Intensity of protein of interest -POI (GFP channel) in nuclei. 3. Ratio of POI (GFP channel) between nuclei and cytoplasm. But I am kind of lost after generating the spreadsheet.
I tried to use cellprofiler analyst to plot the per-object nuclei intensity against each well (scatter).

  1. How to analyse statistical significances? Is it required to learn R, Python etc., to make a proper plot?
  2. Is it possible to simply use the values from Spreadsheet generated in a graphpad or origin spreadsheet?

Ramya,
RWTH Aachen, Germany.

#2

Hi @Ramya,

Generally the exported sheets consist of one row per object (or image for the Images sheet). While CellProfiler does include some ‘Data Tools’ modules to help generate graphs, most users will make use of other software for plotting.

You can certainly use R or Python for statistical analysis and plotting, but this is not essential. It should be relatively straightforward to copy columns of interest into suites like GraphPad Prism or even MS Excel. Prism’s stats functions are pretty good in my experience, but some of the older versions can struggle plotting very large numbers of points onto a graph.

So by all means, feel free to import data into whatever software you’re comfortable with.