CellProfiler Speckle Counting

CellProfiler Newbie here. But why re-invent the wheel if there is a pipeline that does what a facility users wants to measure…

I have downloaded the speckle counting pipeline from the example page of the CellProfiler documentation. It works and I get a speckle count per cell on user data which is what I am after, great!

I cannot find the options for a few things I would like to check during quality control though or have as a reference for reproducability purposes:

  • Can CP display/export the cell labels 1-n overlaying over the mask? I can find an export outline option but not labels? This is for QC purposes. In the pipeline the speckles and the corresponding cells are displayed with the same colour following the relate objects step and the foci are related to cells in the excel table but it would be good to know which cell is cell 1 and which foci are the respective foci. I guess I am after something similar to the numbering of the ROIs in Fiji.
  • Can I output the area of the identified cells/speckles - it does not seem to be included in the output excel files. There are location parameters for the centre of mass in x, y, and z but not area.
  • Is there a way to export all the processing parameters used for a particular Image Analysis session as a text or csv file? This item is for repeoducability purposes.

Any pointers would be much appreciated. Thank you very much!


  1. Yes, you can do this with the DisplayDataOnImage module
  2. Yes, if you include a “MeasureObjectSizeShape” module and measure any objects whose size that you need
  3. The “.cppipe” file extension in CellProfiler actually is a text file for exactly that purpose. Additionally, any time you run an analyses the “Experiment” CSV and/or database table contains a copy of the pipeline, the version of CellProfiler run, the date, etc.

Thanks for the rapid response, Beth.

  1. Done. Thanks!
  2. Done. Thanks!
  3. I tried to open it with Notepad++ and that resulted in gibberish, simple notepad was fine though and I can see all the parameters. :smiley: