Basic Questions for New User

Hello Mike,

I heard about cell profiler at the ASCB meeting in December. I am very excited about it and have now started using it. I have a couple of questions, very basic.

  1. I remember that there is a way to quantitate the cell size, and although I have been able to get images that represent the cells, I am unable to get a data sheet that shows a numerical readout of the cell size.

  2. Is there a way to edit the image after it has been produced. With my current settings the cells are correctly identified in about 90% of the cases, but I would like to be able to correct the other 10% after the image is created (or better yet figure the settings out so that it works more accurately).

  3. I have also been having problems in that the settings that correctly identify cells for some of my images are different than those that correctly identify cells for some of my other images. This results from some variation in morphology between cells. Is this something that can be componsated for?

  4. (and this may sound silly) but I have the oddest problems opening cellprofiler. I click on the computer screen button looking button, which opens a black window and then somehow eventually, usually after some random clicking on other icons, the nice looking blue screen with the cellprofiler logo opens up and I can start working.

Thanks very much for any help you can provide with these matters.


Hi Alexandra,

  1. Your measurements are stored in the .mat output file (which is named in the bottom right corner of the main CellProfiler window, to the left of the Analyze Images button). You can export the measurements from the .mat file by going to the menu Data Tools -> ExportData. From here, you select the output file and then export. This will produce excel files with all of your data in the same folder as the OUT.mat file. We have already developed a module to export data as excel files from the pipeline as this seems to be a re-occuring question. The next update will include this module.

  2. During processing, it is not possible to “correct” the identified images. The software is designed for high-throughput automatic analysis. Generally, you can alter the settings of the IdentPrimAutomatic module to get the desired segmentation. However, it is unreasonable to expect 100% accuracy 100% of the time.

  3. This depends on how different the morphology is. In most cases you can broaden your settings to compensate for many morphologies. I suggest reading all of the help for the identify module and learn what the settings are doing, this way you can pinpoint what to adjust. There are some cases where different pipelines must be used for different morphologies.

  4. Since CellProfiler is compiled from MatLab, you will always have the background “black” prompt window. This cannot be avoided. You simply have to wait for CellProfiler to load, since it does take some time to start.

I hope this answers all of your questions! If you can post your images/pipeline somewhere on the web I may be able to look at your settings and suggests some things to change.


Just in case other users are reading this thread, I also wanted to point out something in response to Alexandra’s question number 1: once you have identified your cells using an Identify module, be sure that you have Measure modules in the pipeline so that you are measuring the features of interest! Then, as Mike suggests, you can use Data Tools > Export Data to get these measurements into a spreadsheet.