Working examples


  1. I have had trouble figuring out the best way to use CP. I downloaded the examples and all seem to have errors with the example pipelines. Are there any updated pipelines this poor novice could use as a template :question:
  2. I am analyzing the morphology of protrusions in single cells, and groups of cells. Is there a kymograph module in the works?




Hello Jon,
With every release of CellProfiler, we update the example images. What type of error message are you receiving? Also, what operating system are you using?



Hi Jon,

We don’t have a kymograph module specifically, however we do have some other modules in the works that may help you, namely:
(1) a “Neurite finding” module, using a probablistic segmentation algorithm, which might work for your protrusions
(2) a TrackObjects module, which allows tracking previously defined objects throughout sequential frames of a movie

The release date for these projects are on the months time scale, I expect.

Feel free to add your suggestion, perhaps with some more details of what you would like and use it for, on the Forum’s “New Modules” section.



I was trying the examples on an older verison of CP. I tried to download the new version. I downloaded the windowsXP version of CP with the MCR 32 (my computer stated its processor was not equipped for the MCR 64.) When I try to run the new CP .exe I get an error that the program is not a valid Win32 application. Any help. Is the new CP exceeding this old dogs WindowsXP processor?


Have you tried rebooting after installing the MCR and CellProfiler? Yours doesn’t sound like exactly the same error, but when I installed a recent version of CellProfiler on my WindowsXP laptop, I got this:

CellProfiler.exe - Unable To Locate Component

This application has failed to start because mclmcrrt76.dll was not found. Re-installing the application may fix this problem.

Once I rebooted, all was fine.


You cannot run the examples on your old version of CellProfiler. Each time we release, I update them to work properly with our newly released version. I’m not sure why you are receiving this error. Would you mind posting the specs of your computer?



I deleted and reloaded the new CP as suggested by David and it works. I have attempted 2 examples so far: ExampleHuman which works perfectly, and the ExampleFly, with some crop problems that I am sure I can figure out.

Thanks for the help! :smiley:



I’m a CP newbie: I downloaded and installed the last version for mac and it seems to work but then I downloaded example pipelines from the CP website at and tried them. Unfortunately it didn’t work (‘spots’ and ‘classified colonies’). I have screenshots with the errors but I don’t know how to insert them in the message here. Basically it seems that the settings of the CorrectIllumnation_Calculate module changed and the pipeline has problem with the new variables, or something like that… :confused:
Thank you in advance for your help

All the best


Hi Gael,
I will double-check them today and upload new pipelines, if necessary. Please download a new copy tomorrow.




[quote=“mvokes”]Hi Gael,
I will double-check them today and upload new pipelines, if necessary. Please download a new copy tomorrow.

Dear Martha,
I reloaded both CP and the example pipelines but I still get the same error message. Any idea how to fix it?
I can send you the screenshots if you need.


I just uploaded the new pipelines. Usually, a message box will popup with the old settings. All you need to do is change the answers in the module to match those that appear in the popup window. Everything should be working fine now.


I was actually trying to change it in the popup window… now it works! Thank you.