Loading a pipline



Hi there,

So I finally was able to launch Cell Profiler after dealing with some previous issues with X11. Now that I have resolved this, I am trying to learn how to use Cell Profiler using the example pipelines that are obtained from the website. My new problem is that when I go to File and ‘load pipeline’ and I choose the ExampleHumanPIPE.mat file that I downloaded from the website (which automatically saved to my desktop), it does not load it but rather gives me the following error:

“the loadimages module could not be found in the directory specified or an error occurred while extracting its variable settings. This error is not common; the module might be corrupt or, if running on the non-developers version of CellProfiler, your preferences may not be set properly…etc”

I didn’t download the developers version so it is possible that my preferences are messed up? or is it something to do with this example being on my desktop and cellprofiler having problems locating it? I really have no idea, so if you can offer assistance to a novice such as myself it would be greatly appreciated



Most likely, the preferences are messed up- basically, CellProfiler is looking for the modules in a place where they aren’t. Go to File>Set Preferences. The box that says, ‘Select the folder where CellProfiler modules are stored’ should be the location of your modules folder. If you downloaded CellProfiler to Applications for example, this would be /Applications/CellProfiler/Modules/.

It shouldn’t matter where the example is downloaded to, as long as the input image folder contains the example images.