CPA 2.2.1 loads same image multiple times



Dear all,

I hope there is somebody who might help me with this problem. I’d like to analyze nuclei (DAPI stained) by using the CPA. Therefore I have to train the program. I received a pipeline from a cooperating group which was set up by using a previous version of CP. So far, I was able to create the database and the properties file. So, I loaded the properties file with CPA 2.2.1. However, the program does not open any windows except the navigation window. Then I tried loading the images with the Image Gallery option and I chose the Excel Csv File. Further the program tells me that there are 360 images to be opened (originally I analyzed 1 example picture with CP3.0.0). Subsequently, CPA opens 360 times the same image as the one I have originally analyzed.


Isn’t the program supposed to load each nuclei as a single image instead of loading the orginal image (which in total shows about 360 nuclei (=objects)) 360 times? Is this a failure due to different program versions?

I’d be happy about any help and please let me know if there is any information left for understanding my problem.
Best regards,



Can you send along your pipeline and properties file? That’ll help us debug this. Thanks!



thanks alot for your help! These are the generated files. I’ve used the SQLite format to generate the database file.

20171113 FPL tox (7.0 KB)

171113 Pipeline Nuclei Analysis_MeBe.cppipe (13.3 KB)


Sorry, just reread your original post and caught something I’d missed the first time-

You’re looking at the ImageGallery, which is designed to show you whole images, so yes that’s the expected behavior. If you want to look at objects, you should open the Classifier tool and have it fetch individual objects.

Sorry for the confusion!


Actually I have tried this before but then I received this error message


What did you push to get that error message? Just the “Fetch!” button or something else?


No I tried loading the training set by using the csv file.


Where did the training set CSV come from?

  • Did someone else already do some training on this image in CPA and then use CPA to export the training set CSV (in which case, the first thing I’d do would be to make sure the paths etc match up against what they are on your machine)?

  • From the ExportToSpreadsheet module in your pipeline? That won’t produce a CSV that’s designed to work with CPA, you should instead hit the “Fetch” button to load some cells from your image, which you can then classify into bins of your choice.