Pipeline 3 TrainModel WormToolBox - error



Hi all,

I am trying to train my own model to Untangle worms using Pipeline 3 of the Worm ToolBox.
I have generated the training images with Pipeline 2 but as I start processing I get this error.

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 2359, in post_group
File “cellprofiler\modules\untangleworms.pyc”, line 721, in post_group
File “numpy\linalg\linalg.pyc”, line 520, in inv
File “numpy\linalg\linalg.pyc”, line 90, in _raise_linalgerror_singular
LinAlgError: Singular matrix

Any suggestions on how to solve this?

Thank you!!



Hi Chiara,

Can you give us a little more information- what version of CellProfiler are you using, what operating system, how did you install it, etc?

Being able to run it here in-house would also be helpful for diagnosis- for that we’d need your pipeline and at least one image we can run.


Hi Beth,

thanks for replying! I am using CellProfiler 2.2.0 on Windows, I have just recently downloaded the program to start using the WormToolbox. I have modified the Pipeline3 from the Tutorial using my images for training, I’m attaching both of them.

Thank you so much for your help!

ChiaraExample images.zip (102.1 KB)
Pipeline3_train_untangle.cpproj (464.4 KB)



I apologize for the delay in getting back to you! Unfortunately we’re having some issues with our forum uploads and downloads at the moment; if you’re still having the issue, can you re-upload them here (or onto dropbox/Google drive/etc)? Thanks.