Untangle worms will not work

Hi everyone,

I am using CellProfiler to analyze pictures of C elegans acquired on a high-content imager. My pipeline looks good until it reaches UntangleWorms. I thought maybe my training set was bad so I switched to train mode and still the module will not work.

Basically, when it gets to UntangleWorms, the time to completion begins to increase as does memory usage. If I do not stop it, the program will run out of memory and crash. When I do stop it, I have to restart the program to clear the memory, otherwise it will continue to increase even if the pipeline is not running.

I had a similar problem before with ‘infinite’ worms at the edges of the images, but I have altered the masking to eliminate that problem.

Please help!

Thank you,


Dear Rachel,
I’m happy to hear you are using the worm tools. Could you please provide us with a set of images, your pipeline, and your training set, and we’ll try to resolve the issue for you. We are about to release an updated version of UntangleWorms, that may also help resolve your memory problems.
Best regards

I’ll take a look at this when we get the images.

I would love to supply the pipeline and images for you, but I am not sure how.

The images are 300Mb each and I cannot attach a .cp file in the forum. Could I email it to you? What is your address?