Error encountered while processing CorrectIlluminationApply


#1

We have CellProfiler set up on a primary workstation. However, because so many of us are using it, we’ve set up some remote instances to use on our private computers to alleviate the bottleneck. I recreated a pipeline that I have used regularly on the workstation without incident on my computer’s remote instance but I get the following error:
https://cvws.icloud-content.com/B/AfGam1tW-6ORUmEk8lkQWTC9bAokAdft2ynFzcSc1-BK5yJK9QLhxrPD/cellprofiler+error.jpg?o=Ah6esXkZ0rvVx7fNd5k9_BrLYfJZZfD40z6_RwnITzqP&v=1&x=3&a=BQniM3B55jjZAxFEPg&e=1507143375&k=rcqpZMNCSjRf34Y3APvn5A&fl=&r=b7b30fb5-98ff-4a54-816f-08082884be9f-1&ckc=com.apple.clouddocs&ckz=com.apple.CloudDocs&p=24&s=JtVt6BFmOJkjRzuAjUz2Z54UC1E&cd=i

So, any idea why the pipeline works on one computer but not the other? Any help would be greatly appreciated. Thanks.

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#2

Hi, @WarhammerTwo, would you mind attaching a pipeline with some sample images (including an illumination image)?


#3

NF2 Seeding Density Instance01 15Sept2017.cpproj (75.9 KB)
There’s the pipeline. I’m working on getting you images.


#6

I’m trying to post the image to the first step, but it says, “sorry cannot post a link to that host.”


#7

And now everything is being flagged by the community?


#8

Hey, it’s because you’re new and you’re trying to post lots of links; I’ll clear the flag on your account, but maybe what’s easier is to make a Dropbox/GoogleDrive/etc folder with your pipeline and image set in it and link that here?

Sorry!


#9

Ah. A folder. Gotcha. Apologies. I’m kind of a luddite when it comes to this Cloud stuff. Thanks. I’ll do that going forward.


#10

Just a quick question. When can I expect the account to be unflagged?


#11

As far as I can tell it has been since yesterday, though as an extra precaution I also just bumped your “trust level”. Can you try now?


#12

Oh. Because on my end, it looks like my previous replies are all still flagged on this thread. Should I just try reposting my my problem here or start a new topic? Apologies for the stupid questions. I almost never use message boards like this.


#13

Yeah, I hadn’t gotten the individual posts un-flagged, but your account was fine to post new things. I figured out how to un-flag the posts now, but please feel free to post links to what we need to help you debug.


#14

Okay, so like I posted the first time, we have CellProfiler set up on a primary workstation. However, because so many of us are using it, we’ve set up some remote instances to use on our private computers to alleviate the bottleneck. I recreated a pipeline that I have used regularly on the workstation without incident on my computer’s remote instance but I get the error that is contained in the following folder:

https://drive.google.com/drive/folders/0B8GVAzHykMAhVll4UXdZcTVMRkU?usp=sharing

I’m trying to measure two things: DNA content by measuring the intensity of Hoechst stain in the nuclei of HUVEC cells via the blue channel and actively replicating DNA in the nuclei signified by 488 azide staining of EdU via the FITC channel. The pipeline and pictures of the first three steps are included in the folder. The pipeline encounters the error at Step 3.

So, any idea why the pipeline works on one computer but not the other? Any help would be greatly appreciated. Thanks.


#15

Sorry, let me clarify; we’d need the actual microscopy images causing the issue so we can try to reproduce it in our hands, not screenshots of the issue occurring.

Have you verified that it fails on one the remote machine but succeeds on the main machine on the EXACT same images? Is the version of CP the same on both? Is it failing as soon as you start up the pipeline or after it’s been running for some amount of time?

Offhand I’d guess that for the image that’s failing what’s actually failing is the generation of the illumination function in step 2, which is then throwing an error in step 3 when it can’t be applied, but that’s just speculation without some more information.


#16

Have you verified that it fails on one the remote machine but succeeds on the main machine on the EXACT same images?
Yes. When I couldn’t do the analysis on the remote instance, I completed it successfully on the main machine.

Is the version of CP the same on both?
Yes.

Is it failing as soon as you start up the pipeline or after it’s been running for some amount of time?
Pretty much immediately.

My apologies about the image confusion. When agoodman asked for an illumination image, I thought he was specifically asking for images from the pipeline. How many images would you need? I’ve been taking images of 9 sites per well using two channels in a 384 well plate. Would a single well worth of images be enough?


#17

If it’s failing immediately, then yes, a single well of images is likely enough. Preferably the exact images that were failing!

Did you check whether or not the function is being created correctly in step 2?


#18

I wanted to thank you for all your help. It turns out it was just a space issue on our end. It’s resolved now and working perfectly. Thanks again.