Memory problem

cellprofiler

#1

Hi,

I have been trying to use a pipeline found on this website for quantifying fibrosis. However, I get an error message that says “Out of memory” every time it reaches the 4th module on the first cycle. I have tried the other suggestions for helping memory problems, like closing all windows, using fewer images, lower resolutions, and speedupcellprofiler, but I have not had any success. I am running version 1.0.7522 on Windows XP. I have attached the pipeline. Any suggestions would be appreciated!

Thanks,
Danielle
2009_05_20_FibrosisPIPE.mat (1.98 KB)


#2

Hi,

Your pipeline seems fine, though it’s hard to debug without images (for example, if you images have millions of tiny objects in them which IdPrimAuto is getting hung up on, this could be the problem). The only thing I can think of is that you have a lot of ImageMath modules, and every time ImageMath is run it creates a an image which is held in memory- so telling SpeedUpCellProfiler that it can trash these images after each cycle is probably your best bet.

-Kate


#3

An additional note: Some memory issues on Windows machines can be resolved by making sure your virtual memory settings are optimized. Take a look at this link, especially section 6.

Regards,
-Mark


#4

Thanks for the speedy replies! However, the suggestions did not seem to work as an error message still appears during the second image math module. I would attach an image, but the reply will not allow me to. It quits after I try to upload. Any suggestions for that? I’ve already tried using a different computer, and a .jpg image instead of a .TIF.
Thanks,
Danielle


#5

If you still run into problems uploading images with your reply, try using YouSendIt and then posting the link to the files back here on the forum.
-Mark


#6

Here’s the link for the example image:
yousendit.com/download/Y1Rx … WUpMWEE9PQ

In addition to the previous suggestions I have tried to run the program using only one image, instead of a batch, but still no luck.

Thanks,
Danielle


#7

Hi Danielle,

Based on the image you uploaded, the images you are using as input are exceedingly large, much more so than the images used when the pipeline was originally devised here. My computer with 4GB RAM is also hitting the memory limit, especially on the IdentifyPrimAuto module.

There are a couple of considerations here that I think are responsible for the memory errors:

  • The pipeline is using such large images

  • Each module is also creating intermediate images, each of which are the same size as the original

Now, the images from the original forum post are much smaller (1392 x 1040 pixels). My question is: Is it essential that the images be so large?

Regards,
-Mark


#8

Hi,

I changed the size of the image, and I’m not getting a memory problem anymore! The program is running faster, but now it’s stopping at the fifth module. I’m still very new to this pipeline, so my new question is, do I need to change all of the settings, or is the pipeline made to be ready-to-use? Currently, it’s telling me that the image ContrastEnh does not exist because it hasn’t been defined yet. Now I’m unclear on which image to choose.

Thanks!
Danielle


#9

Hi,

I think I just solved my own problem. Some of the variables were jumbled up. Thank you so much for your help, I really appreciate it!

Best,
Danielle


#10

Hi,

Good to hear that things have cleared up!

One last item: We noticed that while you said that you are running version 1.0.7522, the pipeline that you posted here was written for an earlier version. When you load the this pipeline into CellProfiler, do you get a message box saying that the some module settings have been updated, and other boxes asking you to check the saved variables?

If you’re not getting these messages, then your CellProfiler may be pointed at the wrong directory for the modules. In that case, go to File > Set Preferences, and make sure that the last box references the Module folder that you installed CellProfiler to.

If you are getting these messages, that means your version of CellProfiler is current but your pipeline version may not be. You may want to check your variables to make sure everything makes sense (which you may already have done), and re-save the pipeline. That will make sure the pipeline is saved with the current version settings.

Again, this is assuming that you are using the pipeline that you posted on the forum. If you have already modified it and saved it, it may be a moot point.

Regards,
-Mark