Crash when using h5 file from ilastic with classifier pixel

I have an interesting case. I load .h5 exported from ilastik in to cell profiler with classify pixel module and It was able to analyse as per requirement.

Suddenly since yesterday, Cellprofiler (r11710) crashes without error message.

Further I have some sets of images with corresponding .h5 file upon which cellprofiler does not crash which indicates there aren’t any issues with CPA

Any clues are highly appreciated.


Hmm, not sure given the info provided. When does CP 11710 crash? Upon launch?
Are you using the version of ilastik bundled with CellProfiler? I am trying to be certain that ilastik has anything to do with the crash.
Have you tried the current release of CP (2.1)?


Thanks for your response logan. CP(r11710) crashes after load images module. when doing ClassfyPixel module.
My piple is as below.


After livePrediction while labeling, train and predict I export classifier in ilastic. it exports with out error. I have done this with more than 5 image sets with each of 5 images.
Out of which two images sets I have this issue.

I get windows error message not cellprofiler errormessage. “Cellprofiler stopped worrking” “A problem caused program to stop working correctly widnows will close the program and notify you if a solution is avilable”

No i have not tried with current release pls.

Your help is very much appreciated.

Bellow is the error details from Windows Event viewer, applciation error specific to cellprofiler

Log Name: Application
Source: Application Error
Date: 07-05-2014 19:54:28
Event ID: 1000
Task Category: (100)
Level: Error
Keywords: Classic
User: N/A
Computer: UTNLab-HPpppp
Faulting application name: CellProfiler.exe, version:, time stamp: 0x4c7cd184
Faulting module name: PYTHON27.DLL, version: 2.7.1150.1013, time stamp: 0x4cf12f78
Exception code: 0xc0000005
Fault offset: 0x000000000011fbb7
Faulting process id: 0x1734
Faulting application start time: 0x01cf69fcf642a90b
Faulting application path: C:\Program Files\CellProfiler\CellProfiler.exe
Faulting module path: C:\Program Files\CellProfiler\PYTHON27.DLL
Report Id: 4b6c3c22-d5f3-11e3-b146-acf1dffa7bf1
Event Xml:



C:\Program Files\CellProfiler\CellProfiler.exe
C:\Program Files\CellProfiler\PYTHON27.DLL

Hmm, I can’t see anything obviously wrong. What version of ilastik did you use to create the classifier? (If you don’t know offhand, look in the top-left corner of the ilastik window).


I have such crashes when the used image isn’t of the exact same bitsize as the images used for the classification. Can this be the reason?


Hi Peter,

That’s a good thought – do you mean bit-depth or size of the image? For bit-depth (e.g. 8-bit, 16-bit, etc) yes, I am pretty sure ClassifyPixels would fail. A different size image would likely be ok, though I haven’t tested it. That brings up somehting - a good test would be to apply ClassifyPixels on one of the very images that was used to train the ilastik classifier, so that these issues are removed from consideration.

@CCMBCCMB, can you run ClassifyPixels on the same image used to train? In addition, you can post the .h5 exported classifer and a training image (possibly need to zip them up to post on the forum) and we can take a look. And don’t forget to tell us the ilastik version you used. CP will NOT work with ilastik 0.6+ afaik.


Hi David,

Sorry for the confusion! Yes I mean bit depth like 8-bit, 24-bit, etc.



I decided to reply here because I am currently having the same issue. I am using the ilastik version that comes bundled with Cell Profiler 2.1.1 and I have tried using images from the batch I used to train the classifier. Still, whenever I run a test, with a ClassifyPixels module, Cell Profiler stops working and closes. Also, when I Analyze images using the same module I get an error message saying that “Analyze_worker.exe” has stopped working and my images are not analyzed.

Any help would be much appreciated.


I am asking my question here because I have basically the same problem. I used the ilastik version bundled with CellProfiler, and tried using the “ClassifyPixels” module with the original images I used to train the Classifier, still Cell Profiler continues to crash. I would appreciate any suggestions.

Thank you!

Hi solvur8, sorry we missed these. Is there any error output you can provide us? From the Windows event viewer perhaps?
Also, what bit-depth are your images? What Windows version are you using?


Hello all,

I believe the ClassifyPixels crash may be due to the bit-depth of the images (32-bit and possibly 24-bit), and/or color RGB images. Does that make sens with the crash reporters here? At least, I confirmed this with one user having ClassifyPixels crashes with 32-bit RGB images, which had classified fine in ilastik bundled with CP, but subsequently crashed in ClassifyPixels.

If you see these immediate ClassifyPixels crash, please ensure that your images are truly grayscale and/or downsample them to 16-bit. Please let us know if that helps.