Cell Profiler 3.1.9 Java Issues


I’m having the following issue with CP 3.1.9. I have ensured the environmental variable was set, I ensured Unicode UTF-8 was disabled. I read on one of the forums that a user installed both java and cell profiler into the Program File folder instead of the (x86). I attempted to install 3.1.8 and follow the trouble shooting steps as well. Having no luck with any of these. Does anyone know a solution for this?

I have also done clean installs of both the latest JRE and Cell profiler to no avail.


have you found a solution?

I’m not sure if this helps but I was having the same problem with CellProfiler 3.1.9, and in my case it was fixed. I uninstalled CellProfiler, then erased the environmental variables (they were still there, and there was more than one with a path related to CellProfiler) called CP_JAVA_HOME, JAVA_HOME, and JDK_HOME. At last, I installed CellProfiler again in my ProgramFile(x86) folder as usual and it started working. The environmental variable CP_JAVA_HOME was created automatically and had the correct path.

Best regards,

Hello, have you found a solution? My computer is a Windows system and I have the same problem.

No solution yet, haven’t been able to get in touch with the user for a couple days. Will try to run another clean install and clearing the environmental variables pre-installation again and post back when I get the chance.

Hi @Sageee,

Have you run through the troubleshooting guide we have here?

Yes, I have gone through the troubleshooting guide.

Okay, is this a packaged version or built from source?

Could you also confirm the directory that the JAVA_HOME environment variable is set to?

this is the packaged version

CP_JAVA_Home is C:\Program Files(x86)\CellProfiler\java

Thanks, is JAVA_HOME also set?

Yes, Ive tried setting it to the normal java install as well as the java folder within the \CellProfiler. Still not working either way.

Okay, could you confirm that there are actually files in the CellProfiler/Java folder? It’d also help if you could send a screenshot of your environment variables.

I was unable to upload the image but here is an imgur link for the environmental variables. I do confirm that there is items inside of the java folder.

Okay, could you try un-setting JAVA_HOME? This can override the default CellProfiler java directory.

I had set it after attempting to run the program without that JAVA_HOME variable set as well. No luck on that front.

That is very peculiar then, just to check - you’re getting exactly the same error in all these cases?

Yes, the error has been the same.

Okay, just to check - is JAVA_HOME also defined in the ‘System Variables’ section? This may override the normal setting so it shouldn’t be.

Could you also check whether there are any contents in C:\Program Files (x86)\CellProfiler\java? It should contain a java installation.

There is no system variable set for JAVA_HOME, there is no install file for JAVA located in (x86)\CellProfiler\java. There is a JDK java.exe located within the bin folder. Looks like the embedded java installed with the program is fine. Also tried installing the latest JDK and pointing to that in environmental variable with no luck. This machine just doesn’t seem to like Cell Profiler. I’m open for other suggestions to try.