CellProfiler 3.1.8 won't open on MacOS

CellProfiler 3.1.8 not working on Mac OSX 10.11.6. It seems that the software is trying to open, but it closes by itself.
Thanks a lot.

Here is my solution:

Make sure your JAVA version is JDK 1.8.0_152 and also try run CellProfiler from terminal:

/Volumes/Macintosh HD/Applications/CellProfiler-3.1.8.app/Contents/MacOS/cellprofiler
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Hi Jun_Ye,

Thanks a lot for your answer. Running CellProfiler from terminal works perfectly. Thank you very much.



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Hi, I get the same problem but Terminal tells me that /Applications/CellProfiler.app/Contents/MacOS/cellprofiler is a directory. I can’t seem to find an app in the “CellProfiler” directory anywhere. Any suggestions?

Can you try open -n /Applications/CellProfiler.app ?

Otherwise, that command is not quite right, try /Applications/CellProfiler.app/Contents/MacOS/

Thank you, but I get a message that the file /Applications/CellProfiler.app/Contents/MacOS (with or without /Contents/MacOS) does not exist. My Java is current.

Did you place CellProfiler.app into the Applications folder? If not you may need to enter the path to where you saved the program.

Yes, I did. I have also made sure I installed Java 8 JDK rather than Java SE.

Java installed on your system shouldn’t matter, CellProfiler downloaded from the website packs its own.

What happens if you type open -n , then a space, then drag and drop CellProfiler from the Applications window to the terminal?

Also, can you confirm your Mac OSX version?

No luck. Terminal tells me error -10810, which means the process table is full, which is plainly wrong.

I’m using 10.13.6. To preserve my sanity I just downloaded 3.1.9 and used that since it seems to work without problem.

Now I have downloaded 4.0.4 on a Win10 machine (latest updates) as a work around…and I get the same error.

Which particular error is this? The Windows version should display a console window with an error message.

It’s the error about not finding the Java folder. Of course I set CP_JAVA_HOME to the right value, but that doesn’t seem to fix it.

That’s odd for 4.0.4, what’s the exact error message, and could you provide a screenshot of your environment variables?

Sure, here you go.

Wow, that’s very unusual. Would you be able to try adding CP_JAVA_HOME as a system variable (the bottom section) rather than a user variable? For some reason the Python environment isn’t seeing CP_JAVA_HOME.

Also - could I check whether you are using a version from an installer or if CellProfiler was built from the source code?

Thank you, adding CP_JAVA_HOME to the System variables worked! I don’t know why that gets added to user variables by default, but at least it’s a simple fix.

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It’s generally best practice to have it in the user environment variables, but on some systems where the user’s account doesn’t have full administrator permissions there are situations where CellProfiler is passed a different set of environment variables. Using the system variables works around this but can interfere with other users if they want to install seperate CellProfiler versions.

Im having a similar problem. My Mac OSX version is Catalina 10.15.6
I have been working perfectly with CellProfiler but suddenly it doesn’t open.
I have installed it again (the new version and version 3.1.9) but when I click to open it… nothing happen. I have also updated JAVA and it is working and I have tried to open it from the Terminal… I cannot see any error but it is still not opening…

Hi Beth. I get the same problem whether trying to install CP3.19 or CP4 onto my Mac (10.12.6).