Windows Java Troubleshooting CP3 - CellProfiler/CellProfiler GitHub Wiki
The instructions below apply to CellProfiler 3.1.9 and earlier versions. Instructions for CellProfiler 4.0 installation can be found here. Please check out the image.sc forum or our Github issues (and submit new issues as needed) if these instructions fail to work for you.
CellProfiler Won't Open
After you've installed CellProfiler you may find that it doesn't start. When running the program you should see a black console window, which flashes a message very quickly before closing, then nothing else happens. The message which appears is hard to catch, but should be as follows:
This is usually caused by CellProfiler having issues detecting it's Java environment. To correct this there are a number of settings we need to check.
Has Windows been told where CellProfiler's Java is?
CellProfiler comes with it's own Java language interpreter bundled inside it. Sometimes there's a problem during the installation process which prevents this Java platform being registered.
You'll be looking for an Environment Variable called CP_JAVA_HOME, which should be pointing to the Java directory in your CellProfiler installation folder. This is usually C:\Program Files (x86)\CellProfiler\java. If that variable is not set CellProfiler won't be able to start.
Setting the environment variable.
You'll want to open up Control Panel and navigate to System. From there, open up Advanced System Settings.
This will bring up the System Properties window. Click on the Advanced tab and click the Environment Variables button.
The resulting Environment Variables window displays several names associated with different directories. In the top, User Variables section, check if CP_JAVA_HOME exists, and if so whether it's pointing to the correct directory where you installed CellProfiler. If it doesn't exist, click the New... button to create it. Hit OK once it's correct.
images/EnvironmentVariables.png
Now see if CellProfiler will launch. If it doesn't, proceed to the next section.
Are your Windows language settings compatible?
Even in English Windows versions, the current release of CellProfiler has trouble with some Unicode characters.
Check Region Settings
Windows 10 recently added a beta version of Unicode support for unsupported programs, this does not work with CellProfiler! You may also want to try setting your system locale to English. Both can be achieved by following these steps:
Open up Control Panel and enter Region settings.
In the Region window, select the Administrative tab and click Change System Locale...
In the resulting Region Settings box, ensure that a variant of English is selected as the system locale, and also make sure that "Use Unicode UTF-8 for worldwide language support" is disabled. Hit OK and test CellProfiler.
Remove non-English characters from names.
CellProfiler can also have trouble with non-standard characters in names, such as non-English or accented characters. Take care to make sure that these aren't present in the path you installed the program to. The same applies to your user folder, since temporary files may be stored there.
If after following this guide you're still having issues, please get in touch on our forum.