Skip to content

Windows Installation Troubleshooting

David Stirling edited this page Jun 24, 2021 · 5 revisions
Clone this wiki locally

The instructions below apply to CellProfiler 4.0 and beyond. Instructions for Windows CellProfiler 3 installations are available 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

First off, make sure you have the Visual C++ Redistributable installed, available here. CellProfiler 4 cannot start without this.

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 before closing, then nothing else happens. The message which appears may be hard to catch, but should be as follows:

Java console error

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\CellProfiler\java. If that variable is not set CellProfiler won't be able to use it's internally bundled java installation.

As of CellProfiler 4.0 the software will first check for java within it's installation folder, what CP_JAVA_HOME is set to will only take effect if the bundled java platform is missing. If you really need to use a non-bundled java installation you may want to only set JAVA_HOME, which is checked if CP_JAVA_HOME is missing.

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.

If your user account doesn't have full administrator permissions, you may want to add CP_JAVA_HOME to the bottom System Variables section instead.

Now see if CellProfiler will launch. If it doesn't, proceed to the next section.


If after following this guide you're still having issues, please get in touch on our forum.