Troubleshooting

Windows: crashes during data saving with long paths

This is often happens during training/inference using Deep Learning tools like Cellpose, but can also happen if your projects are deep within the hierarchy of directories. The cause is the (by default) very short supported path length of 260 characters on Windows. You can follow the official tutorial to support long paths.

JIPipe will mitigate some issues starting with version 5.0.0 due to the usage of shorter paths.

Unable to find compatible artifact

This can happen if you use projects from other operating systems are utilized. There is also a known bug with JIPipe versions 4.0.0 and 4.1.0 where an error with the automatic artifact selection fails to find a replacement.

If you encounter issues with artifacts, please open the artifact settings by navigating to Info & settings | Settings | Plugins and selecting the affected third-party artifact. Select another artifact via the Configure ... button.

Here you can learn more about artifacts.

Cellpose/Omnipose: no images found

According to our tests, this can happen on Linux (and maybe macOS) if your project's path contains a space. This bug will be fixed in JIPipe 5.0.0. Until this software is released, please rename directories to ensure that the path to your project does not contain any spaces.

Example

Rename directories so that the path

/data/projects/important collaborator/my project/

is

/data/projects/important-collaborator/my-project/

Cache resets unexpectedly

Usually, cached data stays within the memory until there is a change in a predecessor or the current node. Due to bugs with some nodes, the cache might fully reset.

Please report this on the JIPipe GitHub if you can reproduce the issue. Do the following steps:

Update the cache to the point of failure
Click the Cache button at the top right and select Clear outdated
Open the Logs viewer (button at the top right) and export the newest log called Clear outdated cache items
Provide the exported file in the issue report

Resetting the application settings

This might be needed if you accidentally misconfigured something and want to restore the default behavior.

Close all instances of JIPipe
Press Windows + R and type into the run dialog:
%appdata%\JIPipe\profiles
and press Enter
Navigate to the directory that corresponds to your JIPipe version, e.g. 4.0.0.
Delete the file settings.json
Start JIPipe. It will generate a new settings file.

Close all instances of JIPipe
Open Finder and navigate to Home/Library/Application Support/JIPipe/profiles.
Navigate to the directory that corresponds to your JIPipe version, e.g. 4.0.0.
Delete the file settings.json
Start JIPipe. It will generate a new settings file.

Close all instances of JIPipe
Open Finder and navigate to ~/.local/share/JIPipe/profiles.
Navigate to the directory that corresponds to your JIPipe version, e.g. 4.0.0.
Delete the file settings.json
Start JIPipe. It will generate a new settings file.

Linux: When JIPipe is started from a *.desktop file, it hangs during startup

This is a known issue caused by the Weka filter. It will be fixed in the next version after 4.0.0.