Troubleshooting
Every effort has been made to make sure the installation and configuration is seamless. However, as it any software there will always be some bugs or issues with configuration. We have tested GAT on Windows and Mac OS to make sure it works well.
If you have any difficulties, suggestions or find any bugs, you can either:
- Use this link to access a Google form for submitting issues or questions.
OR
- Create a post under Issues
OR
- Post the problem on the Imagesc forum and tag @pr4deepr
Make sure you follow the installation and configuration first.
We will list some common issues we've come across
When running StarDist on really large images or if your computer has low RAM, it is possible that you may run out of memory. You can check your Task Manager in Windows or Activity monitor in Mac.
For example, you may get an error printed on your console window:
Specifically you may see: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
This means you ran out of memory. If you keep getting this error and if GAT says no cells found even though there are, then you may have to either:
- use a computer with more RAM (32 GB or higher, depends on image size)
- use QuPath for analysis as it is more memory efficient. You could export the ROIs and use it within FIJI as well.
CLIJ is a powerful and user-friendly GPU-acclerated image proceesing library. GAT uses CLIJ under the hood to speed up things and future development will use GAT extensively. If you get errors related to CLIJ, please have a look at this webpage. Make sure you update your GPU drivers as well.