Wiki

Question	Answer
How do I cite the program?	See here
Why does the program produce an error message on launch saying "ClassLoadException on major.minor version"?	The Java version is too low. The program needs at least Java 16; if you are using the version bundled with Java, check that you don't have another older Java version taking precedence.
How can I save my preferred UI settings?	Some options can be saved in a configuration file. See the config options for the available settings.
How do I map FISH data to pre-FISH nuclei?	See the guide here
What values are calculated for nuclei?	See the list here
Microns and pixels have the same value. How do I get microns to show properly?	Select a dataset in the populations panel. Choose 'Dataset' > 'Set scale'. Enter the pixels per micron for your images. Click OK. The charts will be updated.
I want to download an old version, but it's not in the downloads page.	The patch version number (z in x.y.z) only fixes bugs. Other behaviour should be the same. If you really want an exact older version, get in touch and I'll give you the files.
How do I get in touch?	You can find my contact details on my university webpage
I'm using a Mac and can't access my folders	Recent versions of MacOS have changed how file permissions work. You need to launch the jar file from the Terminal rather than double clicking. Open the Terminal, navigate to the directory containing the jar file, and launch the jar using `java -jar Nuclear_Morphology_Analysis_x.y.z.jar`, changing x, y and z to the appropriate numbers for your version.
How do I build NMA myself from the source code?	See the guide here
Can I contribute to this project?	I'm happy to discuss new ideas, suggestions or contributions. Get in touch with me to talk further.
I have a problem / I think I found a bug in the program	Please check if you are using the most recent version - older issues may have already been fixed (see the changelog). If the issue has not already been fixed, please raise a new issue using the issue tracker. You will need to register a free account to post new issues.