the default property file is overriden when a custom property file is used

[julou]

I figured out that when a custom property file is used (with -p), then the values in the default mm.properties sitting in the MoMA directory are updated to the values of the custom files.
This is very counterintuitive and affects which parameters are used for image analysis at the next run without custom property file…

I imagine that this comes from the fact that MoMA saves things like its window position.
It should be saved back to the custom file imho, or saving of analysis-related parameters and gut-related parameters would have to be done in separate files.