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The configuration file is located in the program folder within the ImageJ plugins folder. For example:

C:\Program Files\ImageJ\plugins\Nuclear_Morphology_Analysis\config.ini

If the file is not present, it will be created when the program is started, with the default values. Any changes you make to the file will be loaded when you next run the program.

The following options can be set:

Key	Allowed Values	Effect
`DEFAULT_NUCLEUS_TYPE`	`ROUND` `RODENT_SPERM` `PIG_SPERM`	Set the default nucleus type to use in new analyses
`DEFAULT_DIR`	directory with backslashes escaped e.g. `C:\\path\\to\\folder`	Sets the default folder for exporting data
`DEFAULT_IMAGE_SCALE`	A positive number e.g. `18.0`	Sets the default scale for converting pixels to microns
`DEFAULT_COLOUR_SWATCH`	`REGULAR_SWATCH` `ACCESSIBLE_SWATCH` `NO_SWATCH`	Sets the default colouring of datasets and segments
`FILL_CONSENSUS`	`true` `false`	Sets the default value for the 'Fill consensus' checkbox in options
`DEFAULT_DISPLAY_SCALE`	`PIXELS` `MICRONS`	Sets the default scale to display charts
`USE_ANTIALIASING`	`true` `false`	Sets the default value for the 'Use anti-aliasing' checkbox in options
`REFOLD_OVERRIDE`	`true` `false`	If true, the 'best-fit nucleus' method will always be used instead of the position averaging method