Preferences.md

+_Settings to customize EpiCure to user specific preferences_
+
+You can customize EpiCure to your specific usage by redefining the key or mouse shortcuts and by saving your default plugin state and parameters.
+
+For this, EpiCure generates a file containing all the user settings in your home directory, in the `.napari` folder (which will be created if not there already). The file will be called `epicure_preferences.pkl`. It can be deleted, but then all the user settings will be lost.
+
+At each start of EpiCure, this preference file, if present in the defined path (`$home_directory/.napari/epicure_preferences.pkl`) will be loaded and applied.
+
+# Update EpiCure settings
+
+To save your prefered plugin set-up (visible options, checked options, some parameter values, default display...), go to the [Display](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Display) option in EpiCure and click on the button `Save current settings`.
+
+
+# Redefine EpiCure shortcuts
+
+You can redefine EpiCure shortcuts to put your favorite keys instead of EpiCure default ones (reminder, you can see the full list of EpiCure shortcuts by pressing <kbd>a</kbd> when EpiCure is open).
+ 
+For this, open the `Preferences` option in `Napari>Plugins>EpiCure>Edit preferences`.
+A panel will open on the right side, with a list of shortcuts for each type of EpiCure action (Edit, Track, Suspect, Output, Display).
+Select the one you wish to edit, change the corresponding shortcut by putting your favorite <kbd>key</kbd> instead of the default one.
+
+🖱️ If the shortcut involves a mouse click, a list of optionnal key (Control, Shift) and of mouse click are proposed instead of a possible key letter.
+
+Click on the button `Save preferences` when all shortcuts have been modified to set them.
+:heavy_exclamation_mark: the new shortcut configuration will be active only at the next EpiCure session. If you already have an EpiCure opened, restart it to apply the new shortcuts.
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