Preferences#

Starting with version 0.4.6, napari provides persistent settings.

Settings are managed by getting the global settings object and modifying settings:

from napari.settings import get_settings

settings = get_settings()
# then modify... e.g:
settings.appearance.theme = 'dark'

Reset to defaults via CLI#

To reset all napari settings to the default values:

napari --reset

The preferences dialog#

Starting with version 0.4.6, napari provides a preferences dialog to manage some of the provided options.

Application#

application

Appearance#

appearance

Plugins#

plugins

Shortcuts#

shortcuts

Experimental#

experimental

Reset to defaults via UI#

To reset the preferences click on the Restore defaults button and continue by clicking on Restore.

Sections#

The settings are grouped by sections and napari core provides the following:

APPLICATION#

Main application settings.

Brush size on mouse move modifiers#

Modifiers to activate changing the brush size by moving the mouse.

  • Access programmatically with SETTINGS.application.brush_size_on_mouse_move_modifiers.

  • Type: BrushSizeOnMouseModifiers.

  • Default: <BrushSizeOnMouseModifiers.ALT: 'Alt'>.

  • UI: This setting can be configured via the preferences dialog.

Confirm window or application closing#

Ask for confirmation before closing a napari window or application (all napari windows).

  • Access programmatically with SETTINGS.application.confirm_close_window.

  • Type: bool.

  • Default: True.

  • UI: This setting can be configured via the preferences dialog.

Console notification level#

Select the notification level for the console.

  • Access programmatically with SETTINGS.application.console_notification_level.

  • Type: NotificationSeverity.

  • Default: <NotificationSeverity.NONE: 'none'>.

  • UI: This setting can be configured via the preferences dialog.

Dask cache#

Settings for dask cache (does not work with distributed arrays)

  • Access programmatically with SETTINGS.application.dask.

  • Type: DaskSettings.

  • Default: DaskSettings(enabled=True, cache=4.193144832).

  • UI: This setting can be configured via the preferences dialog.

Depth Axis Orientation#

Orientation of the depth axis in 3D view. Default is “Towards”; <0.6.0 was “Away”.

  • Access programmatically with SETTINGS.application.depth_axis_orientation.

  • Type: DepthAxisOrientation.

  • Default: <DepthAxisOrientation.TOWARDS: 'towards'>.

  • UI: This setting can be configured via the preferences dialog.

First time#

Indicate if napari is running for the first time. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.first_time.

  • Type: bool.

  • Default: True.

Grid Height#

Number of rows in the grid.

  • Access programmatically with SETTINGS.application.grid_height.

  • Type: ConstrainedIntValue.

  • Default: -1.

  • UI: This setting can be configured via the preferences dialog.

Grid Spacing#

The amount of spacing inbetween grid viewboxes. If between 0 and 1, it is interpreted as a proportion of the size of the viewboxes. If equal or greater than 1, it is interpreted as screen pixels.

  • Access programmatically with SETTINGS.application.grid_spacing.

  • Type: ConstrainedFloatValue.

  • Default: 0.

  • UI: This setting can be configured via the preferences dialog.

Grid Stride#

Number of layers to place in each grid viewbox before moving on to the next viewbox. A negative stride will cause the order in which the layers are placed in the grid to be reversed. 0 is not a valid entry.

  • Access programmatically with SETTINGS.application.grid_stride.

  • Type: ConstrainedIntValue.

  • Default: 1.

  • UI: This setting can be configured via the preferences dialog.

Grid Width#

Number of columns in the grid.

  • Access programmatically with SETTINGS.application.grid_width.

  • Type: ConstrainedIntValue.

  • Default: -1.

  • UI: This setting can be configured via the preferences dialog.

GUI notification level#

Select the notification level for the user interface.

  • Access programmatically with SETTINGS.application.gui_notification_level.

  • Type: NotificationSeverity.

  • Default: <NotificationSeverity.INFO: 'info'>.

  • UI: This setting can be configured via the preferences dialog.

Delay to treat button as hold in seconds#

This affects certain actions where a short press and a long press have different behaviors, such as changing the mode of a layer permanently or only during the long press.

  • Access programmatically with SETTINGS.application.hold_button_delay.

  • Type: float.

  • Default: 0.5.

  • UI: This setting can be configured via the preferences dialog.

Horizontal Axis Orientation#

Orientation of the horizontal axis in 2D and 3D view. Default is “Right”.

  • Access programmatically with SETTINGS.application.horizontal_axis_orientation.

  • Type: HorizontalAxisOrientation.

  • Default: <HorizontalAxisOrientation.RIGHT: 'right'>.

  • UI: This setting can be configured via the preferences dialog.

IPython interactive#

Toggle the use of interactive %gui qt event loop when creating napari Viewers in IPython.

  • Access programmatically with SETTINGS.application.ipy_interactive.

  • Type: bool.

  • Default: True.

Language#

Select the display language for the user interface.

  • Access programmatically with SETTINGS.application.language.

  • Type: Language.

  • Default: 'en'.

  • UI: This setting can be configured via the preferences dialog.

New labels data type#

data type for labels layers created with the “new labels” button.

  • Access programmatically with SETTINGS.application.new_labels_dtype.

  • Type: LabelDTypes.

  • Default: <LabelDTypes.uint8: 'uint8'>.

  • UI: This setting can be configured via the preferences dialog.

Opened folders history#

Last saved list of opened folders. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.open_history.

  • Type: List[str].

  • Default: [].

Playback frames per second#

Playback speed in frames per second.

  • Access programmatically with SETTINGS.application.playback_fps.

  • Type: int.

  • Default: 10.

  • UI: This setting can be configured via the preferences dialog.

Playback loop mode#

Loop mode for playback.

  • Access programmatically with SETTINGS.application.playback_mode.

  • Type: LoopMode.

  • Default: <LoopMode.LOOP: 'loop'>.

  • UI: This setting can be configured via the preferences dialog.

Plugin widget positions#

Per-widget last saved position of plugin dock widgets. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.plugin_widget_positions.

  • Type: Mapping[str, str].

  • Default: {}.

Preferences size#

Last saved width and height for the preferences dialog. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.preferences_size.

  • Type: Optional[Tuple[int, int]].

  • Default: None.

Saved folders history#

Last saved list of saved folders. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.save_history.

  • Type: List[str].

  • Default: [].

Save window geometry#

Toggle saving the main window size and position.

  • Access programmatically with SETTINGS.application.save_window_geometry.

  • Type: bool.

  • Default: True.

  • UI: This setting can be configured via the preferences dialog.

Save window state#

Toggle saving the main window state of widgets.

  • Access programmatically with SETTINGS.application.save_window_state.

  • Type: bool.

  • Default: False.

  • UI: This setting can be configured via the preferences dialog.

Vertical Axis Orientation#

Orientation of the vertical axis in 2D and 3D view. Default is “Down”.

  • Access programmatically with SETTINGS.application.vertical_axis_orientation.

  • Type: VerticalAxisOrientation.

  • Default: <VerticalAxisOrientation.DOWN: 'down'>.

  • UI: This setting can be configured via the preferences dialog.

Window fullscreen#

Last saved fullscreen state for the main window. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.window_fullscreen.

  • Type: bool.

  • Default: False.

Window maximized state#

Last saved maximized state for the main window. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.window_maximized.

  • Type: bool.

  • Default: False.

Window position#

Last saved x and y coordinates for the main window. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.window_position.

  • Type: Optional[Tuple[int, int]].

  • Default: None.

Window size#

Last saved width and height for the main window. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.window_size.

  • Type: Optional[Tuple[int, int]].

  • Default: None.

Window state#

Last saved state of dockwidgets and toolbars for the main window. This setting is managed by the application.

  • Access programmatically with SETTINGS.application.window_state.

  • Type: Optional[str].

  • Default: None.

Show status bar#

Toggle diplaying the status bar for the main window.

  • Access programmatically with SETTINGS.application.window_statusbar.

  • Type: bool.

  • Default: True.

APPEARANCE#

User interface appearance settings.

Font size#

Select the user interface font size.

  • Access programmatically with SETTINGS.appearance.font_size.

  • Type: ConstrainedIntValue.

  • Default: 9.

  • UI: This setting can be configured via the preferences dialog.

Highlight#

Select the highlight color and thickness to use when hovering over shapes/points.

  • Access programmatically with SETTINGS.appearance.highlight.

  • Type: HighlightSettings.

  • Default: HighlightSettings(highlight_thickness=1, highlight_color=[0.0, 0.6, 1.0, 1.0]).

  • UI: This setting can be configured via the preferences dialog.

Show layer tooltips#

Toggle to display a tooltip on mouse hover.

  • Access programmatically with SETTINGS.appearance.layer_tooltip_visibility.

  • Type: bool.

  • Default: False.

  • UI: This setting can be configured via the preferences dialog.

Theme#

Select the user interface theme.

  • Access programmatically with SETTINGS.appearance.theme.

  • Type: Theme.

  • Default: 'dark'.

  • UI: This setting can be configured via the preferences dialog.

Update status based on layer#

Calculate status bar based on current active layer and mouse position.

  • Access programmatically with SETTINGS.appearance.update_status_based_on_layer.

  • Type: bool.

  • Default: True.

  • UI: This setting can be configured via the preferences dialog.

PLUGINS#

Plugins settings.

Shimmed plugins already warned#

Set of installed shimmed plugins that have already been warned about.

  • Access programmatically with SETTINGS.plugins.already_warned_shimmed_plugins.

  • Type: Set[str].

  • Default: set().

Plugin sort order#

Sort plugins for each action in the order to be called.

  • Access programmatically with SETTINGS.plugins.call_order.

  • Type: Mapping[str, list[napari.settings._plugins.PluginHookOption]].

  • Default: {}.

  • UI: This setting can be configured via the preferences dialog.

Disabled plugins#

Plugins to disable on application start.

  • Access programmatically with SETTINGS.plugins.disabled_plugins.

  • Type: Set[str].

  • Default: set().

File extension readers#

Assign file extensions to specific reader plugins

  • Access programmatically with SETTINGS.plugins.extension2reader.

  • Type: Mapping[str, str].

  • Default: {}.

  • UI: This setting can be configured via the preferences dialog.

Writer plugin extension association.#

Assign file extensions to specific writer plugins

  • Access programmatically with SETTINGS.plugins.extension2writer.

  • Type: Mapping[str, str].

  • Default: {}.

Only warn for new adapted plugins#

Only warn about newly installed adapted plugins. Leave unchecked to receive warning with each startup.

  • Access programmatically with SETTINGS.plugins.only_new_shimmed_plugins_warning.

  • Type: bool.

  • Default: False.

  • UI: This setting can be configured via the preferences dialog.

Use npe2 adaptor#

Use npe2-adaptor for first generation plugins. When an npe1 plugin is found, this option will import its contributions and create/cache a ‘shim’ npe2 manifest that allows it to be treated like an npe2 plugin (with delayed imports, etc…)

  • Access programmatically with SETTINGS.plugins.use_npe2_adaptor.

  • Type: bool.

  • Default: True.

  • UI: This setting can be configured via the preferences dialog.

SHORTCUTS#

Shortcut settings.

shortcuts#

Set keyboard shortcuts for actions.

  • Access programmatically with SETTINGS.shortcuts.shortcuts.

  • Type: Mapping[str, list[app_model.types._keys._keybindings.KeyBinding]].

  • Default: {'napari:toggle_console_visibility': [<KeyBinding at 0x7f7260dbc3d0: Ctrl+Shift+C>], 'napari:toggle_ndisplay': [<KeyBinding at 0x7f7260dbc5b0: Ctrl+Y>], 'napari:toggle_theme': [<KeyBinding at 0x7f7260dbcb80: Ctrl+Shift+T>], 'napari:reset_view': [<KeyBinding at 0x7f7260dbcd60: Ctrl+R>], 'napari:delete_selected_layers': [<KeyBinding at 0x7f7260dbc4f0: Ctrl+Delete>, <KeyBinding at 0x7f7260dbc370: Ctrl+Backspace>], 'napari:show_shortcuts': [<KeyBinding at 0x7f7260dbc0d0: Ctrl+Alt+/>], 'napari:increment_dims_left': [<KeyBinding at 0x7f7260dbc190: Left>], 'napari:increment_dims_right': [<KeyBinding at 0x7f7260dbfb20: Right>], 'napari:focus_axes_up': [<KeyBinding at 0x7f7260dbfbb0: Alt+Up>], 'napari:focus_axes_down': [<KeyBinding at 0x7f7260dbfc40: Alt+Down>], 'napari:roll_axes': [<KeyBinding at 0x7f7260dbfcd0: Ctrl+E>], 'napari:transpose_axes': [<KeyBinding at 0x7f7260dbfd60: Ctrl+T>], 'napari:rotate_layers': [<KeyBinding at 0x7f7260dbfdc0: Ctrl+Alt+T>], 'napari:toggle_grid': [<KeyBinding at 0x7f7260dbfe20: Ctrl+G>], 'napari:toggle_selected_visibility': [<KeyBinding at 0x7f7260dbfeb0: V>], 'napari:toggle_unselected_visibility': [<KeyBinding at 0x7f7260dbff40: Shift+V>], 'napari:select_layer_above': [<KeyBinding at 0x7f7260dbffa0: Ctrl+Up>], 'napari:select_layer_below': [<KeyBinding at 0x7f7260dd4040: Ctrl+Down>], 'napari:show_only_layer_above': [<KeyBinding at 0x7f7260dd40a0: Shift+Alt+Up>], 'napari:show_only_layer_below': [<KeyBinding at 0x7f7260dd4100: Shift+Alt+Down>], 'napari:hold_for_pan_zoom': [<KeyBinding at 0x7f7260dd4160: Space>], 'napari:activate_labels_erase_mode': [<KeyBinding at 0x7f7260dd41f0: 1>, <KeyBinding at 0x7f7260dd4280: E>], 'napari:activate_labels_paint_mode': [<KeyBinding at 0x7f7260dd42e0: 2>, <KeyBinding at 0x7f7260dd4370: P>], 'napari:activate_labels_polygon_mode': [<KeyBinding at 0x7f7260dd4400: 3>], 'napari:activate_labels_fill_mode': [<KeyBinding at 0x7f7260dd4490: 4>, <KeyBinding at 0x7f7260dd4520: F>], 'napari:activate_labels_picker_mode': [<KeyBinding at 0x7f7260dd45b0: 5>, <KeyBinding at 0x7f7260dd4640: L>], 'napari:activate_labels_pan_zoom_mode': [<KeyBinding at 0x7f7260dd46d0: 6>, <KeyBinding at 0x7f7260dd4760: Z>], 'napari:activate_labels_transform_mode': [<KeyBinding at 0x7f7260dd47f0: 7>], 'napari:new_label': [<KeyBinding at 0x7f7260dd4880: M>], 'napari:swap_selected_and_background_labels': [<KeyBinding at 0x7f7260dd4910: X>], 'napari:decrease_label_id': [<KeyBinding at 0x7f7260dd49a0: ->], 'napari:increase_label_id': [<KeyBinding at 0x7f7260dd4a30: =>], 'napari:decrease_brush_size': [<KeyBinding at 0x7f7260dd4ac0: [>], 'napari:increase_brush_size': [<KeyBinding at 0x7f7260dd4b50: ]>], 'napari:toggle_preserve_labels': [<KeyBinding at 0x7f7260dd4be0: B>], 'napari:reset_polygon': [<KeyBinding at 0x7f7260dd4c70: Escape>], 'napari:complete_polygon': [<KeyBinding at 0x7f7260dd4d00: Enter>], 'napari:activate_points_add_mode': [<KeyBinding at 0x7f7260dd4d90: 2>, <KeyBinding at 0x7f7260dd4df0: P>], 'napari:activate_points_select_mode': [<KeyBinding at 0x7f7260dd4e50: 3>, <KeyBinding at 0x7f7260dd4eb0: S>], 'napari:activate_points_pan_zoom_mode': [<KeyBinding at 0x7f7260dd4f40: 4>, <KeyBinding at 0x7f7260dd4fa0: Z>], 'napari:activate_points_transform_mode': [<KeyBinding at 0x7f7260dd5000: 5>], 'napari:select_all_in_slice': [<KeyBinding at 0x7f7260dd5060: A>, <KeyBinding at 0x7f7260dd50f0: Ctrl+A>], 'napari:select_all_data': [<KeyBinding at 0x7f7260dd5150: Shift+A>], 'napari:delete_selected_points': [<KeyBinding at 0x7f7260dd51b0: 1>, <KeyBinding at 0x7f7260dd5210: Delete>, <KeyBinding at 0x7f7260dd5270: Backspace>], 'napari:activate_add_rectangle_mode': [<KeyBinding at 0x7f7260dd52d0: R>], 'napari:activate_add_ellipse_mode': [<KeyBinding at 0x7f7260dd5330: E>], 'napari:activate_add_line_mode': [<KeyBinding at 0x7f7260dd5390: L>], 'napari:activate_add_path_mode': [<KeyBinding at 0x7f7260dd53f0: T>], 'napari:activate_add_polyline_mode': [<KeyBinding at 0x7f7260dd5450: Shift+L>], 'napari:activate_add_polygon_mode': [<KeyBinding at 0x7f7260dd54b0: P>], 'napari:activate_add_polygon_lasso_mode': [<KeyBinding at 0x7f7260dd5510: Shift+P>], 'napari:activate_direct_mode': [<KeyBinding at 0x7f7260dd5570: 4>, <KeyBinding at 0x7f7260dd55d0: D>], 'napari:activate_select_mode': [<KeyBinding at 0x7f7260dd5660: 5>, <KeyBinding at 0x7f7260dd56c0: S>], 'napari:activate_shapes_pan_zoom_mode': [<KeyBinding at 0x7f7260dd5720: 6>, <KeyBinding at 0x7f7260dd5780: Z>], 'napari:activate_shapes_transform_mode': [<KeyBinding at 0x7f7260dd57e0: 7>], 'napari:activate_vertex_insert_mode': [<KeyBinding at 0x7f7260dd5840: 2>, <KeyBinding at 0x7f7260dd58a0: I>], 'napari:activate_vertex_remove_mode': [<KeyBinding at 0x7f7260dd5930: 1>, <KeyBinding at 0x7f7260dd5990: X>], 'napari:copy_selected_shapes': [<KeyBinding at 0x7f7260dd59f0: Ctrl+C>], 'napari:paste_shape': [<KeyBinding at 0x7f7260dd5a50: Ctrl+V>], 'napari:move_shapes_selection_to_front': [<KeyBinding at 0x7f7260dd5ab0: F>], 'napari:move_shapes_selection_to_back': [<KeyBinding at 0x7f7260dd5b10: B>], 'napari:select_all_shapes': [<KeyBinding at 0x7f7260dd5b70: A>, <KeyBinding at 0x7f7260dd5bd0: Ctrl+A>], 'napari:delete_selected_shapes': [<KeyBinding at 0x7f7260dd5c30: 3>, <KeyBinding at 0x7f7260dd5c90: Delete>, <KeyBinding at 0x7f7260dd5cf0: Backspace>], 'napari:finish_drawing_shape': [<KeyBinding at 0x7f7260dd5d50: Enter>, <KeyBinding at 0x7f7260dd5db0: Escape>], 'napari:orient_plane_normal_along_x': [<KeyBinding at 0x7f7260dd5e10: X>], 'napari:orient_plane_normal_along_y': [<KeyBinding at 0x7f7260dd5e70: Y>], 'napari:orient_plane_normal_along_z': [<KeyBinding at 0x7f7260dd5ed0: Z>], 'napari:orient_plane_normal_along_view_direction': [<KeyBinding at 0x7f7260dd5f30: O>], 'napari:activate_image_pan_zoom_mode': [<KeyBinding at 0x7f7260dd5fc0: 1>], 'napari:activate_image_transform_mode': [<KeyBinding at 0x7f7260dd6020: 2>], 'napari:activate_vectors_pan_zoom_mode': [<KeyBinding at 0x7f7260dd6080: 1>], 'napari:activate_vectors_transform_mode': [<KeyBinding at 0x7f7260dd60e0: 2>], 'napari:activate_tracks_pan_zoom_mode': [<KeyBinding at 0x7f7260dd6140: 1>], 'napari:activate_tracks_transform_mode': [<KeyBinding at 0x7f7260dd61a0: 2>], 'napari:activate_surface_pan_zoom_mode': [<KeyBinding at 0x7f7260dd6200: 1>], 'napari:activate_surface_transform_mode': [<KeyBinding at 0x7f7260dd6260: 2>]}.

  • UI: This setting can be configured via the preferences dialog.

EXPERIMENTAL#

Experimental settings.

Render Images Asynchronously#

Asynchronous loading of image data. This setting partially loads data while viewing.

  • Access programmatically with SETTINGS.experimental.async_.

  • Type: bool.

  • Default: False.

  • UI: This setting can be configured via the preferences dialog.

Enable autoswapping rendering buffers.#

Autoswapping rendering buffers improves quality by reducing tearing artifacts, while sacrificing some performance.

  • Access programmatically with SETTINGS.experimental.autoswap_buffers.

  • Type: bool.

  • Default: False.

  • UI: This setting can be configured via the preferences dialog.

Colormap backend to use for Labels layer#

*Color mapping backend to use for Labels layer. ‘partsegcore’ requires the optional ‘partsegcore-compiled-backend’ package. ‘numba’ requires the optional ‘numba’ package. ‘pure python’ uses only NumPy and Python. The ‘fastest available’ backend will select the fastest installed backend. *

  • Access programmatically with SETTINGS.experimental.colormap_backend.

  • Type: ColormapBackend.

  • Default: fastest_available.

  • UI: This setting can be configured via the preferences dialog.

Unused option. Use “triangulation backend” instead.#

This option was removed in napari 0.6.0. Use “triangulation backend” instead.

  • Access programmatically with SETTINGS.experimental.compiled_triangulation.

  • Type: bool.

  • Default: False.

Double-click Labels polygon completion radius (-1 to always complete)#

Max radius in pixels from first vertex for double-click to complete a polygon; set -1 to always complete.

  • Access programmatically with SETTINGS.experimental.completion_radius.

  • Type: int.

  • Default: -1.

  • UI: This setting can be configured via the preferences dialog.

Minimum distance threshold of shapes lasso and path tool#

Value determines how many screen pixels one has to move before another vertex can be added to the polygonor path.

  • Access programmatically with SETTINGS.experimental.lasso_vertex_distance.

  • Type: ConstrainedIntValue.

  • Default: 10.

  • UI: This setting can be configured via the preferences dialog.

Shapes polygon lasso and path RDP epsilon#

Setting this higher removes more points from polygons or paths. Setting this to 0 keeps all vertices of a given polygon or path.

  • Access programmatically with SETTINGS.experimental.rdp_epsilon.

  • Type: ConstrainedFloatValue.

  • Default: 0.5.

  • UI: This setting can be configured via the preferences dialog.

Triangulation backend to use for Shapes layer#

*Triangulation backend to use for Shapes layer. The ‘bermuda’ requires the optional ‘bermuda’ package. The ‘partsegcore’ requires the optional ‘partsegcore-compiled-backend’ package. The ‘triangle’ requires the optional ‘triangle’ package. The ‘numba’ backend requires the optional ‘numba’ package. The ‘pure python’ backend uses the default Python triangulation from vispy. The ‘fastest available’ backend will select the fastest available backend. *

  • Access programmatically with SETTINGS.experimental.triangulation_backend.

  • Type: TriangulationBackend.

  • Default: fastest_available.

  • UI: This setting can be configured via the preferences dialog.

Support for plugin specific settings will be provided in an upcoming release.