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 0x7f68a452c430: Ctrl+Shift+C>], 'napari:toggle_ndisplay': [<KeyBinding at 0x7f68a452c2e0: Ctrl+Y>], 'napari:toggle_theme': [<KeyBinding at 0x7f68a452cc10: Ctrl+Shift+T>], 'napari:reset_view': [<KeyBinding at 0x7f68a452cfa0: Ctrl+R>], 'napari:delete_selected_layers': [<KeyBinding at 0x7f68a452c550: Ctrl+Delete>, <KeyBinding at 0x7f68a452c0a0: Ctrl+Backspace>], 'napari:show_shortcuts': [<KeyBinding at 0x7f68a452c220: Ctrl+Alt+/>], 'napari:increment_dims_left': [<KeyBinding at 0x7f68a452c160: Left>], 'napari:increment_dims_right': [<KeyBinding at 0x7f68a452f880: Right>], 'napari:focus_axes_up': [<KeyBinding at 0x7f68a452f910: Alt+Up>], 'napari:focus_axes_down': [<KeyBinding at 0x7f68a452f9a0: Alt+Down>], 'napari:roll_axes': [<KeyBinding at 0x7f68a452fa30: Ctrl+E>], 'napari:transpose_axes': [<KeyBinding at 0x7f68a452fac0: Ctrl+T>], 'napari:rotate_layers': [<KeyBinding at 0x7f68a452fb20: Ctrl+Alt+T>], 'napari:toggle_grid': [<KeyBinding at 0x7f68a452fb80: Ctrl+G>], 'napari:toggle_selected_visibility': [<KeyBinding at 0x7f68a452fc10: V>], 'napari:toggle_unselected_visibility': [<KeyBinding at 0x7f68a452fca0: Shift+V>], 'napari:select_layer_above': [<KeyBinding at 0x7f68a452fd00: Ctrl+Up>], 'napari:select_layer_below': [<KeyBinding at 0x7f68a452fd60: Ctrl+Down>], 'napari:show_only_layer_above': [<KeyBinding at 0x7f68a452fdc0: Shift+Alt+Up>], 'napari:show_only_layer_below': [<KeyBinding at 0x7f68a452fe20: Shift+Alt+Down>], 'napari:hold_for_pan_zoom': [<KeyBinding at 0x7f68a452fe80: Space>], 'napari:activate_labels_erase_mode': [<KeyBinding at 0x7f68a452ff10: 1>, <KeyBinding at 0x7f68a452ffa0: E>], 'napari:activate_labels_paint_mode': [<KeyBinding at 0x7f68a453c040: 2>, <KeyBinding at 0x7f68a453c0d0: P>], 'napari:activate_labels_polygon_mode': [<KeyBinding at 0x7f68a453c160: 3>], 'napari:activate_labels_fill_mode': [<KeyBinding at 0x7f68a453c1f0: 4>, <KeyBinding at 0x7f68a453c280: F>], 'napari:activate_labels_picker_mode': [<KeyBinding at 0x7f68a453c310: 5>, <KeyBinding at 0x7f68a453c3a0: L>], 'napari:activate_labels_pan_zoom_mode': [<KeyBinding at 0x7f68a453c430: 6>, <KeyBinding at 0x7f68a453c4c0: Z>], 'napari:activate_labels_transform_mode': [<KeyBinding at 0x7f68a453c550: 7>], 'napari:new_label': [<KeyBinding at 0x7f68a453c5e0: M>], 'napari:swap_selected_and_background_labels': [<KeyBinding at 0x7f68a453c670: X>], 'napari:decrease_label_id': [<KeyBinding at 0x7f68a453c700: ->], 'napari:increase_label_id': [<KeyBinding at 0x7f68a453c790: =>], 'napari:decrease_brush_size': [<KeyBinding at 0x7f68a453c820: [>], 'napari:increase_brush_size': [<KeyBinding at 0x7f68a453c8b0: ]>], 'napari:toggle_preserve_labels': [<KeyBinding at 0x7f68a453c940: B>], 'napari:reset_polygon': [<KeyBinding at 0x7f68a453c9d0: Escape>], 'napari:complete_polygon': [<KeyBinding at 0x7f68a453ca60: Enter>], 'napari:activate_points_add_mode': [<KeyBinding at 0x7f68a453caf0: 2>, <KeyBinding at 0x7f68a453cb50: P>], 'napari:activate_points_select_mode': [<KeyBinding at 0x7f68a453cbb0: 3>, <KeyBinding at 0x7f68a453cc10: S>], 'napari:activate_points_pan_zoom_mode': [<KeyBinding at 0x7f68a453cca0: 4>, <KeyBinding at 0x7f68a453cd00: Z>], 'napari:activate_points_transform_mode': [<KeyBinding at 0x7f68a453cd60: 5>], 'napari:select_all_in_slice': [<KeyBinding at 0x7f68a453cdc0: A>, <KeyBinding at 0x7f68a453ce50: Ctrl+A>], 'napari:select_all_data': [<KeyBinding at 0x7f68a453ceb0: Shift+A>], 'napari:delete_selected_points': [<KeyBinding at 0x7f68a453cf10: 1>, <KeyBinding at 0x7f68a453cf70: Delete>, <KeyBinding at 0x7f68a453cfd0: Backspace>], 'napari:activate_add_rectangle_mode': [<KeyBinding at 0x7f68a453d030: R>], 'napari:activate_add_ellipse_mode': [<KeyBinding at 0x7f68a453d090: E>], 'napari:activate_add_line_mode': [<KeyBinding at 0x7f68a453d0f0: L>], 'napari:activate_add_path_mode': [<KeyBinding at 0x7f68a453d150: T>], 'napari:activate_add_polyline_mode': [<KeyBinding at 0x7f68a453d1b0: Shift+L>], 'napari:activate_add_polygon_mode': [<KeyBinding at 0x7f68a453d210: P>], 'napari:activate_add_polygon_lasso_mode': [<KeyBinding at 0x7f68a453d270: Shift+P>], 'napari:activate_direct_mode': [<KeyBinding at 0x7f68a453d2d0: 4>, <KeyBinding at 0x7f68a453d330: D>], 'napari:activate_select_mode': [<KeyBinding at 0x7f68a453d3c0: 5>, <KeyBinding at 0x7f68a453d420: S>], 'napari:activate_shapes_pan_zoom_mode': [<KeyBinding at 0x7f68a453d480: 6>, <KeyBinding at 0x7f68a453d4e0: Z>], 'napari:activate_shapes_transform_mode': [<KeyBinding at 0x7f68a453d540: 7>], 'napari:activate_vertex_insert_mode': [<KeyBinding at 0x7f68a453d5a0: 2>, <KeyBinding at 0x7f68a453d600: I>], 'napari:activate_vertex_remove_mode': [<KeyBinding at 0x7f68a453d690: 1>, <KeyBinding at 0x7f68a453d6f0: X>], 'napari:copy_selected_shapes': [<KeyBinding at 0x7f68a453d750: Ctrl+C>], 'napari:paste_shape': [<KeyBinding at 0x7f68a453d7b0: Ctrl+V>], 'napari:move_shapes_selection_to_front': [<KeyBinding at 0x7f68a453d810: F>], 'napari:move_shapes_selection_to_back': [<KeyBinding at 0x7f68a453d870: B>], 'napari:select_all_shapes': [<KeyBinding at 0x7f68a453d8d0: A>, <KeyBinding at 0x7f68a453d930: Ctrl+A>], 'napari:delete_selected_shapes': [<KeyBinding at 0x7f68a453d990: 3>, <KeyBinding at 0x7f68a453d9f0: Delete>, <KeyBinding at 0x7f68a453da50: Backspace>], 'napari:finish_drawing_shape': [<KeyBinding at 0x7f68a453dab0: Enter>, <KeyBinding at 0x7f68a453db10: Escape>], 'napari:orient_plane_normal_along_x': [<KeyBinding at 0x7f68a453db70: X>], 'napari:orient_plane_normal_along_y': [<KeyBinding at 0x7f68a453dbd0: Y>], 'napari:orient_plane_normal_along_z': [<KeyBinding at 0x7f68a453dc30: Z>], 'napari:orient_plane_normal_along_view_direction': [<KeyBinding at 0x7f68a453dc90: O>], 'napari:activate_image_pan_zoom_mode': [<KeyBinding at 0x7f68a453dd20: 1>], 'napari:activate_image_transform_mode': [<KeyBinding at 0x7f68a453dd80: 2>], 'napari:activate_vectors_pan_zoom_mode': [<KeyBinding at 0x7f68a453dde0: 1>], 'napari:activate_vectors_transform_mode': [<KeyBinding at 0x7f68a453de40: 2>], 'napari:activate_tracks_pan_zoom_mode': [<KeyBinding at 0x7f68a453dea0: 1>], 'napari:activate_tracks_transform_mode': [<KeyBinding at 0x7f68a453df00: 2>], 'napari:activate_surface_pan_zoom_mode': [<KeyBinding at 0x7f68a453df60: 1>], 'napari:activate_surface_transform_mode': [<KeyBinding at 0x7f68a453dfc0: 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.