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=4.191603712).

  • 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#

Proportional spacing between grid layers.

  • Access programmatically with SETTINGS.application.grid_spacing.

  • Type: ConstrainedFloatValue.

  • Default: 0.0.

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

Grid Stride#

Number of layers to place in each grid square.

  • 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 0x7fe87c29d7e0: Ctrl+Shift+C>], 'napari:reset_scroll_progress': [<KeyBinding at 0x7fe87c29ce80: Ctrl>], 'napari:toggle_ndisplay': [<KeyBinding at 0x7fe87c29d000: Ctrl+Y>], 'napari:toggle_theme': [<KeyBinding at 0x7fe87c29cca0: Ctrl+Shift+T>], 'napari:reset_view': [<KeyBinding at 0x7fe87c29d6c0: Ctrl+R>], 'napari:delete_selected_layers': [<KeyBinding at 0x7fe87c29d0c0: Ctrl+Delete>, <KeyBinding at 0x7fe87c29d450: Ctrl+Backspace>], 'napari:show_shortcuts': [<KeyBinding at 0x7fe87c29d4b0: Ctrl+Alt+/>], 'napari:increment_dims_left': [<KeyBinding at 0x7fe87c29ddb0: Left>], 'napari:increment_dims_right': [<KeyBinding at 0x7fe87c29d420: Right>], 'napari:focus_axes_up': [<KeyBinding at 0x7fe87c29d7b0: Alt+Up>], 'napari:focus_axes_down': [<KeyBinding at 0x7fe87c29d810: Alt+Down>], 'napari:roll_axes': [<KeyBinding at 0x7fe87c29dc90: Ctrl+E>], 'napari:transpose_axes': [<KeyBinding at 0x7fe87c29db70: Ctrl+T>], 'napari:rotate_layers': [<KeyBinding at 0x7fe87c29db10: Ctrl+Alt+T>], 'napari:toggle_grid': [<KeyBinding at 0x7fe87c29db40: Ctrl+G>], 'napari:toggle_selected_visibility': [<KeyBinding at 0x7fe87c29da80: V>], 'napari:toggle_unselected_visibility': [<KeyBinding at 0x7fe87c29dfc0: Shift+V>], 'napari:show_only_layer_above': [<KeyBinding at 0x7fe87c29dd20: Shift+Alt+Up>], 'napari:show_only_layer_below': [<KeyBinding at 0x7fe87c2ad930: Shift+Alt+Down>], 'napari:hold_for_pan_zoom': [<KeyBinding at 0x7fe87c2ad990: Space>], 'napari:activate_labels_erase_mode': [<KeyBinding at 0x7fe87c2ada20: 1>, <KeyBinding at 0x7fe87c2adab0: E>], 'napari:activate_labels_paint_mode': [<KeyBinding at 0x7fe87c2adb10: 2>, <KeyBinding at 0x7fe87c2adba0: P>], 'napari:activate_labels_polygon_mode': [<KeyBinding at 0x7fe87c2adc30: 3>], 'napari:activate_labels_fill_mode': [<KeyBinding at 0x7fe87c2adcc0: 4>, <KeyBinding at 0x7fe87c2add50: F>], 'napari:activate_labels_picker_mode': [<KeyBinding at 0x7fe87c2adde0: 5>, <KeyBinding at 0x7fe87c2ade70: L>], 'napari:activate_labels_pan_zoom_mode': [<KeyBinding at 0x7fe87c2adf00: 6>, <KeyBinding at 0x7fe87c2adf90: Z>], 'napari:activate_labels_transform_mode': [<KeyBinding at 0x7fe87c2ae020: 7>], 'napari:new_label': [<KeyBinding at 0x7fe87c2ae0b0: M>], 'napari:swap_selected_and_background_labels': [<KeyBinding at 0x7fe87c2ae140: X>], 'napari:decrease_label_id': [<KeyBinding at 0x7fe87c2ae1d0: ->], 'napari:increase_label_id': [<KeyBinding at 0x7fe87c2ae260: =>], 'napari:decrease_brush_size': [<KeyBinding at 0x7fe87c2ae2f0: [>], 'napari:increase_brush_size': [<KeyBinding at 0x7fe87c2ae380: ]>], 'napari:toggle_preserve_labels': [<KeyBinding at 0x7fe87c2ae410: B>], 'napari:reset_polygon': [<KeyBinding at 0x7fe87c2ae4a0: Escape>], 'napari:complete_polygon': [<KeyBinding at 0x7fe87c2ae530: Enter>], 'napari:activate_points_add_mode': [<KeyBinding at 0x7fe87c2ae5c0: 2>, <KeyBinding at 0x7fe87c2ae620: P>], 'napari:activate_points_select_mode': [<KeyBinding at 0x7fe87c2ae680: 3>, <KeyBinding at 0x7fe87c2ae6e0: S>], 'napari:activate_points_pan_zoom_mode': [<KeyBinding at 0x7fe87c2ae770: 4>, <KeyBinding at 0x7fe87c2ae7d0: Z>], 'napari:activate_points_transform_mode': [<KeyBinding at 0x7fe87c2ae830: 5>], 'napari:select_all_in_slice': [<KeyBinding at 0x7fe87c2ae890: A>, <KeyBinding at 0x7fe87c2ae920: Ctrl+A>], 'napari:select_all_data': [<KeyBinding at 0x7fe87c2ae980: Shift+A>], 'napari:delete_selected_points': [<KeyBinding at 0x7fe87c2ae9e0: 1>, <KeyBinding at 0x7fe87c2aea40: Delete>, <KeyBinding at 0x7fe87c2aeaa0: Backspace>], 'napari:activate_add_rectangle_mode': [<KeyBinding at 0x7fe87c2aeb00: R>], 'napari:activate_add_ellipse_mode': [<KeyBinding at 0x7fe87c2aeb60: E>], 'napari:activate_add_line_mode': [<KeyBinding at 0x7fe87c2aebc0: L>], 'napari:activate_add_path_mode': [<KeyBinding at 0x7fe87c2aec20: T>], 'napari:activate_add_polyline_mode': [<KeyBinding at 0x7fe87c2aec80: Shift+L>], 'napari:activate_add_polygon_mode': [<KeyBinding at 0x7fe87c2aece0: P>], 'napari:activate_add_polygon_lasso_mode': [<KeyBinding at 0x7fe87c2aed40: Shift+P>], 'napari:activate_direct_mode': [<KeyBinding at 0x7fe87c2aeda0: 4>, <KeyBinding at 0x7fe87c2aee00: D>], 'napari:activate_select_mode': [<KeyBinding at 0x7fe87c2aee90: 5>, <KeyBinding at 0x7fe87c2aeef0: S>], 'napari:activate_shapes_pan_zoom_mode': [<KeyBinding at 0x7fe87c2aef50: 6>, <KeyBinding at 0x7fe87c2aefb0: Z>], 'napari:activate_shapes_transform_mode': [<KeyBinding at 0x7fe87c2af010: 7>], 'napari:activate_vertex_insert_mode': [<KeyBinding at 0x7fe87c2af070: 2>, <KeyBinding at 0x7fe87c2af0d0: I>], 'napari:activate_vertex_remove_mode': [<KeyBinding at 0x7fe87c2af160: 1>, <KeyBinding at 0x7fe87c2af1c0: X>], 'napari:copy_selected_shapes': [<KeyBinding at 0x7fe87c2af220: Ctrl+C>], 'napari:paste_shape': [<KeyBinding at 0x7fe87c2af280: Ctrl+V>], 'napari:move_shapes_selection_to_front': [<KeyBinding at 0x7fe87c2af2e0: F>], 'napari:move_shapes_selection_to_back': [<KeyBinding at 0x7fe87c2af340: B>], 'napari:select_all_shapes': [<KeyBinding at 0x7fe87c2af3a0: A>], 'napari:delete_selected_shapes': [<KeyBinding at 0x7fe87c2af400: 3>, <KeyBinding at 0x7fe87c2af460: Delete>, <KeyBinding at 0x7fe87c2af4c0: Backspace>], 'napari:finish_drawing_shape': [<KeyBinding at 0x7fe87c2af520: Enter>, <KeyBinding at 0x7fe87c2af580: Escape>], 'napari:orient_plane_normal_along_x': [<KeyBinding at 0x7fe87c2af5e0: X>], 'napari:orient_plane_normal_along_y': [<KeyBinding at 0x7fe87c2af640: Y>], 'napari:orient_plane_normal_along_z': [<KeyBinding at 0x7fe87c2af6a0: Z>], 'napari:orient_plane_normal_along_view_direction': [<KeyBinding at 0x7fe87c2af700: O>], 'napari:activate_image_pan_zoom_mode': [<KeyBinding at 0x7fe87c2af790: 1>], 'napari:activate_image_transform_mode': [<KeyBinding at 0x7fe87c2af7f0: 2>], 'napari:activate_vectors_pan_zoom_mode': [<KeyBinding at 0x7fe87c2af850: 1>], 'napari:activate_vectors_transform_mode': [<KeyBinding at 0x7fe87c2af8b0: 2>], 'napari:activate_tracks_pan_zoom_mode': [<KeyBinding at 0x7fe87c2af910: 1>], 'napari:activate_tracks_transform_mode': [<KeyBinding at 0x7fe87c2af970: 2>], 'napari:activate_surface_pan_zoom_mode': [<KeyBinding at 0x7fe87c2af9d0: 1>], 'napari:activate_surface_transform_mode': [<KeyBinding at 0x7fe87c2afa30: 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.

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.