Preferences#

napari settings#

napari provides persistent settings that are stored on a per environment basis. This means that if you have multiple Python environments, each with a napari installation (e.g. different versions), the napari in each environment will have its own set of stored preferences. So, for example, you could have an environment where napari always uses the Light theme and another one where napari always uses the Dark theme.

A wide range of settings are available, organized into sections, and described in more detail below.

Where settings are stored#

Settings are stored in a settings.yaml file and napari uses appdirs to determine the save location: the platform-specific user configuration directory. You can check where a napari installation has stored settings by looking for “Settings path” in the output of:

napari --info

Resetting settings to defaults using the command line (CLI)#

Sometimes, for example due to a version change, an issue with the stored settings can prevent napari from launching or cause other issues. In those cases, it can be useful to reset the settings to the defaults from the command line. To reset all napari settings to the default values:

napari --reset

Programmatic access to the 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'

You can get more information about individual settings, their types, and default values in each of the settings section descriptions below.

The Preferences dialog#

napari provides a Preferences dialog to manage the settings using a graphical user interface (GUI). Importantly, this dialog also allows you to customize napari keyboard shortcuts (keybindings).

On Windows and Linux, the Preferences dialog can be accessed in the File menu. On macOS, it can be accessed in the napari menu.

The settings are grouped by sections that are accessible in a list on the left side of the dialog.

Application Settings#

Main application settings.

application

More details on the individual 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.

  • Environmental variable: NAPARI_APPLICATION_BRUSH_SIZE_ON_MOUSE_MOVE_MODIFIERS

  • Type: BrushSizeOnMouseModifiers

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

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.

  • Environmental variable: NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW

  • Type: bool

  • Default: True.

Console notification level

Select the notification level for the console.

  • Access programmatically with SETTINGS.application.console_notification_level.

  • Environmental variable: NAPARI_APPLICATION_CONSOLE_NOTIFICATION_LEVEL

  • Type: NotificationSeverity

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

Dask cache

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

  • Access programmatically with SETTINGS.application.dask.

  • Environmental variable: NAPARI_APPLICATION_DASK

  • Type: DaskSettings

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

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.

  • Environmental variable: NAPARI_APPLICATION_DEPTH_AXIS_ORIENTATION

  • Type: DepthAxisOrientation

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

Grid Height

Number of rows in the grid.

  • Access programmatically with SETTINGS.application.grid_height.

  • Environmental variable: NAPARI_APPLICATION_GRID_HEIGHT

  • Type: ConstrainedIntValue

  • Default: -1.

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.

  • Environmental variable: NAPARI_APPLICATION_GRID_SPACING

  • Type: ConstrainedFloatValue

  • Default: 0.

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.

  • Environmental variable: NAPARI_APPLICATION_GRID_STRIDE

  • Type: ConstrainedIntValue

  • Default: 1.

Grid Width

Number of columns in the grid.

  • Access programmatically with SETTINGS.application.grid_width.

  • Environmental variable: NAPARI_APPLICATION_GRID_WIDTH

  • Type: ConstrainedIntValue

  • Default: -1.

GUI notification level

Select the notification level for the user interface.

  • Access programmatically with SETTINGS.application.gui_notification_level.

  • Environmental variable: NAPARI_APPLICATION_GUI_NOTIFICATION_LEVEL

  • Type: NotificationSeverity

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

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.

  • Environmental variable: NAPARI_APPLICATION_HOLD_BUTTON_DELAY

  • Type: float

  • Default: 0.5.

Horizontal Axis Orientation

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

  • Access programmatically with SETTINGS.application.horizontal_axis_orientation.

  • Environmental variable: NAPARI_APPLICATION_HORIZONTAL_AXIS_ORIENTATION

  • Type: HorizontalAxisOrientation

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

Language

Select the display language for the user interface.

  • Access programmatically with SETTINGS.application.language.

  • Environmental variable: NAPARI_APPLICATION_LANGUAGE

  • Type: Language

  • Default: 'en'.

New labels data type

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

  • Access programmatically with SETTINGS.application.new_labels_dtype.

  • Environmental variable: NAPARI_APPLICATION_NEW_LABELS_DTYPE

  • Type: LabelDTypes

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

Playback frames per second

Playback speed in frames per second.

  • Access programmatically with SETTINGS.application.playback_fps.

  • Environmental variable: NAPARI_APPLICATION_PLAYBACK_FPS

  • Type: int

  • Default: 10.

Playback loop mode

Loop mode for playback.

  • Access programmatically with SETTINGS.application.playback_mode.

  • Environmental variable: NAPARI_APPLICATION_PLAYBACK_MODE

  • Type: LoopMode

  • Default: <LoopMode.LOOP: 'loop'>.

Save window geometry

Toggle saving the main window size and position.

  • Access programmatically with SETTINGS.application.save_window_geometry.

  • Environmental variable: NAPARI_APPLICATION_SAVE_WINDOW_GEOMETRY

  • Type: bool

  • Default: True.

Save window state

Toggle saving the main window state of widgets.

  • Access programmatically with SETTINGS.application.save_window_state.

  • Environmental variable: NAPARI_APPLICATION_SAVE_WINDOW_STATE

  • Type: bool

  • Default: False.

Full path to a startup script

Path to a Python script that will be executed on napari startup. This can be used to customize the behavior of napari or load specific plugins automatically.

  • Access programmatically with SETTINGS.application.startup_script.

  • Environmental variable: NAPARI_APPLICATION_STARTUP_SCRIPT

  • Type: Path

  • Default: PosixPath('.').

Vertical Axis Orientation

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

  • Access programmatically with SETTINGS.application.vertical_axis_orientation.

  • Environmental variable: NAPARI_APPLICATION_VERTICAL_AXIS_ORIENTATION

  • Type: VerticalAxisOrientation

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

Appearance Settings#

User interface appearance settings.

appearance

More details on the individual Appearance settings

Font size

Select the user interface font size.

  • Access programmatically with SETTINGS.appearance.font_size.

  • Environmental variable: NAPARI_APPEARANCE_FONT_SIZE

  • Type: ConstrainedIntValue

  • Default: 9.

Highlight

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

  • Access programmatically with SETTINGS.appearance.highlight.

  • Environmental variable: NAPARI_APPEARANCE_HIGHLIGHT

  • Type: HighlightSettings

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

Show layer tooltips

Toggle to display a tooltip on mouse hover.

  • Access programmatically with SETTINGS.appearance.layer_tooltip_visibility.

  • Environmental variable: NAPARI_APPEARANCE_LAYER_TOOLTIP_VISIBILITY

  • Type: bool

  • Default: False.

Theme

Select the user interface theme.

  • Access programmatically with SETTINGS.appearance.theme.

  • Environmental variable: NAPARI_APPEARANCE_THEME

  • Type: Theme

  • Default: 'dark'.

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.

  • Environmental variable: NAPARI_APPEARANCE_UPDATE_STATUS_BASED_ON_LAYER

  • Type: bool

  • Default: True.

Plugins Settings#

Plugins settings.

plugins

More details on the individual Plugins settings

Plugin sort order

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

  • Access programmatically with SETTINGS.plugins.call_order.

  • Environmental variable: NAPARI_PLUGINS_CALL_ORDER

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

  • Default: {}.

File extension readers

Assign file extensions to specific reader plugins

  • Access programmatically with SETTINGS.plugins.extension2reader.

  • Environmental variable: NAPARI_PLUGINS_EXTENSION2READER

  • 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.

  • Environmental variable: NAPARI_PLUGINS_ONLY_NEW_SHIMMED_PLUGINS_WARNING

  • Type: bool

  • Default: False.

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.

  • Environmental variable: NAPARI_PLUGINS_USE_NPE2_ADAPTOR

  • Type: bool

  • Default: True.

Shortcuts Settings#

Shortcut settings.

shortcuts

More details on the individual Shortcuts settings

shortcuts

Set keyboard shortcuts for actions.

  • Access programmatically with SETTINGS.shortcuts.shortcuts.

  • Environmental variable: NAPARI_SHORTCUTS_SHORTCUTS

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

Default Shortcuts

Action

Shortcut

napari:toggle_console_visibility

[<KeyBinding at 0x7f0a7058a300: Ctrl+Shift+C>]

napari:toggle_ndisplay

[<KeyBinding at 0x7f0a7058a570: Ctrl+Y>]

napari:toggle_theme

[<KeyBinding at 0x7f0a70588350: Ctrl+Shift+T>]

napari:reset_view

[<KeyBinding at 0x7f0a70588200: Ctrl+R>]

napari:delete_selected_layers

[<KeyBinding at 0x7f0a7058b290: Ctrl+Delete>, <KeyBinding at 0x7f0a7058b9b0: Ctrl+Backspace>]

napari:show_shortcuts

[<KeyBinding at 0x7f0a708a2600: Ctrl+Alt+/>]

napari:increment_dims_left

[<KeyBinding at 0x7f0a705b3ad0: Left>]

napari:increment_dims_right

[<KeyBinding at 0x7f0a705b2ba0: Right>]

napari:focus_axes_up

[<KeyBinding at 0x7f0a705b2270: Alt+Up>]

napari:focus_axes_down

[<KeyBinding at 0x7f0a705b16a0: Alt+Down>]

napari:roll_axes

[<KeyBinding at 0x7f0a705b0830: Ctrl+E>]

napari:transpose_axes

[<KeyBinding at 0x7f0a705b0680: Ctrl+T>]

napari:rotate_layers

[<KeyBinding at 0x7f0a705b0500: Ctrl+Alt+T>]

napari:toggle_grid

[<KeyBinding at 0x7f0a705b14c0: Ctrl+G>]

napari:toggle_selected_visibility

[<KeyBinding at 0x7f0a705b09e0: V>]

napari:toggle_unselected_visibility

[<KeyBinding at 0x7f0a705b1310: Shift+V>]

napari:select_layer_above

[<KeyBinding at 0x7f0a705b2150: Ctrl+Up>]

napari:select_layer_below

[<KeyBinding at 0x7f0a705b1880: Ctrl+Down>]

napari:show_only_layer_above

[<KeyBinding at 0x7f0a705b1fa0: Shift+Alt+Up>]

napari:show_only_layer_below

[<KeyBinding at 0x7f0a705b2a50: Shift+Alt+Down>]

napari:hold_for_pan_zoom

[<KeyBinding at 0x7f0a705b2390: Space>]

napari:activate_labels_erase_mode

[<KeyBinding at 0x7f0a705b2930: 1>, <KeyBinding at 0x7f0a705b3920: E>]

napari:activate_labels_paint_mode

[<KeyBinding at 0x7f0a705b2d80: 2>, <KeyBinding at 0x7f0a705b3740: P>]

napari:activate_labels_polygon_mode

[<KeyBinding at 0x7f0a705b3e00: 3>]

napari:activate_labels_fill_mode

[<KeyBinding at 0x7f0a70883fb0: 4>, <KeyBinding at 0x7f0a70a16ae0: F>]

napari:activate_labels_picker_mode

[<KeyBinding at 0x7f0a70d1e540: 5>, <KeyBinding at 0x7f0a70538380: L>]

napari:activate_labels_pan_zoom_mode

[<KeyBinding at 0x7f0a70538c50: 6>, <KeyBinding at 0x7f0a70538200: Z>]

napari:activate_labels_transform_mode

[<KeyBinding at 0x7f0a70538470: 7>]

napari:new_label

[<KeyBinding at 0x7f0a70538620: M>]

napari:swap_selected_and_background_labels

[<KeyBinding at 0x7f0a70538710: X>]

napari:decrease_label_id

[<KeyBinding at 0x7f0a705388f0: ->]

napari:increase_label_id

[<KeyBinding at 0x7f0a70538b60: =>]

napari:decrease_brush_size

[<KeyBinding at 0x7f0a70539d90: [>]

napari:increase_brush_size

[<KeyBinding at 0x7f0a7053a5a0: ]>]

napari:toggle_preserve_labels

[<KeyBinding at 0x7f0a7053aab0: B>]

napari:reset_polygon

[<KeyBinding at 0x7f0a7053af90: Escape>]

napari:complete_polygon

[<KeyBinding at 0x7f0a70528560: Enter>]

napari:activate_points_add_mode

[<KeyBinding at 0x7f0a70528c20: 2>, <KeyBinding at 0x7f0a70528fb0: P>]

napari:activate_points_select_mode

[<KeyBinding at 0x7f0a70529520: 3>, <KeyBinding at 0x7f0a70529700: S>]

napari:activate_points_pan_zoom_mode

[<KeyBinding at 0x7f0a705299a0: 4>, <KeyBinding at 0x7f0a70529f70: Z>]

napari:activate_points_transform_mode

[<KeyBinding at 0x7f0a7052a4b0: 5>]

napari:select_all_in_slice

[<KeyBinding at 0x7f0a7052a5a0: A>, <KeyBinding at 0x7f0a7052a720: Ctrl+A>]

napari:select_all_data

[<KeyBinding at 0x7f0a7052a7e0: Shift+A>]

napari:delete_selected_points

[<KeyBinding at 0x7f0a7052aab0: 1>, <KeyBinding at 0x7f0a7052ac90: Delete>, <KeyBinding at 0x7f0a7052af60: Backspace>]

napari:activate_add_rectangle_mode

[<KeyBinding at 0x7f0a7052b230: R>]

napari:activate_add_ellipse_mode

[<KeyBinding at 0x7f0a7052b3b0: E>]

napari:activate_add_line_mode

[<KeyBinding at 0x7f0a7052b530: L>]

napari:activate_add_path_mode

[<KeyBinding at 0x7f0a7052b680: T>]

napari:activate_add_polyline_mode

[<KeyBinding at 0x7f0a7052b860: Shift+L>]

napari:activate_add_polygon_mode

[<KeyBinding at 0x7f0a7052bb90: P>]

napari:activate_add_polygon_lasso_mode

[<KeyBinding at 0x7f0a7052bda0: Shift+P>]

napari:activate_direct_mode

[<KeyBinding at 0x7f0a7052bfe0: 4>, <KeyBinding at 0x7f0a70516b10: D>]

napari:activate_select_mode

[<KeyBinding at 0x7f0a70516c00: 5>, <KeyBinding at 0x7f0a7057ba70: S>]

napari:activate_shapes_pan_zoom_mode

[<KeyBinding at 0x7f0a7057a330: 6>, <KeyBinding at 0x7f0a7057a960: Z>]

napari:activate_shapes_transform_mode

[<KeyBinding at 0x7f0a7057b140: 7>]

napari:activate_vertex_insert_mode

[<KeyBinding at 0x7f0a7057b410: 2>, <KeyBinding at 0x7f0a7057bd10: I>]

napari:activate_vertex_remove_mode

[<KeyBinding at 0x7f0a70597a40: 1>, <KeyBinding at 0x7f0a70595f40: X>]

napari:copy_selected_shapes

[<KeyBinding at 0x7f0a70596f00: Ctrl+C>]

napari:paste_shape

[<KeyBinding at 0x7f0a705940b0: Ctrl+V>]

napari:move_shapes_selection_to_front

[<KeyBinding at 0x7f0a70594da0: F>]

napari:move_shapes_selection_to_back

[<KeyBinding at 0x7f0a70594260: B>]

napari:select_shapes_in_slice

[<KeyBinding at 0x7f0a70594bc0: A>, <KeyBinding at 0x7f0a70595760: Ctrl+A>]

napari:delete_selected_shapes

[<KeyBinding at 0x7f0a70594f50: 3>, <KeyBinding at 0x7f0a70595580: Delete>, <KeyBinding at 0x7f0a70597e00: Backspace>]

napari:finish_drawing_shape

[<KeyBinding at 0x7f0a70595940: Enter>, <KeyBinding at 0x7f0a70597140: Escape>]

napari:orient_plane_normal_along_x

[<KeyBinding at 0x7f0a70595b20: X>]

napari:orient_plane_normal_along_y

[<KeyBinding at 0x7f0a70596b70: Y>]

napari:orient_plane_normal_along_z

[<KeyBinding at 0x7f0a70597860: Z>]

napari:orient_plane_normal_along_view_direction

[<KeyBinding at 0x7f0a705a7a10: O>]

napari:activate_image_pan_zoom_mode

[<KeyBinding at 0x7f0a705a6cc0: 1>]

napari:activate_image_transform_mode

[<KeyBinding at 0x7f0a705a5d00: 2>]

napari:activate_vectors_pan_zoom_mode

[<KeyBinding at 0x7f0a705a4f20: 1>]

napari:activate_vectors_transform_mode

[<KeyBinding at 0x7f0a705a4200: 2>]

napari:activate_tracks_pan_zoom_mode

[<KeyBinding at 0x7f0a705a4b60: 1>]

napari:activate_tracks_transform_mode

[<KeyBinding at 0x7f0a705a5460: 2>]

napari:activate_surface_pan_zoom_mode

[<KeyBinding at 0x7f0a705a5b20: 1>]

napari:activate_surface_transform_mode

[<KeyBinding at 0x7f0a705a5100: 2>]

Experimental Settings#

Experimental settings.

experimental

More details on the individual Experimental settings

Render Images Asynchronously

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

  • Access programmatically with SETTINGS.experimental.async_.

  • Environmental variable: NAPARI_EXPERIMENTAL_ASYNC_

  • Type: bool

  • Default: False.

Enable autoswapping rendering buffers.

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

  • Access programmatically with SETTINGS.experimental.autoswap_buffers.

  • Environmental variable: NAPARI_EXPERIMENTAL_AUTOSWAP_BUFFERS

  • Type: bool

  • Default: False.

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.

  • Environmental variable: NAPARI_EXPERIMENTAL_COLORMAP_BACKEND

  • Type: ColormapBackend

  • Default: fastest_available.

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.

  • Environmental variable: NAPARI_EXPERIMENTAL_COMPLETION_RADIUS

  • Type: int

  • Default: -1.

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.

  • Environmental variable: NAPARI_EXPERIMENTAL_LASSO_VERTEX_DISTANCE

  • Type: ConstrainedIntValue

  • Default: 10.

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.

  • Environmental variable: NAPARI_EXPERIMENTAL_RDP_EPSILON

  • Type: ConstrainedFloatValue

  • Default: 0.5.

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.

  • Environmental variable: NAPARI_EXPERIMENTAL_TRIANGULATION_BACKEND

  • Type: TriangulationBackend

  • Default: fastest_available.

Reset settings to defaults using the Preferences dialog#

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

Overriding settings#

napari settings can also be overridden by using environment variables. The variable names follow a pattern: they start with NAPARI, followed by the Preference section name, yielding, for example, NAPARI_APPLICATION, followed by the setting name, yielding, for example, NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW. (This specific setting controls whether napari will prompt you to confirm closing the application.) You can also find the environmentvariable names for each setting in the descriptions for each of the Preference sections above.

You can override settings for a single napari session by setting environment variables at launch:

On Mac and Linux:

NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW=False napari

On Windows:

set NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW=False && napari

Or programatically in a script/notebook:

import os
os.environ['NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW'] = 'False'

Or, depending on your shell, you can persist environment variables for a shell session using the export command (e.g. bash, zsh):

export NAPARI_APPLICATION_CONFIRM_CLOSE_WINDOW=False

Or, to persist between shell sessions, add the above command to your shell configuration file e.g ~/.bashrc or ~/.zshrc.