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: <enum '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: <class '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: <enum '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: <class 'napari.settings._application.DaskSettings'>
Default: DaskSettings(enabled=True, cache=4.19160576).

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

Float display precision

Number of significant digits when displaying float values in the status bar and layer tooltips.

Access programmatically with SETTINGS.application.float_display_precision.
Environmental variable: NAPARI_APPLICATION_FLOAT_DISPLAY_PRECISION
Type: <class 'int'>
Default: 3.

Grid Height

Number of rows in the grid.

Access programmatically with SETTINGS.application.grid_height.
Environmental variable: NAPARI_APPLICATION_GRID_HEIGHT
Type: <class 'int'>
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: <class 'float'>
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: <class 'int'>
Default: 1.

Grid Width

Number of columns in the grid.

Access programmatically with SETTINGS.application.grid_width.
Environmental variable: NAPARI_APPLICATION_GRID_WIDTH
Type: <class 'int'>
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: <enum '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: <class '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: <enum 'HorizontalAxisOrientation'>
Default: <HorizontalAxisOrientation.RIGHT: 'right'>.

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: <enum '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: <class 'int'>
Default: 10.

Playback loop mode

Loop mode for playback.

Access programmatically with SETTINGS.application.playback_mode.
Environmental variable: NAPARI_APPLICATION_PLAYBACK_MODE
Type: <enum '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: <class '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: <class '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: <class 'pathlib.Path'>
Default: PosixPath('.').

Synced Camera

Controls how camera state is managed when switching between 2D and 3D views. When checked, camera center and zoom are shared between views, with the depth (Z) component synced via the dims slider. When unchecked, each mode remembers its own camera state independently.

Access programmatically with SETTINGS.application.synced_camera.
Environmental variable: NAPARI_APPLICATION_SYNCED_CAMERA
Type: <class 'bool'>
Default: True.

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

Appearance Settings#

User interface appearance settings.

appearance

Plugins Settings#

Plugins settings.

plugins

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: dict[str, list[app_model.types._keys._keybindings.KeyBinding]]

Default Shortcuts

Action	Shortcut
napari:toggle_console_visibility	[<KeyBinding at 0x7f45bcc8daf0: Ctrl+Shift+C>]
napari:toggle_ndisplay	[<KeyBinding at 0x7f45bcc8ecf0: Ctrl+Y>]
napari:toggle_theme	[<KeyBinding at 0x7f45bcb37170: Ctrl+Shift+T>]
napari:reset_view	[<KeyBinding at 0x7f45bcc94800: Ctrl+R>]
napari:delete_selected_layers	[<KeyBinding at 0x7f45bcc946e0: Ctrl+Delete>, <KeyBinding at 0x7f45bcc96e10: Ctrl+Backspace>]
napari:show_shortcuts	[<KeyBinding at 0x7f45bcb3c5f0: Ctrl+Alt+/>]
napari:increment_dims_left	[<KeyBinding at 0x7f45bcb3d190: Left>]
napari:increment_dims_right	[<KeyBinding at 0x7f45bcb3d1c0: Right>]
napari:focus_axes_up	[<KeyBinding at 0x7f45bcb3d220: Alt+Up>]
napari:focus_axes_down	[<KeyBinding at 0x7f45bcb3d2b0: Alt+Down>]
napari:roll_axes	[<KeyBinding at 0x7f45bcb3d310: Ctrl+E>]
napari:transpose_axes	[<KeyBinding at 0x7f45bcb3d370: Ctrl+T>]
napari:rotate_layers	[<KeyBinding at 0x7f45bcb3d3d0: Ctrl+Alt+T>]
napari:toggle_grid	[<KeyBinding at 0x7f45bcb3d430: Ctrl+G>]
napari:toggle_selected_visibility	[<KeyBinding at 0x7f45bcb3d490: V>]
napari:toggle_unselected_visibility	[<KeyBinding at 0x7f45bcb3d4f0: Shift+V>]
napari:select_layer_above	[<KeyBinding at 0x7f45bcb3d550: Ctrl+Up>]
napari:select_layer_below	[<KeyBinding at 0x7f45bcb3d5b0: Ctrl+Down>]
napari:show_only_layer_above	[<KeyBinding at 0x7f45bcb3d610: Shift+Alt+Up>]
napari:show_only_layer_below	[<KeyBinding at 0x7f45bcb3d670: Shift+Alt+Down>]
napari:hold_for_pan_zoom	[<KeyBinding at 0x7f45bcb3d6d0: Space>]
napari:activate_labels_erase_mode	[<KeyBinding at 0x7f45bcb3d730: 1>, <KeyBinding at 0x7f45bcb3d790: E>]
napari:activate_labels_paint_mode	[<KeyBinding at 0x7f45bcb3d7f0: 2>, <KeyBinding at 0x7f45bcb3d850: P>]
napari:activate_labels_polygon_mode	[<KeyBinding at 0x7f45bcb3d8b0: 3>]
napari:activate_labels_fill_mode	[<KeyBinding at 0x7f45bcb3d910: 4>, <KeyBinding at 0x7f45bcb3d970: F>]
napari:activate_labels_picker_mode	[<KeyBinding at 0x7f45bcb3d9d0: 5>, <KeyBinding at 0x7f45bcb3da30: L>]
napari:activate_labels_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3da90: 6>, <KeyBinding at 0x7f45bcb3daf0: Z>]
napari:activate_labels_transform_mode	[<KeyBinding at 0x7f45bcb3db50: 7>]
napari:new_label	[<KeyBinding at 0x7f45bcb3dbb0: M>]
napari:swap_selected_and_background_labels	[<KeyBinding at 0x7f45bcb3dc10: X>]
napari:decrease_label_id	[<KeyBinding at 0x7f45bcb3dc70: ->]
napari:increase_label_id	[<KeyBinding at 0x7f45bcb3dd30: =>]
napari:decrease_brush_size	[<KeyBinding at 0x7f45bcb37f80: [>]
napari:increase_brush_size	[<KeyBinding at 0x7f45bcb37fb0: ]>]
napari:toggle_preserve_labels	[<KeyBinding at 0x7f45bcb37e00: B>]
napari:reset_polygon	[<KeyBinding at 0x7f45bcb37e60: Escape>]
napari:complete_polygon	[<KeyBinding at 0x7f45bcb37d70: Enter>]
napari:activate_points_add_mode	[<KeyBinding at 0x7f45bcb37a10: 2>, <KeyBinding at 0x7f45bcb378f0: P>]
napari:activate_points_select_mode	[<KeyBinding at 0x7f45bcca13a0: 3>, <KeyBinding at 0x7f45bcc3ff80: S>]
napari:activate_points_pan_zoom_mode	[<KeyBinding at 0x7f45bcc959d0: 4>, <KeyBinding at 0x7f45bcc955e0: Z>]
napari:activate_points_transform_mode	[<KeyBinding at 0x7f45bcb2b1a0: 5>]
napari:select_all_in_slice	[<KeyBinding at 0x7f45bcb2b1d0: A>]
napari:select_append_all_in_slice	[<KeyBinding at 0x7f45bcc18950: Shift+A>]
napari:select_all_data	[<KeyBinding at 0x7f45bff17860: Ctrl+A>]
napari:delete_selected_points	[<KeyBinding at 0x7f45bcc8fa10: 1>, <KeyBinding at 0x7f45bcc8c320: Delete>, <KeyBinding at 0x7f45bcc8c740: Backspace>]
napari:activate_add_rectangle_mode	[<KeyBinding at 0x7f45bcc8c9e0: R>]
napari:activate_add_ellipse_mode	[<KeyBinding at 0x7f45c06062a0: E>]
napari:activate_add_line_mode	[<KeyBinding at 0x7f45bcc83ec0: L>]
napari:activate_add_path_mode	[<KeyBinding at 0x7f45bcc84d10: T>]
napari:activate_add_polyline_mode	[<KeyBinding at 0x7f45bcb3dd60: Shift+L>]
napari:activate_add_polygon_mode	[<KeyBinding at 0x7f45bcb3d010: P>]
napari:activate_add_polygon_lasso_mode	[<KeyBinding at 0x7f45bcb3d0a0: Shift+P>]
napari:activate_direct_mode	[<KeyBinding at 0x7f45bcb3cef0: 4>, <KeyBinding at 0x7f45bcb3cf50: D>]
napari:activate_select_mode	[<KeyBinding at 0x7f45bcb3cdd0: 5>, <KeyBinding at 0x7f45bcb3ce30: S>]
napari:activate_shapes_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3ccb0: 6>, <KeyBinding at 0x7f45bcb3cd10: Z>]
napari:activate_shapes_transform_mode	[<KeyBinding at 0x7f45bcb3cb90: 7>]
napari:activate_vertex_insert_mode	[<KeyBinding at 0x7f45bcb3cbf0: 2>, <KeyBinding at 0x7f45bcb3ca70: I>]
napari:activate_vertex_remove_mode	[<KeyBinding at 0x7f45bcb3cad0: 1>, <KeyBinding at 0x7f45bcb3c950: X>]
napari:copy_selected_shapes	[<KeyBinding at 0x7f45bcb3c9b0: Ctrl+C>]
napari:paste_shape	[<KeyBinding at 0x7f45bcb3c830: Ctrl+V>]
napari:move_shapes_selection_to_front	[<KeyBinding at 0x7f45bcb3c890: F>]
napari:move_shapes_selection_to_back	[<KeyBinding at 0x7f45bcb3c710: B>]
napari:select_shapes_in_slice	[<KeyBinding at 0x7f45bcb3c770: A>, <KeyBinding at 0x7f45bcb3c620: Ctrl+A>]
napari:delete_selected_shapes	[<KeyBinding at 0x7f45bcb3c650: 3>, <KeyBinding at 0x7f45bcb3c4d0: Delete>, <KeyBinding at 0x7f45bcb3c500: Backspace>]
napari:finish_drawing_shape	[<KeyBinding at 0x7f45bcb3c3e0: Enter>, <KeyBinding at 0x7f45bcb3c290: Escape>]
napari:orient_plane_normal_along_x	[<KeyBinding at 0x7f45bcb3c2f0: X>]
napari:orient_plane_normal_along_y	[<KeyBinding at 0x7f45bcb3c170: Y>]
napari:orient_plane_normal_along_z	[<KeyBinding at 0x7f45bcb3c1d0: Z>]
napari:orient_plane_normal_along_view_direction	[<KeyBinding at 0x7f45bcb3c050: O>]
napari:auto_contrast_once	[<KeyBinding at 0x7f45bcb3c0b0: C>]
napari:activate_image_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3e0c0: 1>]
napari:activate_image_transform_mode	[<KeyBinding at 0x7f45bcb3f1a0: 2>]
napari:activate_vectors_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3ddc0: 1>]
napari:activate_vectors_transform_mode	[<KeyBinding at 0x7f45bcb3de20: 2>]
napari:activate_tracks_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3de80: 1>]
napari:activate_tracks_transform_mode	[<KeyBinding at 0x7f45bcb3e270: 2>]
napari:activate_surface_pan_zoom_mode	[<KeyBinding at 0x7f45bcb3deb0: 1>]
napari:activate_surface_transform_mode	[<KeyBinding at 0x7f45bcb40110: 2>]

Experimental Settings#

Experimental settings.

experimental

More details on the individual Experimental settings

Render Layers Asynchronously

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

Access programmatically with SETTINGS.experimental.async_.
Environmental variable: NAPARI_EXPERIMENTAL_ASYNC_
Type: <class '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: <class '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: <enum 'ColormapBackend'>
Default: fastest_available.

Enable fuzzy search in the command palette

When searching for commands via the command palette, use fuzzy finding instead of matching exact words.

Access programmatically with SETTINGS.experimental.command_palette_fuzzy_search.
Environmental variable: NAPARI_EXPERIMENTAL_COMMAND_PALETTE_FUZZY_SEARCH
Type: <enum 'PaletteFuzzySearch'>
Default: <PaletteFuzzySearch.enabled_if_available: 'Enabled if available'>.

Similarity threshold (%) for fuzzy search in the command palette

When searching commands via the command palette, if a command’s similarity to the query is lower than this threshold, it won’t be shown as a match.

Access programmatically with SETTINGS.experimental.command_palette_fuzzy_search_threshold.
Environmental variable: NAPARI_EXPERIMENTAL_COMMAND_PALETTE_FUZZY_SEARCH_THRESHOLD
Type: <class 'int'>
Default: 60.

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: <class '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: <class 'int'>
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: <class 'float'>
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: <enum '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.