Using the shapes layer#

In this document, you will learn about the napari shapes layer, including how to display and edit shapes like rectangle, ellipses, polygons, paths, and lines. You will also understand how to add a shapes layer and edit it from the GUI and from the console.

For more information about layers, refer to Layers at a glance.

When to use the shapes layer#

The shapes layer allows you to display a list of an NxD arrays, where each array corresponds to one shape, specified by N points in D coordinates. You can adjust the position, size, face color, edge color, and opacity of all the shapes independently, both programmatically and from the GUI.

Controlling the shapes layer using the GUI#

Before we start talking about all the controls on the GUI, here is an overview of how to handle the shapes layer.

Selecting, resizing, moving, editing, and deleting shapes#

All shapes are edited in the same way:

  1. Click the select shapes tool.

  2. Draw a box around the shape you want to edit.

  3. Adjust the size or contour of the shape using the square handles that appear on the bounding box of the shape. When resizing a layer, hold down the shift key to lock the aspect ratio of the shape. Then you can continue to resize the shape with a fixed aspect ratio. Note: you have to hold the shift key down and when finished release the mouse button first! Here is a shape being resized:

  4. Change the face or edge color by clicking on the thumbnail to the right of face color: or edge color: and choosing or creating a color from the pallette.

  5. Change the edge width of a shape or the width of a line or path by clicking the circle next to edge width: and dragging it to a new width.

  6. Move the shape by dragging it.

  7. Rotate the shape by clicking and dragging on the rotation handle above the shape bounding box.

  8. Select multiple shapes by continuing to shift+click additional shapes after the first, or drag a box around the shapes to select.

  9. Select all the shapes in the current slice by clicking the a key if you are in select mode. Once selected you can delete the shapes by clicking the delete button in the layer controls panel or pressing the delete key on the keyboard.

Copying and pasting shapes#

Copy and paste any selected shapes using the ctrl-c and ctrl-v keybindings respectively. If you have a multidimensional shapes layer you can copy shapes from one slice to another by pasting them into the new slice. The coordinates of the shapes in the visible dimensions will be in the same place on the new slice as in the old slice, but the rest of the coordinates will be updated with the new slice values.

Adding (inserting), editing, and deleting (removing) individual vertices#

Creating a new shapes layer#

You can create a brand-new empty shapes layer by clicking the New shapes layer button at the top of the layer list panel. The shape of the new layer is defined by the shapes inside it, as new shapes are added the new shape layer will adjust as needed. The dimension of the new shapes layer will default to the largest dimension of any layer currently in the viewer, or to 2 if no other layers are present in the viewer.

shapes layer buttons and controls#

Here are the buttons and controls that are available in the GUI for the shapes layer. This is the order they are presented in, not necessarily the order they are used. i.e. You can’t remove a vertex before you have created a shape.

  • Buttons

    • Remove vertex

    • Insert vertex

    • Delete selected shape

    • Select vertices

    • Select shapes

    • Pan/zoom

    • Transform

    • Move to back

    • Move to front

    • Add ellipses

    • Add rectangles

    • Add polygons

    • Add polygons lasso

    • Add lines

    • Add path

  • Controls

    • Opacity

    • Edge width

    • Blending

    • Face color

    • Edge color

    • Display text

  • Other tools

    • 2D/3D button or Toggle ndisplay button

    • New shapes layer button

Buttons#

  • Remove vertex image: Remove vertex

    To remove a vertex, click this button and then click the vertex you want to remove.

  • Insert vertex (Add vertex) image: Insert vertex

    Click this button and then click where you want to insert (add) a vertex.

  • Delete selected shape image: Delete shape

    Select the vertex to delete using the select vertices tool (below), then click this button, or hit the delete key on your keyboard.

  • Select vertices image: Select vertices

    Use this tool to select the vertex or vertices you want to move or delete. To select more than one vertex, select one, hold down the shift key and select the rest. Once a vertex is selected, it can be moved by dragging it to a new location.

  • Select shapes image: Select shapes

    Use this tool to select the shape or shapes you want to delete. To select more than one shape, select one, hold down the shift key and select the rest.

  • Pan/zoom image: Pan/zoom

    Use this tool to pan around the layer or zoom in. Pan functionality is disabled when using the adding and editing tools; however, zoom using the mouse-wheel will typically continue to work. To activate the tool, you can press 6. Temporarily re-enable pan and zoom by pressing and holding the spacebar. This feature can be useful if you want to move around the shapes layer as you edit it.

  • Transform image: Transform

    Use this tool to rotate, scale, or translate the layer. Note: at present this feature is limited to 2D viewer display mode. To activate the tool, you can press 7. To reset the transformation, you can Option/Alt-click the transform button (a confirmation dialog will open to confirm the reset).

  • Move to back image: Move to back

    Using the select shapes tool, select the shape to move behind other shapes and then click this button.

  • Move to front image: Move to front

    Using the select shapes tool, select the shape to move in front of other shapes and then click this button.

  • Add ellipses image: Add ellipses

    Use this tool to draw ovals or circles. Click the tool or press e (the default keybinding for this tool); next, click the point where you want the ellipse to begin. Hold down the left button on the mouse and go to the point where you want the ellipse to end. Release the mouse button. Add other ellipses as needed. A single click creates an ellipse of default size centered on that click.

  • Add rectangles image: Add rectangles

    Select Add rectangles from the layer controls panel or by pressing the r key when the shapes layer is selected. Click and drag the rectangle to the desired size. Releasing the mouse completes the rectangle. Add other rectangles as needed. A single click creates a rectangle of default size centered on that click.

  • Add polygons image: Add polygons

    The Add polygon tool can be selected from the layer controls panel or by pressing the p key when the shapes layer is selected. When adding a polygon, each click will add a vertex at the clicked location. To finish, double click or press the Esc key: this adds a final vertex at the current mouse position and completes the polygon. You can then add another polygon.

  • Add polygons lasso image: Add polygons lasso

    Polygons can also be created with the polygon lasso creation tool, which can be found in the layer control panel or by pressing shift+p. The tool can be used to draw complex Polygons with the mouse or tablet.

    More details on the lasso tool

    When using the mouse, the sequence of events to draw a polygon is as follows:

    1. Click mouse (left-click) to begin drawing.

    2. Move mouse – without holding down the mouse button – to draw the polygon.

    3. Click mouse (left-click) or press Esc to end drawing—the polygon will auto-complete.

    The polygon lasso tool can also be used to draw Polygons using a tablet. In this case, drawing the polygon is started by touching the tablet screen with the tablet stylus and drawing will continue for as long as the pencil is moved while touching the tablet screen. Note that similar behavior is also available when using a macOS trackpad, using three-finger drag mode.

    For both modes, vertices are added only if the vertex to be added is at a certain number of screen pixels away from the previous vertex. This value can be adjusted in the settings in napari by going to File -> Preferences (or control + shift + p), then in the menu on the left-clicking on Experimental and then adjusting the value of Minimum distance threshold of shapes lasso tool. The default is 10 and can be any integer higher than 0 and lower than 50. As with the polygon creation tool, drawing the shape can also be finished by pressing the Esc key.

    After finishing drawing a polygon using the polygon lasso tool, an implementation of the Ramer–Douglas–Peucker algorithm is applied to reduce the number of vertices that make up the shape, while preserving its contours. The aggressiveness with which the algorithm reduces the number of vertices of the polygon is determined by an epsilon parameter, which is a perpendicular distance threshold. Any vertices beyond the threshold will be preserved, so if epsilon is set to 0, no vertices will be removed. With increasing values of epsilon, more and more vertices will be removed. The value of epsilon can be set in napari by going to File -> Preferences (or control + shift + p), then in the menu on the left-clicking on Experimental and then adjusting the value of RDP epsilon. The default value is 0.5 and cannot be set lower than 0.

  • Add lines image: Add lines

    Select the Add lines tool from the layer controls panel or by pressing the l key when the shapes layer is selected. Lines consist of two vertices representing the end points of the line. Click where you want the line to start and then click where you want it to stop. The first click marks the coordinates of the first endpoint and the second click marks the coordinates of the second endpoint. Add other lines as needed.

  • Add path image: Add path

    Select the Add path tool from the layer controls panel or by pressing the t key when the shapes layer is selected. Click where you want the path to start and then click each location where the direction of the path changes, this adds a vertex at that location. When you have drawn the complete path, hit Esc. This adds a final vertex at the current mouse position and completes the path. You can then add another path.

Controls#

  • Opacity

    Click and hold the oval on the opacity slider bar and adjust it to any value between 0.00 (clear) and 1.00 (completely opaque).

  • Edge width

    Click and drag the circle on the edge width slider bar to adjust edge width from 0 to 40.

  • Blending

    blending has the options of opaque, translucent, translucent no depth, additive, and minimum in the dropdown. Refer to the Blending layers section of Layers at a glance for an explanation of each type of blending.

  • Face and edge colors

    To change the shape color properties from the GUI, first select the shapes whose properties you want to change, otherwise you will just be initializing the color for the next shape to add. Select the shape you want to change, click the thumbnail next to face color: or edge color: to select or create a color from the pallette.

  • Display text

    Check this box to turn display text on or off. Text can be added to the points only programmatically and not through the GUI. Refer to Add points with multicolor text for more information.

Other tools#

  • 2D/3D button or Toggle ndisplay button

    All layers can be rendered in both 2D and 3D. The Toggle ndisplay button at the bottom of the left panel toggles between these 2 modes. When in 2D, the button looks like this: image: 2D/3D button, ready to switch to 3D mode. When in 3D, the button looks like this: image: 2D/3D button, ready to switch to 2D mode.

    You can also switch modes by pressing ctrl+y.

    Note that when entering 3D rendering mode the GUI Add point, Delete selected points, and Select points tools are all disabled. Those options are supported only when viewing a layer using 2D rendering.

  • New shapes layer button

    Create a brand new empty shapes layer by clicking the New shapes layer button at the top of the layers list panel. The shape of this layer is defined by the shapes inside it, as new shapes are added the layer will adjust as needed.

Controlling the shapes layer programmatically#

A simple example#

You can create a new viewer and add a list of shapes in one go using the napari.view_shapes() method, or if you already have an existing viewer, you can add shapes to it using viewer.add_shapes. The API of both methods is the same. In these examples we’ll mainly use add_shapes to overlay shapes onto an existing image.

In this example, we will overlay shapes on the image of a photographer:

import napari
import numpy as np
from skimage import data

# create the list of polygons
triangle = np.array([[11, 13], [111, 113], [22, 246]])

person = np.array([[505, 60], [402, 71], [383, 42], [251, 95],
                   [212, 59], [131, 137], [126, 187], [191, 204],
                   [171, 248], [211, 260], [273, 243], [264, 225],
                   [430, 173], [512, 160]])

building = np.array([[310, 382], [229, 381], [209, 401], [221, 411],
                     [258, 411], [300, 412], [306, 435], [268, 434],
                     [265, 454], [298, 461], [307, 461], [307, 507],
                     [349, 510], [352, 369], [330, 366], [330, 366]])

polygons = [triangle, person, building]

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# add the polygons
shapes_layer = viewer.add_shapes(
    polygons,
    shape_type='polygon',
    edge_width=5,
    edge_color='coral',
    face_color='royalblue'
)
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Shapes overlaid on image")
Shapes overlaid on image

Arguments of view_shapes and add_shapes#

view_shapes() and add_shapes() accept the same layer-creation parameters.

help(napari.view_shapes)
Hide code cell output 
Help on function view_shapes in module napari.view_layers:

view_shapes(data=None, ndim=None, *, affine=None, blending='translucent', cache=True, edge_color='#777777', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, edge_width=1, experimental_clipping_planes=None, face_color='white', face_color_cycle=None, face_colormap='viridis', face_contrast_limits=None, feature_defaults=None, features=None, metadata=None, name=None, opacity=0.7, projection_mode='none', properties=None, property_choices=None, rotate=None, scale=None, shape_type='rectangle', shear=None, text=None, translate=None, units=None, visible=True, z_index=0, title='napari', ndisplay=2, order=(), show=True, camera: napari.components.camera.Camera = None, cursor: napari.components.cursor.Cursor = None, dims: napari.components.dims.Dims = None, grid: napari.components.grid.GridCanvas = None, layers: napari.components.layerlist.LayerList = None, help: str = '', status: Union[str, dict] = 'Ready', tooltip: napari.components.tooltip.Tooltip = None, theme: str = None, mouse_over_canvas: bool = False) -> napari.viewer.Viewer
    Create a viewer and add a shapes layer.
    
    Parameters
    ----------
    data : list or array
        List of shape data, where each element is an (N, D) array of the
        N vertices of a shape in D dimensions. Can be an 3-dimensional
        array if each shape has the same number of vertices.
    ndim : int
        Number of dimensions for shapes. When data is not None, ndim must be D.
        An empty shapes layer can be instantiated with arbitrary ndim.
    affine : n-D array or napari.utils.transforms.Affine
        (N+1, N+1) affine transformation matrix in homogeneous coordinates.
        The first (N, N) entries correspond to a linear transform and
        the final column is a length N translation vector and a 1 or a napari
        `Affine` transform object. Applied as an extra transform on top of the
        provided scale, rotate, and shear values.
    axis_labels : tuple of str, optional
        Dimension names of the layer data.
        If not provided, axis_labels will be set to (..., 'axis -2', 'axis -1').
    blending : str
        One of a list of preset blending modes that determines how RGB and
        alpha values of the layer visual get mixed. Allowed values are
        {'opaque', 'translucent', and 'additive'}.
    cache : bool
        Whether slices of out-of-core datasets should be cached upon retrieval.
        Currently, this only applies to dask arrays.
    edge_color : str, array-like
        If string can be any color name recognized by vispy or hex value if
        starting with `#`. If array-like must be 1-dimensional array with 3
        or 4 elements. If a list is supplied it must be the same length as
        the length of `data` and each element will be applied to each shape
        otherwise the same value will be used for all shapes.
    edge_color_cycle : np.ndarray, list
        Cycle of colors (provided as string name, RGB, or RGBA) to map to edge_color if a
        categorical attribute is used color the vectors.
    edge_colormap : str, napari.utils.Colormap
        Colormap to set edge_color if a continuous attribute is used to set face_color.
    edge_contrast_limits : None, (float, float)
        clims for mapping the property to a color map. These are the min and max value
        of the specified property that are mapped to 0 and 1, respectively.
        The default value is None. If set the none, the clims will be set to
        (property.min(), property.max())
    edge_width : float or list
        Thickness of lines and edges. If a list is supplied it must be the
        same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
    experimental_clipping_planes : list of dicts, list of ClippingPlane, or ClippingPlaneList
        Each dict defines a clipping plane in 3D in data coordinates.
        Valid dictionary keys are {'position', 'normal', and 'enabled'}.
        Values on the negative side of the normal are discarded if the plane is enabled.
    face_color : str, array-like
        If string can be any color name recognized by vispy or hex value if
        starting with `#`. If array-like must be 1-dimensional array with 3
        or 4 elements. If a list is supplied it must be the same length as
        the length of `data` and each element will be applied to each shape
        otherwise the same value will be used for all shapes.
    face_color_cycle : np.ndarray, list
        Cycle of colors (provided as string name, RGB, or RGBA) to map to face_color if a
        categorical attribute is used color the vectors.
    face_colormap : str, napari.utils.Colormap
        Colormap to set face_color if a continuous attribute is used to set face_color.
    face_contrast_limits : None, (float, float)
        clims for mapping the property to a color map. These are the min and max value
        of the specified property that are mapped to 0 and 1, respectively.
        The default value is None. If set the none, the clims will be set to
        (property.min(), property.max())
    feature_defaults : dict[str, Any] or Dataframe-like
        The default value of each feature in a table with one row.
    features : dict[str, array-like] or Dataframe-like
        Features table where each row corresponds to a shape and each column
        is a feature.
    metadata : dict
        Layer metadata.
    name : str
        Name of the layer.
    opacity : float
        Opacity of the layer visual, between 0.0 and 1.0.
    projection_mode : str
        How data outside the viewed dimensions but inside the thick Dims slice will
        be projected onto the viewed dimenions.
    properties : dict {str: array (N,)}, DataFrame
        Properties for each shape. Each property should be an array of length N,
        where N is the number of shapes.
    property_choices : dict {str: array (N,)}
        possible values for each property.
    rotate : float, 3-tuple of float, or n-D array.
        If a float convert into a 2D rotation matrix using that value as an
        angle. If 3-tuple convert into a 3D rotation matrix, using a yaw,
        pitch, roll convention. Otherwise assume an nD rotation. Angles are
        assumed to be in degrees. They can be converted from radians with
        np.degrees if needed.
    scale : tuple of float
        Scale factors for the layer.
    shape_type : string or list
        String of shape shape_type, must be one of "{'line', 'rectangle',
        'ellipse', 'path', 'polygon'}". If a list is supplied it must be
        the same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
    shear : 1-D array or n-D array
        Either a vector of upper triangular values, or an nD shear matrix with
        ones along the main diagonal.
    text : str, dict
        Text to be displayed with the shapes. If text is set to a key in properties,
        the value of that property will be displayed. Multiple properties can be
        composed using f-string-like syntax (e.g., '{property_1}, {float_property:.2f}).
        A dictionary can be provided with keyword arguments to set the text values
        and display properties. See TextManager.__init__() for the valid keyword arguments.
        For example usage, see /napari/examples/add_shapes_with_text.py.
    translate : tuple of float
        Translation values for the layer.
    units : tuple of str or pint.Unit, optional
        Units of the layer data in world coordinates.
        If not provided, the default units are assumed to be pixels.
    visible : bool
        Whether the layer visual is currently being displayed.
    z_index : int or list
        Specifier of z order priority. Shapes with higher z order are
        displayed ontop of others. If a list is supplied it must be the
        same length as the length of `data` and each element will be
        applied to each shape otherwise the same value will be used for all
        shapes.
        title : string, optional
        The title of the viewer window. By default 'napari'.
    ndisplay : {2, 3}, optional
        Number of displayed dimensions. By default 2.
    order : tuple of int, optional
        Order in which dimensions are displayed where the last two or last
        three dimensions correspond to row x column or plane x row x column if
        ndisplay is 2 or 3. By default None
    axis_labels : list of str, optional
        Dimension names. By default they are labeled with sequential numbers
    show : bool, optional
        Whether to show the viewer after instantiation. By default True.
    
    
    Returns
    -------
    viewer : :class:`napari.Viewer`
        The newly-created viewer.

Shapes data#

The input data to the shapes layer must be a list of NxD NumPy array, with each array containing the coordinates of the N vertices in D dimensions that make up the shape. The ordering of these dimensions is the same as the ordering of the dimensions for image layers. This list of arrays is always accessible through the layer.data property and will grow or shrink as new shapes are added or deleted. By storing data as a list of arrays it is possible for each shape to have a different number of vertices in it. This is especially useful when drawing polygons and paths.

Adding different shape types#

Right now the shapes layer supports 5 types of shapes, Lines, Rectangles, Ellipses, Polygons, and Paths. When adding new data can set the shape type through the shape_type keyword argument, as either a single shape type if all the shapes to be added have the same type or as a list of shape types if some of the shapes have different types. The actual shape types of all the shapes is accessible through the layer.shape_types property.

  • Lines consist of two vertices representing the end points of the line. The line creation tool can be selected from the layer control panel or by pressing the l key when the shapes layer is selected. When adding a new line the first click will coordinates of the first endpoint and the second click will mark the coordinates of the second endpoint. You’ll then be able to add another line.

  • Rectangles can be added using two vertices representing the corners of the rectangle for axis aligned rectangle, or using four corners so that non-axis aligned rectangle can be represented. Internally we use the four vertex representation so we can always support rotated rectangles.

  • Ellipses can be added using either two vectors, one representing the center position of the ellipse and the other representing the radii of the ellipse in all dimensions for an axis aligned ellipse, or by using the four corners of the ellipse bounding box for a non-axis aligned ellipse. Internally we use the four vertex representation so we can always support rotated ellipses.

  • Polygons can be added using an array of N vertices. Polygons are closed by default, so you don’t also need to include the first point at the end of the array. The order of the vertices will determine the triangulation of the polygon, which can be non-convex, but cannot have holes. For drawing polygons, multiple tools can be used.

  • Paths are like polygons but are not closed or filled in. They can be added using an array of N vertices.

Adding new shapes#

You can add new shapes to an existing shapes layer programmatically using the add method. This allows you to pass in a shape_type list when there is mixed shape data (data for different types of shapes).

import napari
import numpy as np
from skimage import data

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# create a triangle
triangle = np.array([[11, 13], [111, 113], [22, 246]])

# create an ellipse
ellipse = np.array([[59, 222], [110, 289], [170, 243], [119, 176]])

# put both shapes in a list
mixed_shapes = [triangle, ellipse]

# add an empty shapes layer
shapes_layer = viewer.add_shapes()

# add mixed shapes using the `add` method
shapes_layer.add(
  mixed_shapes,
  shape_type=['polygon', 'ellipse'],
  edge_width=5,
  edge_color='coral',
  face_color='royalblue'
)
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Add new shapes to an existing shapes layer")
Add new shapes to an existing shapes layer

Finally, each shape type has its own convenience method for adding new shapes to a layer. Their arguments are identical to those of the add method, but they do not take a shape_type.

import napari
import numpy as np
from skimage import data

# add the image
viewer = napari.view_image(data.camera(), name='photographer')

# create some ellipses
ellipse = np.array([[59, 222], [110, 289], [170, 243], [119, 176]])

ellipse2 = np.array([[165, 329], [165, 401], [234, 401], [234, 329]])

# put both shapes in a list
ellipses = [ellipse, ellipse2]

# add an empty shapes layer
shapes_layer = viewer.add_shapes()

# add ellipses using their convenience method
shapes_layer.add_ellipses(
  ellipses,
  edge_width=5,
  edge_color='coral',
  face_color='royalblue'
)
Hide code cell source 
from napari.utils import nbscreenshot

nbscreenshot(viewer, alt_text="Add new ellipses to an existing shapes layer using the specific method for this layer type")
Add new ellipses to an existing shapes layer using the specific method for this layer type

Non-editable mode#

To disable editing of the shapes layer, set the editable property of the layer to False.

As noted in 3D rendering, below, the shapes layer is not editable when using 3D rendering.

3D rendering#

All layers can be rendered in both 2D and 3D.

The number of dimensions sliders will be 2 or 3 less than the total number of dimensions of the layer, allowing you to browse volumetric timeseries data and other high dimensional data. See nD shapes to see shapes in both 2D and 3D:

Also note that for a multidimensional shape to be displayed on a given view slice, all of its non-displayed coordinates must match the coordinates of that view slice, i.e. the shape must be entirely defined within that plane.

For paths that are defined by coordinates spanning more than two dimensions, it is possible to visualize them as 3D cylinders, see 3D Paths for examples.

image: 3D paths

Note

Right now, it is not possible to display 3D cuboids or 3D spheroids, but we will be supporting those options soon.

Changing shape edge and face colors#

Individual shapes can each have different edge and face colors. You can initially set these colors by providing a list of colors to the edge_color or face_color keyword arguments respectively. The colors of each of the shapes are available as lists under the layer.edge_color and layer.face_color properties. These properties are different from the layer.current_edge_color and layer.current_face_color properties that will determine the color of the next shape to be added or any currently selected shapes.

Changing shape edge widths#

Individual shapes can each have different edge widths. You can initially set the edge widths by providing a list of values to the edge_width keyword arguments respectively, or you can edit them from the GUI. The widths of each of the shapes are available as a list under the layer.edge_width property. Similar to the edge and face colors, these property is different from the layer.current_edge_width property that will determine the edge width of the next shape to be added or any currently selected shapes.

Layer ordering#

You can get the ordering of all the shapes using the layer.z_indices property. You can also set the initial ordering of shapes by passing a list to the layer.z_index property.

shapes layer opacity#

The opacity value applies to all shapes. You can initialize the shape opacities using the opacity keyword argument which accepts a single opacity value that will be applied globally. You can then access the opacity using the layer.opacity property. In order to adjust the opacity of individual shapes you need to adjust the alpha value in the layer.edge_color and layer.face_color properties.

Putting it all together#

Here you can see an example of adding, selecting, and editing shapes and changing their properties:

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