Graphical User Interface#

The movement graphical user interface (GUI), powered by our custom plugin for napari, makes it easy to view and explore movement motion tracks. Currently, you can use it to visualise 2D movement datasets as points, tracks, and rectangular bounding boxes (if defined) overlaid on video frames, as well as to define regions of interest (RoIs).

Warning

The GUI is still in early stages of development but we are working on ironing out the kinks. Please get in touch if you find any bugs or have suggestions for improvements!

The napari plugin is shipped with the movement package starting from version 0.1.0. To use it, you need to install the package with a method that includes the napari dependency.

Launch the GUI#

To launch the movement GUI, type the following command in your terminal:

movement launch

This is equivalent to running napari -w movement and will open the napari window with the movement widget docked on the right-hand side, as in the screenshot below.

In napari, data is typically loaded into layers, which can be reordered and toggled for visibility in the layers list panel. For example, keypoint data can be added as a points layer or a tracks layer, while image stacks (including videos) can be added as image layers. Below, we’ll explain how to do this.

Load a background layer#

Though this is not strictly necessary, it is usually informative to view the keypoints overlaid on a background that provides some spatial context. You can either load the video corresponding to the dataset, or load a single image (e.g., a still frame derived from that video). You can do this by dragging and dropping the corresponding video or image file onto the napari window or by using the File > Open File(s) menu option.

Load a video#

Upon loading a video file into napari, you will be prompted via a pop-up dialog to select the reader. Choose the video reader—corresponding to the napari-video plugin—and click OK. You can optionally select to remember this reader for all files with the same extension.

napari video reader

napari-video will load the video as an image stack with a slider at the bottom that you can use to navigate through frames. You may also use the left and right arrow keys to navigate frame-by-frame.

napari video slider

Clicking on the play button will start the video playback at a default rate of 10 frames per second. You can adjust the playback speed by right-clicking on the play button, or by opening the napari > Preferences menu (File > Preferences on Windows) and changing the Playback frames per second setting.

Video playback limitations

  • The video playback may freeze or stutter if you jump to a specific frame while the video is playing. We recommended pausing the playback first.

  • napari-video may struggle to play videos at a high frame rate, depending on your hardware, the video resolution and codec. If you experience performance issues, such as the video freezing or skipping frames, try reducing the playback speed or fall back to using a single image as a background.

Load an image#

This usually means using a still frame extracted from the video, but in theory you could use any image that’s in the same coordinate system as the tracking data. For example, you could use a schematic diagram of the arena, as long as it has the same width and height as the video and is properly aligned with the tracking data.

Extracting a still frame from a video

You can use the command line tool ffmpeg to extract a still frame from a video.

To extract the first frame of a video:

ffmpeg -i video.mp4 -frames:v 1 first-frame.png

To extract a frame at a specific time stamp (e.g. at 2 seconds):

ffmpeg -i video.mp4 -ss 00:00:02 -frames:v 1 frame-2sec.png

Dragging and dropping the image file onto the napari window (or opening it via the File menu) will load the image as a single 2D frame without a slider.

Load the tracked dataset#

Now you are ready to load some motion tracks over your chosen background layer.

On the right-hand side of the window you should see an expanded Load tracked data menu. You can load data from one of the supported third-party formats or from a netCDF file saved with movement (expand the dropdown below for the precise requirements).

netCDF files compatible with the GUI

Only netCDF files that store a valid movement dataset can be opened in the GUI. Practically, this means:

  • The dataset’s ds_type attribute must be set to poses or bboxes.

  • The data variables, dimensions, and coordinates must satisfy the dataset structure requirements for that ds_type. For example, a poses dataset must provide both position and confidence.

Below is a small example showing how to save a GUI-compatible netCDF file with movement:

from movement.io import load_dataset
from movement.filtering import rolling_filter

ds_orig = load_dataset(
    "path/to/my_data.h5", source_software="DeepLabCut", fps=30
)

# Create a copy to avoid modifying the original dataset
ds_new = ds_orig.copy()

# Apply some processing to the position data variable.
# e.g. a rolling median filter
ds_new["position"] = rolling_filter(
  ds_orig["position"], window=5, statistic="median"
)

# Save the processed dataset to a netCDF file
ds_new.to_netcdf("my_data_processed.nc")

Because ds_new is copied from the original dataset, it retains all required attributes and structure. Note that the data variable remains named position after processing, as expected.

To load tracked data in napari:

  1. From the source software dropdown menu select the name of the tracking software you used to generate the data (e.g. “DeepLabCut”), or choose “movement (netCDF)”.

  2. Set the fps (frames per second) of the video the data refers to. This only changes the time units shown when you hover over a keypoint. An unknown fps can be set to 1, which makes the displayed time equal to the frame index. The fps option is disabled when loading a netCDF file because the fps is directly read from the file’s attributes.

  3. Select the file containing the tracked data. You can paste the path to the file directly in the text box, or you can use the file browser button.

  4. Click Load.

The data will be loaded into the viewer as a points layer and as a tracks layer. If the input file is a bounding boxes dataset, an additional napari shapes layer is loaded. By default, the data is added at the top of the layer list and the points layer is selected.

For a poses dataset, you will see a view similar to this:

napari with poses dataset loaded

And for a bounding boxes dataset, you will see a view more like the one below:

napari with bboxes dataset loaded

Note the additional bounding boxes layer that is loaded for bounding boxes datasets. For both poses and bounding boxes datasets, you can toggle the visibility of any of these layers by clicking on the eye icon.

The points layer#

The points layer shows the data for the current frame.

The keypoints are represented as points, colour-coded by keypoint for single-individual datasets, or by individual for multi-individual datasets. In datasets with one keypoint per individual, or no keypoint dimension, the points are always colour-coded by individual.

With the points layer selected, if we enable the display_text option in the layer controls panel, the keypoint name will be displayed on the lower right corner of each point. If the dataset has no keypoint dimension, the individual name is shown instead.

Hovering with your mouse over a point (with the points layer selected) will bring up a tooltip containing the properties of that point: the individual and keypoint it represents, the point-wise confidence score (provided by the source software), and the time in seconds (calculated based on the frame number and the fps value).

napari points tooltip

Using the frame slider at the bottom of the window, you can move through the frames of the dataset, and the points and video (if loaded) will update in sync.

Changing markers size, colour and shape

You can change the size, the colour and the shape of any selected markers using the points layer controls panel.

You can use the following keyboard shortcuts to toggle the markers selection:

  • To select all the markers in the current frame, press A.

  • To select all the markers in all the loaded frames, press Shift + A.

  • To unselect the currently selected markers, press the relevant keyboard shortcut again.

You can find all the keyboard shortcuts in the top menu of the napari window, under Preferences > Shortcuts.

The tracks layer#

The tracks layer allows us to visualise data before and after the current frame. Remember that the current frame is determined by the position of the frame slider.

The trajectory made up of all positions of a keypoint on all frames before the current frame is called tail. Similarly, its trajectory on all frames after the current frame is called head.

Both tail and head tracks are represented as lines connecting a single keypoint across frames. The colour of the tracks follows the colour of the markers, and the length of the tracks can be adjusted in the tracks layer controls panel, with the tail length and head length sliders.

When the tail length slider is at its maximum position, the tail track show the trajectory of the keypoints from the start of the video until the current frame. When the head length slider is at its maximum position, the head track shows the trajectory of the keypoints from the current frame until the end of the video.

For example, in the screenshot below, we can see from the tracks layer control panel that the selected layer shows the trajectories of the keypoints from the current frame until the end of the video.

napari tracks sliders

You can also use the tracks layer controls panel to change the colormap of a selected tracks layer.

Some caveats regarding the tracks layer

  • Currently there is no support in napari for fine control over the length of the tail and head tracks. However, we are working on a workaround, stay tuned!

  • You may occasionally see a warning message in the GUI upon loading a datafile, that says:

    UserWarning: Previous color_by key 'keypoint_factorized'
not present in features. Falling back to track_id!

    This is a known issue and can be safely ignored. It does not currently affect the functionality of the GUI.

  • Also note that currently the show ID checkbox in the tracks layer controls panel refers to an internal napari track ID, rather than the individual or the keypoint ID. This is a known issue and we are working on a fix or workaround.

The boxes layer#

The boxes layer is loaded for bounding boxes datasets only. It shows the bounding boxes for the current frame, as rectangles color-coded by individual.

The name of the individual is shown in the lower left of the bounding box by default. This can be toggled by selecting the shapes layer in the layer list and clicking the display text checkbox in the layer controls panel.

As with tracks and points, you can use the frame slider at the bottom of the viewer to move through the frames of the dataset. This will update the bounding boxes and the rest of the loaded data in sync.

Changing bounding box size, colour and shape

You can change edge and face colour as well as the positions of a bounding box’s corner vertices using the shapes layer controls panel.

You can use the following keyboard shortcuts to toggle the bounding boxes selection:

  • To select all the bounding boxes in the current frame, enable the select shapes tool (5 or S) and press A.

  • To deselect, click off of the bounding boxes.

  • Individual vertices can be selected instead of the entire rectangle using the select vertex tool: 4 or D.

You can find all the keyboard shortcuts in the top menu of the napari window, under Preferences > Shortcuts.

Define regions of interest#

The Define regions of interest menu allows you to draw shapes on the viewer and use them as regions of interest (RoIs) for analysis.

Each shape you draw represents a static region that remains fixed across all frames.

Terminology

Shape

Any geometric object you draw on the napari canvas (e.g. a polygon or a line). Shapes are grouped together in napari shapes layers.

Region

A named napari shape that movement recognises as a region of interest (RoI) for analysis.

Region layer

A napari shapes layers managed by movement, whose shapes are treated as regions.

Create a region layer#

To define a region for your data, start by creating a region layer, which will serve as a container. To do this:

  1. Ensure a background layer is loaded so that you can see where you are drawing.

  2. Expand the Define regions of interest menu on the right-hand side of the napari window.

  3. Click the Add new layer button.

This will create a new region layer in the layer list and select it. The layer also appears in the dropdown next to the Add new layer button. The layer’s default name is regions, but you can change it by double-clicking on it in the layer list (this is the case for any napari layer).

napari new region layer

Draw and edit regions#

With the region layer selected, you can use the native napari shape tools in the layer controls panel to draw shapes on the canvas. Convenient keyboard shortcuts are available to select the shape drawing tools, for example:

  • R: rectangle tool

  • E: ellipse tool

  • P: polygon tool

  • L: line tool

Tools are also provided for selecting, moving, transforming, and deleting shapes, as well as for editing their vertices. You can also copy-paste shapes within a layer. See the napari shapes layer guide for details on the drawing tools and how to use them.

Each shape you draw is automatically added to the widget’s table of regions on the right-hand side and auto-assigned a unique name (e.g. region, region_1, region_2, etc.).

napari drawing regions

You can interact with the table in the following ways:

  • Select: clicking a row in the table selects the corresponding shape on the canvas, and vice versa. This makes it easy to identify which shape corresponds to which table entry.

  • Rename: double-click the name cell of a region to edit its name. Press Enter to confirm the change or Escape to cancel.

  • Delete: select a shape on the canvas and press Delete (or Backspace) to remove it. The corresponding row will be removed from the table.

Changing shape appearance

You can change the edge colour, face colour, edge width, and opacity of shapes by selecting a shape (or multiple shapes) and using the napari layer controls panel. Once a shape’s appearance has been adjusted, all subsequent shapes drawn in the same layer will inherit those properties by default.

To display region names on the canvas, tick the display text checkbox in the layer controls panel. The text colour follows the shape’s edge colour.

Save and load regions#

Save and load functionality for region layers is coming soon. You will be able to save a region layer to a GeoJSON file, and load it back later or share it with others. This will also allow you to import drawn regions into your Python code using the load_rois() function.

Stay tuned!

Working with multiple region layers#

You can use region layers to group related regions together. For example, you might use one layer for “nesting zones” and another for “foraging zones”.

To add another region layer, click the Add new layer button again. You can switch between region layers using the layers dropdown, or by selecting the layer directly in the napari layer list—both are kept in sync. The regions table updates to show only the shapes belonging to the selected layer.