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 and tracks overlaid on video frames.

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 widget 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 widget 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.

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. To load tracked data in napari:

Select one of the supported formats from the source software dropdown menu.
Set the fps (frames per second) of the video the data refers to. Note this will only affect the units of the time variable shown when hovering over a keypoint. If the fps is not known, you can set it to 1, which will effectively make the time variable equal to the frame number.
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.
Click Load.

The data will be loaded into the viewer as a points layer and as a tracks layer. By default, the data is added at the top of the layer list and the points layer is selected.

You will see a view similar to the one above. Notice the three layers on the left-hand side list: the image layer, that holds the background information (i.e., the loaded video or image), the points layer and the tracks layer. You can toggle the visibility of each 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 you provided).

napari points layer 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 the keypoints of the same individual 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 layer head length

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.