Knowledge Base

Edit the Tracks

Introduction to Editing Tracks

Why Edit Data?

Correcting Tracking Errors

Sometimes EthoVision XT tracks a reflection instead of the subject, or confuses the nose-point and tail-base. If that occurs, you can correct such errors in the Track Editor screen.

Examples

• Reflections in a water maze. EthoVision XT tracks accidentally a reflection next to the maze's border. There are "spikes" in the resulting track. Make sure that light is not directed to the water surface.
• Nose-tail base swaps. In experiments set to nose-tail base tracking, the nose-point could be detected as the tail-base, and vice versa. In the last sample of the following track, the two body points are inverted. The Track Editor offers some ways to correct such swaps. Try out the Deep Learning tracking technique, which is superior at finding the subject's nose-point.

Notes

• The Edit Tracks function in EthoVision XT is only intended for minor changes of a few points. If you have many errors, there is a problem with your experimental set-up, trial control or detection settings, and you should correct those problems rather than try to manipulate the raw data. For example, if EthoVision XT tracks the arm of the operator who released the animal in the water maze, do one or both of the following:
  • In the Trial Control Settings, select to start tracking a few seconds after the subject is detected in the arena.
  • In the Detection Settings, set a maximum subject size.

Important Definitions in Track Editing

Sample vs. Body Point

A sample is the set of coordinates found at any sampling time. This means that:

• If your experiment is set to Only center-point detection, a sample is the subject's center point (one pair of X, Y coordinates).
• If your experiment is set to Center-point, nose-point and tail-base detection, a sample includes the center-point, nose-point and tail-base point (three pairs of X, Y coordinates).

Within a sample, one or more points can be missing. Missing points are shown in a different color.

Sample List

The Sample List is the list of coordinates of the subject's body points and surface area, for each sample time. It is the actual raw data used in all the subsequent analysis functions (from Track Smoothing to Results).

To access the Sample List window, choose Acquisition > Edit Tracks. If the Sample List is not shown, choose Show/Hide > Sample List.

When you select samples in the Sample List, selected samples are highlighted in green, while the sample time that corresponds to the current video image is the one shown in blue in the Time column. These two selections are independent of each other, meaning that the video image may show a sample time that is not within the range selected.

Save Edits

You can save a copy of the track that includes the last edits. If you make changes after clicking Save, you can always go back to that copy if you are not satisfied with those changes.

Customize Your Screen Before Editing

Visualize the Tracks in the Track Editor Screen

To access the Track Editor screen, choose Acquisition > Edit Tracks, or in the Experiment Explorer, under Acquisition click Track Editor.

In the track editing screen you can view the following objects:

• A. The track area, where you can view:
  • The background. This can be of uniform color, the captured image of the arenas from the Arena Settings, or the content of the video file.
  • Arenas and zones as overlay objects.
  • Tracks (samples and paths).
• B. The toolbar, which contains tools for:
  • Selecting the trials to be edited.
  • Managing track edits and reverting to the original data if needed.
  • Selecting and editing data points.
  • The Show/Hide button for choosing the elements to display.
• C. The Playback Control window.
• D. The Samples List window, listing the coordinates of the data points and the surface area of the subjects tracked.
  • The Time column shows the time elapsed since the start of the trial. If data recording started after the start of the trial or ended before the end of the trial, the Samples List shows asterisks (*) for the samples not collected before the start and after the end of data recording.
  • The current time (also shown in the Playback Control window) is marked in blue.
  • Missing points are listed with coordinates and surface area '-'.
• E. The Track Plot Settings pane, for customizing the tracks and body points.

To display the Playback Control window, the Samples List and the Track Plot Settings pane, click the Show/Hide button on the toolbar and make sure they are selected.

To visualize the track you want to edit, select the trial name from the list on the toolbar. You can visualize one trial at a time. To switch from one trial to the previous or next, click the Previous Trial button or the Next Trial button on the toolbar, respectively.

To play back tracks, use the buttons in the Playback Control window. Set the playback speed you require.

To visualize the whole tracks, clear the options under Filter in the Track Plot Settings pane and click the Jump to End button in the Playback Control window.

Colors

In the Colors tab of the Track Plot Settings pane, by default, Subject is selected under Level, that is, the track color does not change between tracks of the same subject. If you select Track, the color of tracks can change between tracks, according to the value of the variable selected under Variable for those tracks.

Improve the Readability of the Tracks Before Editing

The following options help you locate and edit the tracks more easily.

Zoom In and Out the Track Plots

Click the Zoom In button (Ctrl+.) or the Zoom Out button (Ctrl+.) on the toolbar, respectively. If the data points are out of view after zooming in, use the scrollbars to find them.

Visualize Part of the Track

In the Track Plot Settings pane, click the Show/Hide tab, and under Filter select Last and enter the time interval. This way, only the last few seconds are visualized before the current sample. The current sample is highlighted in blue in the Samples List.

Visualize One Sample Every N-th

This option is handy when you edit tracks with high sample rates or of slow-moving animals. To show one sample every n-th, click the Show/Hide tab, and under Filter select Every and enter n in the corresponding field.

• If you select 0, only the current sample point is shown.
• If you select 1, this is the same as not selecting the Last option (all samples are displayed).

Hide the Tracks You Do Not Need

When two or more subjects move in the same arena, the tracks become a dense population of points. If you edit the track of subject A, you can hide the tracks of the other subject B which you do not edit at that time. To hide tracks of subjects, in the Track Plot Settings pane click the Show/Hide tab. Under Subjects, clear the box corresponding to those subjects.

Hide Unnecessary Track Features

To hide unnecessary features like body points and connectors, in the Track Plot Settings pane click the Show/Hide tab. Under Features, clear the corresponding box for Sample or Trail.

• The nose-point and the tail-base point are not selected by default.
• What you choose under Features also determines which body points are shown in the Sample List.

Adjust the Line Thickness and Dot Size

Sometimes dots are too small and therefore scarcely visible, or too large and make the tracks difficult to edit. The tracks may be hardly visible especially when using high resolution video. In the Track Plot Settings pane click the Show/Hide tab. Under Features, adjust the following:

• Line thickness. Adjust the thickness of the trails and the segments joining the body points (Connectors).
• Dot size. Adjust the size of the body points visualized.

Customize the Missing Sample Points

Missing sample points are always visualized in the track plot. You can change the color of missing points to distinguish them more easily from the actual data. The current color for missing points is indicated next to Missing Samples Color at the bottom of the Colors tab in the Track Plot Settings pane. To change the color for missing points, click this button and select the new color in the Color window.

• Remember that within a sample, nose-point and tail-base can be missing independently. For example, the nose-point may be missing, while the corresponding tail-base may not. However, if the center-point is missing, then the other two points are too.
• If the experiment is set to Only center-point detection or Color marker tracking, the term sample coincides with the only point (center).