Knowledge Base

Auto-Start Data Analysis

The Auto-start data analysis option in the Acquisition Settings window allows you to automatically start batch calculations immediately after data acquisition has ended, without the need to give any additional command.

Example: You have a large set of video files, and you plan to start the batch data acquisition before leaving the lab in the evening. By selecting Auto-start data analysis, you make sure that analysis starts immediately after the end of the last trial, so that the results are ready the next morning.

To Enable Auto-Start Data Analysis

1. Define your series of trials in the Trial List.
2. In the Acquisition module, before starting acquisition, in the Acquisition Settings window, under Options, select Auto-start data analysis.
3. Select one of the two options:
   • Active profiles only. To calculate the statistics using only the combination of the Track smoothing profile, Data profile and Analysis profile currently active (highlighted in blue in the Experiment Explorer).
   • All profile combinations. To calculate the statistics using all combinations of the Track smoothing profiles, Data profiles and Analysis profiles in your experiment.
4. Carry out data acquisition as usual.

Notes

• If you choose the second option, to minimize processing time and disk space occupied by results, make sure that the Track smoothing, Data and Analysis profiles in your experiment are those you want to use for analysis. Remove any duplicate or non-interesting profiles.
• If you want to analyze data using certain profile combinations, not others, do not select Auto-start data analysis. Instead, do batch analysis after acquisition; there you can choose those profile combinations.
• The analysis does not start automatically when you stop tracking manually.
• If you move to another window and then return to the Data acquisition screen, you have to set the Auto-start data analysis option again.
• The Auto-start data analysis option is not available when you select Save video only, track later as acquisition method.
• Once analysis is started, a window with a progress bar opens. You can see that there are a few stages:
  • Step 1 - Data Preparation (for when tracking two subjects with Deep learning). For details see Prepare the data in multi-subject trials.
  • Step 2 - Track Smoothing, for adjusting the tracks based on a Track smoothing profile.
  • Step 3 - Data Selection, for choosing tracks, and track segments based on a Data profile.
  • Step 4 - Analysis, for calculating the values of the dependent variables specified in an Analysis profile.

Score Behaviors Manually

What do you want to do?

• Score behaviors manually during acquisition
• Score behaviors manually after acquisition
• Edit the duration of manually-scored behaviors
• Replace a behavior with another one
• Score behaviors in different arenas
• Score behaviors of two or more subjects
• Delete a manually-scored behavior

Score Behaviors Manually During Acquisition

Aim

To record behaviors manually, while EthoVision XT tracks the subjects.

Note: You can also score behaviors manually after acquisition.

Prerequisites

• You have defined behaviors in the Manual Scoring Settings.
• In the Acquisition screen locate the Analysis Results and Scoring pane, and click the Manual scoring tab. If you do not see the Analysis Results and Scoring pane, click the Show/Hide button and select Analysis Results and Scoring.
• If you track from video files, in the Playback Control window, deselect DDS. This ensures that the video file is played at the normal speed.

Behavior Buttons and Key Codes

Each behavior has its corresponding buttons (with key code, if defined) for each arena and subject. Mutually-exclusive behaviors are shown under their group name.

For multiple animals per arena, you can use the fill color as a reference to identify animals.

If at least one trial is set to Planned in your Trial List, the buttons for behaviors defined as Initially active in the Manual Scoring Settings are highlighted in green, indicating that when you start the trial this is recorded automatically as initial behavior.

Procedure

1. Start the trial.
2. To score a behavior for a specific subject, arena and behavior, press the key for that combination, or click the button for that combination. The button of the scored behavior is highlighted in green and the behavior's start has been scored. For mutually-exclusive behaviors, the button of the previous behavior is reset.
3. When the subject no longer shows that behavior, do the following:
   • For Mutually-exclusive states, score the behavior that is active next.
   • For Start-Stop states, press the stop key or click the button for that behavior.
   The button of the behavior is reset. For mutually-exclusive behaviors, the button of the new behavior is highlighted in green.

Notes

• Data can only be recorded after tracking has started. If you start the trial and tracking starts some time later as a result of Trial control conditions setting some delay, any scoring action between the start of the trial and the tracking is not recorded.
• You cannot pause recording behaviors even when you track from a video file. However, after acquisition you can score behaviors manually after acquisition.
• If you want to change the initial state of a subject for the next trials, do so in the Manual Scoring Settings. Initial behavior for trials already acquired remains as it is.
• To modify the coding scheme, stop the trial and click Manual Scoring Settings in the Experiment Explorer.
• To improve clarity in the video image during the observation, choose which body points to show, and adjust their size. See The video window > Show/hide body points and other track features.
• If you want to show the arena and zones during the scoring sessions, click the Show/Hide button at the top-left corner, and choose Arena features.