Body elongation state
A discrete (state event) variable with three possible states: Stretched, Normal and Contracted, depending on where the running average elongation measure (E) of the subject's contour calculated for the current sample lays relative to two user-defined thresholds (see Calculation below).
note Body elongation state is not available if your experiment is set to:
▪Center-point detection.
▪Color marker tracking.
▪Live Mouse Tracker (but see Stretch attend posture).
▪Center-point, nose-point and tail-base detection, with two subjects per arena tracked with Deep learning.
Calculation
1.The Body elongation is calculated for each sample. See Body elongation
2.The running average of Body elongation is calculated for each sample using the number of samples specified by the Averaging interval.
3.The Body elongation state variable is determined for each sample:
▪If the running average elongation percentage is greater than the Stretched above value, the state is Stretched.
▪If the running average elongation percentage is smaller than the Contracted below value, the state is Contracted.
▪In all the other cases, the state is Normal.
Below: Visualization of Body elongation state (top) and Body elongation (bottom). The two variables have been set with the same Averaging interval (10 samples). Stretched is scored when Body elongation is above 80%. Contracted is scored when the resampled variable is below 50%.
How to specify Body elongation state
1.Click the Add button next to Body elongation state and click the Body Elongation State tab.
2.Enter the following:
▪Averaging interval: The number of samples over which the running average elongation is based. The default value is 1, that is, the elongation measure is not smoothed before calculating Body Elongation state.
▪Stretched above: The elongation measure above which the subject is considered to be Stretched.
▪Contracted below: The elongation measure below which the subject is considered to be Contracted.
To find the optimal Stretched above and Contracted below, run a few test trials and check in the Analysis Results and Scoring pane the values of Body elongation state when the animal shows such behavior. These values are calculated real-time during acquisition.
Values of elongation percentage between Stretched above and Contracted below result in the subject being scored as Normal.
3.Under Calculate statistics for, select which state you want to calculate statistic for: Stretched, Normal o Contracted. Select at least one state.
4.Complete the procedure to add the variable. See Calculate statistics: procedure.
▪The elongation measure is independent of video size and the subject's position and orientation.
▪When a body point is missing for more than three samples, the current Body elongation state ends and the remaining missing samples are ignored.
▪The Body elongation thresholds set in Acquisition are not used in analysis. When you specify the Body elongation dependent variable in your Analysis profile, enter the new values in the appropriate fields.
▪By increasing the averaging interval, you can increase the reliability of detection of stretching and contracting. A running average elongation based on more samples diminishes the effect of random changes in elongation measure between consecutive samples that would be detected as state transitions. However, a drawback of increasing the Averaging interval is that it causes a delay in the determination of a state transition, proportional to the length of the interval. See Averaging interval
▪In some cases the number of samples available for smoothing can be less than the averaging interval entered. For example, when there are missing samples or at the beginning of the track. In such cases EthoVision XT uses the samples available in the specified interval. For example, the value of Elongation for the first sample of the track is always calculated over one sample.
▪In the Detection Settings, under Subject Contour, select Erosion and then Dilation to remove the animal's tail from the detected image of the subjects. This way you get a more accurate measurement of Body elongation.
▪Body elongation is not calculated with Live Mouse Tracker data.
The Body elongation state variable can help you assess the frequency and cumulative duration of stretch attend postures in a more objective way.