Knowledge Base

Nesting Over Activity State

Aim

To pick out the data collected when the subject was in one of the states defined by the dependent variable Activity State.

Example: Select all samples when the rat was inactive (freezing), and based on this selection, make a heatmap to highlight where freezing occurred.

Procedure

1. In the Data Profile, under Nesting, click the button next to Activity state.
2. In the Activity State window:
   • Under Outlier filter, enter an Averaging interval to smooth the values of acceleration.
   • Under Number of states, enter how many different categories you want to split the data in.
   • Under Thresholds, enter the thresholds that define the various activity states.
   • Under Calculate nesting for, select the state that the intervals are based on.
   • Under State duration threshold, enter the minimal duration of the state chosen in the previous step.
   For details about how Activity state is calculated, see Dependent Variables in Detail > Activity State.
3. Click OK. Proceed with step 4 in How to Select Track Segments.

Notes

• You can only nest over Activity state if you selected Activity analysis in the Experiment Settings, and for experiments with one subject per arena.
• If you want to select track segments based on more states (e.g., Active and Highly active), create one Nest box for each state, and combine them with OR logic. This selects the time when the subject was in one of those states (e.g., either Active or Highly active). See Basic Rules for Combining Selection Boxes.
• For Activity state, it is possible to select different thresholds for nesting (see above) and for analysis (see Activity State in the Analysis Profile). You should either use the same thresholds or make the thresholds in your analysis profile more restrictive, so that the variable specified in the Analysis Profile is in effect a fine-tuning of your nesting criteria.

Nesting Over Acceleration State

Aim

To pick out the data collected when one or more subjects were in one of the states High acceleration or Low acceleration.

Example: Select the time intervals when the fish performed swim bursts (for this, use Acceleration state). Next, calculate how much time the fish was in the stimulus zone compared with the rest of the arena during those time fragments (for this, use the variable In zone).

Nesting vs. Nesting Over Subjects

Notice the difference when there are multiple subjects in the same arena:

• To select data of a subject based on the Acceleration state of that subject, choose Acceleration state under Nesting. See the procedure below.
• To select data of a subject based on the Acceleration state of other subjects, choose Acceleration state under Nesting over Subjects. There you find the Actors tab where you can specify which subjects (Actors) were in a certain Acceleration state. See Nesting Over Subjects.

Procedure

1. In the Data Profile, under Nesting, click the button next to Acceleration state.
2. In the Acceleration State window:
   • Under Outlier filter, enter an Averaging interval to smooth the values of acceleration.
   • Under Threshold, enter the threshold that defines the states High acceleration and Low acceleration.
   • Under Calculate nesting for, select the state that the intervals are based on.
   For details about how Acceleration state is calculated, see Dependent Variables in Detail > Acceleration State.
3. Click the Body Points tab (when available), and specify the body points that Acceleration is based on. Choose whether Acceleration state is based on all the chosen points being in the same state simultaneously (All selected points) or at least one being in that state (Any selected point).
4. Click OK. Proceed with step 4 in How to Select Track Segments.

See Also

• Nesting Over Subjects

Nesting Over Body Elongation State

Aim

To pick out data collected when the subject was in one of the Body elongation states: Stretched, Normal, or Contracted.

Example: Analyze the time that the subject spent in the zones Object and Rest of Arena when it was in the Stretched state. The aim is to test whether the subject spent more time stretched near the object than when in the rest of the arena.

Nesting vs. Nesting Over Subjects

Notice the difference when there are multiple subjects in the same arena:

• To select data of a subject based on the Body elongation state of that subject, choose Body elongation state under Nesting. See the procedure below.
• To select data of a subject based on the Body elongation state of other subjects, choose Body elongation state under Nesting over Subjects. There you find the Actors tab where you can specify which subjects (Actors) were in a certain Body elongation state. See Nesting Over Subjects.

Procedure

1. In the Data Profile, under Nesting, click the button next to Body elongation state.
2. In the Body Elongation State window:
   • Under Outlier filter, enter an Averaging interval to smooth the body elongation values.
   • Under Threshold, enter the thresholds that define the states Stretched, Normal, and Contracted.
   • Under Calculate nesting for, select the state that the intervals are based on.
   For details about how Body elongation state is calculated, see Dependent Variables in Detail > Body Elongation State.
3. Click OK. Proceed with step 4 in How to Select Track Segments.

See Also

• Nesting Over Subjects