Knowledge Base

Data Analysis in EthoVision XT

Once you acquire your trials, you want to pair the behavioral tracking with the calcium imaging/optogenetic stimulation events. To view and analyze those events, you must first define them in the Analysis profile. Here we report a few examples.

Choose Analysis > Analysis Profile > New.

Define a Simple Event

With the variable Hardware command you can visualize the time that the USB-IO box sends a trigger command to nVista/nVoke.

1. In the Dependent Variables pane, under Hardware, choose Hardware command.
2. Choose the device and the output state, for example Output 1 High. Note that Output represents one of the two communication lines present in each TTL port of the USB-IO box. Choose the line that you used in the Action box in the Trial Control Settings to trigger the device.
3. Visualize the event (Analysis > Results > Integrated Visualization).

Analyze Intervals (Global)

You can analyze the behavior of the subject within an interval based on events. For example, calculate the average velocity of the subject from the time that stimulation starts (i.e., when the TTL Output 1 is High) to the time that stimulation ends (i.e., nVoke is triggered with Output 1 Low). To analyze the behavior within intervals, you must use the Nesting function in the Data profile.

1. Choose Analysis > Data Profile > New.
2. In the Components pane, under Nesting, choose Hardware state.
3. Select the device and the status of the device. For example, Device A - Is Output 1 High - true. This selects the time that the TTL Output 1 signal remains high.
4. Insert the box in the flow line.
5. Visualize the interval (Analysis > Results > Integrated Visualization).

Note: If Output 1 stays high multiple times during one trial, EthoVision XT considers the cumulative time that Output 1 stays High, and that is used as the analysis interval. When you want to analyze the time defined by a specific triggering event, see below for a different solution.

Analyze Specific Intervals

You can use Free Intervals to specify a single interval based on one of the occurrences of a triggering event. Suppose that nVoke is triggered in ten intervals, and you want to analyze the second interval.

1. Choose Analysis > Data Profile > New.
2. In the Components pane, under Nesting, choose Free interval.
3. For both Start criterion and Stop criterion, select Hardware. Define the start and stop event. For example, Start criterion: Output 1 High; Stop criterion: Output 1 Low.
4. Select Calculate Result for interval and choose the occurrence. In this example, 2.
5. Insert the box in the flow line.
6. Visualize the interval (Analysis > Results > Integrated Visualization).
7. In the Analysis profile, define the variable that you want to calculate within the interval (e.g. velocity).

Note: You can also use the commands of Trial Control to define intervals. For example, define an interval that starts when the tone cue is given (i.e. when the Action Tone cue becomes active). You can also use Conditions (e.g. the interval starts when the Condition Wait 30 seconds becomes active). If an Action follows immediately a Condition, then the time that the condition becomes true is essentially the same as the time that the following action becomes active, because both boxes are processed in the same sample time. In that case it does not matter which box you use for defining the interval.

Export the Raw Data

You can export the raw data (behavior and hardware events) with their time stamps, for example to sync EthoVision XT data with calcium imaging in a third-party application.

• Choose Analysis > Export > Raw data.
• Note that Raw data also includes the Trial Control events and states (e.g. a condition being true) once you include them in the Analysis profile.
• Select the Hardware log option if you want to export hardware events.

Align EthoVision XT and Inscopix Data

Computer Clocks

Ensure that the two computers used for data acquisition (EthoVision XT and Inscopix IDAS) have their clocks synchronized, for example using Network Time Protocol. Point all PCs at a time server or point one and set it up to act as a time server to the other.

Unix Time

Inscopix software often exports time stamps to Unix (Epoch) time. Unix time is also known as Epoch Time or Unix timestamp. It is a system that counts the number of seconds that have elapsed since the Unix Epoch, i.e. January 1st, 1970. In simple terms, Unix time is the total number of seconds that have elapsed since 00:00:00 UTC Thursday, 1 January 1970.

Convert EthoVision XT Time to Unix Time

You can use an Excel formula to convert the trial time in EthoVision XT to Unix time. In general, the formula is:

Because the trial (or recording) time in EthoVision XT is relative time (e.g. 0.200), you need to convert it to absolute time using the Reference time cell in the raw data. Then use a second formula that adds the trial (or recording) time to the reference time.

Source: EthoVision XT 18 - Application Manual, Noldus Information Technology