Knowledge Base

Data Preparation

Track Smoothing

Track Smoothing profiles are available in the template experiment:

• No Smoothing – Smoothing filters are not activated.
• MDM 0.2 mm – With this Minimal Distance Moved filter, you can reduce the effect of 'jitter' on the Distance Moved variable. Applying this filter is recommended, however, it results in longer calculation times in the analysis.

Change these settings for your setup, if necessary.

More Options

Use the Maximum Distance Moved filter to remove outliers in the track, due to erratic detection of objects within the arena, such as when the margin of the well is sometimes detected as the fish.

For more information on smoothing data, see Smooth the Tracks in the EthoVision XT Help.

Select Data

Data profiles available in the template experiment:

• All Data – With this Data profile you analyze all tracks separately.
• Treated vs. Control – The data are split for analysis based on the two values of the user-defined variable Treatment: Treated and Control. This Data profile assumes that you have assigned a label (either Control or Treated) to each of your trials or arenas (wells).

Analyze Dark vs. Light Periods

In this example, the researcher wants to analyze the data in different light and dark periods, determined by the activation of the white light. In the Data profile, the function Trial Control State under Nesting is used to create intervals corresponding to the state of the white light.

1. Choose Analysis > Data Profile > New. Give the new Data profile a name and click OK.
2. In the Components pane, under Nesting, click the button next to Trial Control State.
3. Select the period you are interested in using the Trial Control actions. For example, From Light On To Light Off (depending on what name the Light On/Off actions have in the Trial Control Settings).
4. Insert the Nest box in the Data profile sequence.
5. If you want to analyze different periods and have the results in the same table, create more Results boxes. To add a Result box, in the Components pane click the button next to Result. In each sequence, add a Nest box that specifies a different Trial Control State.
6. Choose the dependent variables and run analysis.

Tip: See also the sample experiment DanioVision with 96 wells XT, which you can download from our website. There you can find the Data profile mentioned here.

Analyze Data Excluding Periods of Inactivity

In this example we want to exclude the interval in which a larva was not moving.

1. Choose Analysis > Data Profile > New. Give the new Data profile a name and click OK.
2. In the Components pane, under Nesting, click the button next to Movement.
3. In the Movement tab, you can set the following:
   • Averaging interval (range 1–1000) – This is the number of samples across which changes in speed are calculated to determine whether the subject is moving or not. In order to reduce the sensitivity of the Movement variable to brief changes in velocity, the velocity data can be smoothed by taking the running average of the last n samples. Enter the averaging interval n, or leave 1 if you do not want to smooth the velocity data.
   • Start velocity – The velocity above which the subject is considered to be moving.
   • Stop velocity – The velocity below which displacements of the subject's body points are no longer attributed to locomotion but to system noise, body wobble, or pivoting on the spot.
4. Under Calculate nesting for, select Not moving.
5. Click OK. Insert the Nest box in the appropriate position between the Start and the Result box.
6. Choose the dependent variables and run analysis.

For more information on the Nesting functions, see Analyze Track Segments in the EthoVision XT Help.

Analyze the Intervals Around the Onset of the White Light

In this example, we want to analyze two intervals:

• From 5 seconds before the onset of the White light stimulus, to the onset of the stimulus.
• From the onset of the White light stimulus, to 5 seconds after the onset of the stimulus.

The aim is to compare activity, speed, and other parameters between the two intervals.

1. Choose Analysis > Data Profile > New. Give the new Data profile a name and click OK.
2. In the Components pane, under Nesting, click the button next to Free interval.
3. Do the following:
   • Under Start criterion, select Trial Control. Choose the appropriate options for your light stimulus action.
   • Under Stop criterion, select Time. Next to Elapsed time, leave 0:00:00.000 after start event selected.

   Note: The term start event refers to the White light selected under Interval start.

   Click OK and insert the Nest box in the sequence.
4. To create the second interval, choose Result under Common elements. Click the middle of the Start box and drag to the Result 2 box to connect the two boxes.
5. Repeat steps 2–3 to create a new Nest box for the interval "from White light to 5 seconds after that". In the settings, choose the criteria for the second interval: from Trial Control – 0 seconds before Action: Light On to Time – Elapsed time 5 seconds after start event. Click OK and insert the Nest box in the sequence.
6. Choose the dependent variables and run analysis.

Tip: Click Settings in the Result boxes and rename them, for example to 5-s Before White Light and 5-s After White Light. Those names will be displayed as headers in your results.

Source: DanioVision DVOC-0050 Reference Manual - Data Preparation, Noldus Information Technology