To create a new experiment

By Willie Cole,2014-01-20 04:27
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To create a new experiment

    ETHOVISION : Fear Conditioning

    To create a new experiment:

? Go to File ? New workspace and then name the file and it will open a new


    ? Next you need to create a specific experiment (i.e. CoFC profile). Go to File ?

    New ? Experiment and name the new experiment (i.e. CoFC)

    ? Finally follow directions below for setting up new tracking profile.

    To set up a new tracking profile:

? Go to Experiment ? Design

    o Go to Variables ? Add user-defined variable

    o Also Feel Free to Add a Description of your Experiment, Controls,

    Experimental Groups

    ? Add variables that you need to identify trials (e.g., Subject ID,

    Genotype, Drug Tx).


    ETHOVISION : Fear Conditioning

    o Go Variables ? Show system variables

    ? Select “status” and any other variables of interest; (ie, movie file,

    average mobility number)

    ? Go to Experiment ? Arena Definition


    ETHOVISION : Fear Conditioning

o Video Source: Picolo, Composite (BNC), NTSC, Medium Resolution

    o Go to Arena ? Add Arena

    o Use the tool icons (e.g. Free Form Tool) to draw your arena (Click around

    each of the Arenas along the plastic walls and the shock grid bars, to form

    an arena around each phenotyper.)

    ? Make sure the label “Arena 1” in pointing in the 1

    st Phenotyper

    you have drawn.

    ? Continue Making a New Arena For Each Phenotyper

    o Now you need to calibrate your arena.

    ? Go to Arena ? Calibrate Arena

    ? For Each Arena, you must calibrate the distance between the

    plastic walls and the opposing grid bars. The distance from Bar to

    Bar should be Calibrated to “27 cm,” while the distance from

    Plastic to Plastic should be “28 cm.”

    ? Rotate between the arenas by selecting them in the Top Right side

    of the Toolbar.


ETHOVISION : Fear Conditioning

? Go to Experiment ? Acquire Data


    ETHOVISION : Fear Conditioning

    o Go to Tracking ? Trial Protocol

    ? Enter the duration (5 min is standard for COFC) & Enter the

    sample rate (standard is 6 samp/sec) and then click OK.

    ? Also Check manually edit Threshold, and Update Noise Threshold

    before each Trial.

    Figure 1: REPLACE

    o Go to Tracking ? Processing ? Detection Method

    ? Select “Grayscale” for Method ? Select “Object is always darker than the background” for Object


    ? Noise removal: select Minimum object size 150 pixels. Max =

    1500 pxls. These may need to be adjusted depending on the size of

    your mice, or the size of the video you are processing.

    ? Select tab at top of Processing Settings window titled “ Image


    ? Select erosion & dilation at 1 pixel.

    ? Select first erode, then dilate and then click OK.


    ETHOVISION : Fear Conditioning

    ? Also, Under “Image Enhancement,” adjust the Contrast and

    Brightness until there is very little background noise around the

    arenas, represented by highlighted Green Noise.

o Go to Tracking ? Experiment Control: Here we set the parameters of the

    Fear Conditioning. Most often or not you will set some sort of US, usually

    a Foot Shock to occur at certain time points during the Trial. Sometimes

    you will also set a CS, in the form of a Tone or Light.

    o To Set the Action Controls Click ? Actions:

    ? Assign the following Actions. The pin numbers for the actions are

    shown below, change the durations as desired.


    ETHOVISION : Fear Conditioning

    ? Click “Add Elapsed Time condition.” This will tell Ethovision

    when to deliver either the Foot Shock or the Light Tone.

    ? Continue to Add Time Lapsed Conditions until you have the

    experiment protocol.

    o Go to Tracking ? Update detection variables

    ? Adjust threshold until only the animal is tracking in Red and only

    background noise is Green.

    o Go to Tracking ? Mobility

    ? Set the Immobility Threshold to “5%”

    ? Set the Strong Mobile Threshold to “95%”

    ? Set the Mobility Average number to “20”

    ? Start Trial:

    o You can start a trial either by going to Tracking ? Start Trial or by

    pressing F5 or clicking the black arrow in the toolbar.

    o Note: you should always have media cruise open so that you can also

    record a video for each trial.

    To Analyze Data after you have run your experiment:

    ? Go to Experiment ? Analyze Data

    o Go to Data ? Select Tracks

    ? You can select tracks by tracking profile or by date by selecting

    them and moving them over to the “selected” box. Hold down the

    Ctrl button to select multiple items.


    ETHOVISION : Fear Conditioning

o Go to Analysis ? Add parameters

    ? Select variables of interest (e.g. Mobility, Time in zone, velocity)

o Go to Analysis ? Calculate


    ETHOVISION : Fear Conditioning

    ? Click on dataset and Ctrl + C to copy & Ctrl + V to paste into


    o Other helpful options are grouping data (by day or subject etc.) by going

    to Data ? Group tracks and select option that best suits your research


    o You can also adjust the layout of your data by right clicking on the data

    and selecting Layout.


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