Knowledge Base

3 - Set up an Experiment 3.1 Start CatWalk XT ................................................................................. Turning on the CatWalk system and starting CatWalk XT. 3.2 Set up the walkway ............................................................................. Define the layout of the walkway and calibrating the walkway. 3.4 Specify the experiment settings ......................................................... Define your treatment groups and run criteria. 3.5 Define the Trial List.............................................................................. In the Trial List you can enter variables for the trials you plan to acquire. 3.6 Experiment setup profiles................................................................... Save the current experiment settings, time points, treatment groups and Trial List to a profile that you can apply to future experiments. Select the Distance Units and number of decimals to be displayed. In the Preferences you can also set the program Folders, the Auto Save interval and the colors in which paws and other prints are displayed. 3 - Set up an Experiment

3.1 Start CatWalk XT

Turn On The Catwalk System

Prerequisites

If you upgrade from CatWalk XT 8/9, you need the CatWalk Control Unit. Contact your nearest Noldus representative for information. If you upgrade from CatWalk XT 10.0, you need to upgrade the firmware of the Control Unit. Contact the Noldus Help desk (see page 14). See the CatWalk XT Assembly Instructions on the installation disc to install the CatWalk system and the Control Unit.

Procedure

1. Check that the on-off switch of the walkway (located on the left side) is turned On. The Control Unit must be connected to the camera, walkway and illuminated ceiling (if this not the case, see the Assembly Instructions for details). The Control Unit must also be connected to the CatWalk XT computer via a USB cable if you want to acquire data.

Make sure the Control Unit is not connected to the mains socket yet!

2. Now connect the Control Unit to the mains socket, and on the Control Unit, turn the switch on. The red lights busy/alive and power on the Control Unit turn on, and the busy alive lights starts flashing. When the Control Unit is finished configuring the LED lights, both red lights turn off. The green and red LED lights of the CatWalk system flash until the correct intensity levels are reached.
3. Make sure you turn on the CatWalk system at least 15 minutes before you start using CatWalk. 3 - Set up an Experiment
4. To turn off the CatWalk system, turn the switch off on the Control Unit.

Start Catwalk Xt

After turning on the CatWalk system, it can take a couple of minutes for the camera to be detected. This is indicated by the Acquiring network icon in the Windows task bar. Note that the yellow triangle does not mean that something went wrong. It means that the PC has not found a network. However, the camera has been detected. Do not start CatWalk XT before this icon appears. To start CatWalk XT, double-click the CatWalk XT icon on the desktop. After starting CatWalk XT, you may get a message that the firmware of the Control Unit needs to be upgraded. Contact the Noldus Help desk (page 14).

3.2 Set Up The Walkway

Setting up the walkway involves: Defining the layout of the walkway - In this step you outline the area of the walkway that you want to record, that is the area inside the corridor. Calibrating the walkway - This is done so CatWalk can convert pixels to real-life dimensions. 3 - Set up an Experiment

Define The Layout Of The Walkway

1. Do one of the following: In the Application Startup Tasks window, select Setup the walkway and then click Define the layout of the walkway. Choose Setup > Define Walkway.

Click the Define Walkway icon in the tool bar

In the Define Walkway window, you see the full camera image. If you do not see an image, open the camera's aperture. Make sure the camera is in focus. If you do not see a camera image, close the Application Startup Tasks window and choose Setup > Camera. In the Camera Selection window, click the Refresh button, select the Gevicam camera in the Camera field and click OK. 2. Adjust the camera's vertical position to the match the type of animal you are using. You should get 5-6 step cycles per run. This corresponds to about 45 cm on the walkway for mice and 70 cm for rats. 3. Position the mouse pointer over the rectangle so it becomes a four-headed arrow; drag the rectangle to the top-left corner of the area of the walkway you want to outline (see the arrow on the left in the figure below). 4. Next, position the mouse pointer at the bottom-right corner of the rectangle so the pointer becomes a resize pointer. Drag the bottom-right corner of the rectangle to the bottom-right corner of the area of interest on the walkway (see the arrow on the right in the figure below). Make sure that all sides of the rectangle are visible within the camera view. 5. Click OK. Figure 3.1 The walkway and the corridor in the CatWalk system. 3 - Set up an Experiment

Calibrate The Walkway

1. Do one of the following: In the Application Startup Tasks window, click Setup the walkway and then Calibrate the walkway. Choose Setup > Calibrate Walkway. Click the Calibrate Walkway icon in the tool bar.
2. Put the Calibration sheet in the middle of the glass plate. If necessary, put the camera in focus using the text on the Calibration sheet. The Calibration sheet is enclosed in the CatWalk box with the assembly instructions. If you do not find it, on the CatWalk XT installation disc open the Documentation folder and print the Calibration sheet PDF file that matches your page size settings.
3. Move and resize the white rectangle to match the 20 x 10 cm rectangle on the calibration sheet. If you use another shape with known dimensions to calibrate the walkway, type in the

Width and Height at the bottom of the Calibrate Walkway window and select the

appropriate Unit. 4. Click OK. For an experiment, with a specific setup of your CatWalk system, you only need to set up the walkway once, unless something changes to the hardware setup of the system (for example, the camera was moved or the width of the corridor was changed). When you close an experiment, the layout of the walkway and the calibration are stored within the application. Next time you open CatWalk, the Application Startup Tasks window shows the last date/ time the walkway was defined and calibrated.

3.3 Create A New Experiment

1. To create a new experiment, do one of the following: In the Application Startup Tasks window, click Create a new experiment. Choose File > New Experiment or press Ctrl+N.

Click the New Experiment icon in the tool bar

2. In the New Experiment window, enter the Name of the experiment. The name cannot contain any of the following characters: /:*?\"<>|'&.; .
3. Select a Setup profile from the list. See Experiment setup profiles on page 43 for more information. 3 - Set up an Experiment
4. Optionally, browse to the location where you want to save your experiment. important Do not save your experiment to a USB stick because this might result in a corrupt experiment.
5. Optionally, add a Description and edit the name in the Created by field.
6. Click the Create experiment button.

3.4 Specify The Experiment Settings

Experiment Settings Screen

In the Experiment Settings screen, you define the animal type, time points, treatment groups and the run criteria. These variables and values stay constant throughout the experiment, but potentially affect the outcome of the experiment.

Open the Experiment Settings screen

Do one of the following:

Choose Setup > Experiment Settings

In the Experiment Tasks window, click Experiment Settings.

Click the Experiment Settings icon in the tool bar

In the Experiment Explorer, under Setup, double-click Experiment Settings.

Animal Type

As Animal Type you can select Rat or Mouse. The Automatic Footprint Classification (AFC) module uses a different algorithm depending on whether you select Rat or Mouse. Furthermore, the Sciatic Functional Index, which is only available if you have the Interactive Footprint Measurements (IFM) module, is calculated differently for rats and mice. When you do not have the AFC or IFM module, it does not matter which Animal Type you choose. However, when you later want to use the AFC and/or IFM module in the same experiment, you should then select the correct Animal Type. For the IFM module, make sure in the Detection Settings that the animals' toes are detected properly! 3 - Set up an Experiment

Time Points

Under Time Points, define the time points at which you carry out data acquisition. Use time points to distinguish between trials of the same animal.

Add time points

1. Click the Add Time Point button once to add one time point, or more than once to add multiple time points.
2. Click the name to type in the name for a time point.
3. Optional: Add a Description for a time point. Click the cell under Fill Style and change the color in which the time point is displayed in the Group statistics and charts screen.
4. Repeat the previous steps to add additional time points.

Delete Time Points

1. Click on a time point name. To select multiple items, click them while holding the Ctrl key.
2. Click the Delete Time Point(s) button and click Yes.

Treatment Groups

Under Treatment Groups, predefine your groups.

Add treatment groups

1. Click the Add Group button.
2. In the new row of the table, from the list in the Type column select one of the predefined types (Undefined, Experimental, Control and Sham).
3. In the Name column, type the name of the Treatment Group. Change the Name of a group to reflect the type of treatment group, because the Name of the treatment group is used in the analysis (see Figure 3.2). 3 - Set up an Experiment
4. Optional: Add a Description for that group. This description is also exported to an export file with the statistics and can be used as an independent variable. Click the cell under Fill Style and change the color in which the treatment group is displayed in the Group statistics and charts screen.

Delete groups

1. Click in the row of the groups you want to remove. You can select multiple groups by clicking rows while holding the Ctrl key.
2. Click the Delete Group(s) button and click Yes.

Copy and paste values from one cell to another

1. Select the contents of the cell.
2. Right-click the cell and select Copy.
3. Select the cell in which you want to paste.
4. Right-click this cell and select Paste or press Ctrl+V.

Run Criteria

Define run criteria to automatically check the quality of your runs in terms of mean running speed and variation in running speed. This automatic check is useful because it enables you to compare runs within and between animals. In order to achieve this, animals should be Figure 3.2 The Treatment Groups table in the Experiment Settings screen. In this example, two groups have been defined. 3 - Set up an Experiment trained to cross the glass plate before they are eventually tested (see Train the animals on page 47).

Under Run Criteria you can set the following criteria:

Minimum run duration - When the animal is slower than this Minimum run duration, the run is marked 'non-compliant'. Maximum run duration - When the animal exceeds the Maximum run duration, the run is marked 'non-compliant'. This does not stop data acquisition of this and the next runs. If you want to automatically abort data acquisition after a specific time, do this in the Acquisition Settings (page 53). Minimum number of compliant runs to acquire - Data Acquisition continues until this number of runs that meet the other three criteria (Minimum and Maximum run duration and Maximum allowed speed variation) has been acquired. The maximum number of runs (compliant + non-compliant) to acquire per trial is '100'. Use maximum allowed speed variation - With this criterion you can check whether the animal walked very slowly during part of the run, and then extremely fast during another part. When this happens, the run can still meet the Minimum and Maximum run duration criteria, but the variation in speed would be too high. The speed variation is calculated as follows: the run is divided into 5 intervals with equal duration. For each interval, the average speed is calculated and this speed is expressed as the percentage difference, from the average speed of the total run. For example, an animal starts very slowly and its speed in the first interval is 5 cm/s. After that, it speeds up, resulting in an average speed of the total run of 20 cm/s. The speed variation is: ([absolute difference (5-20)] / 20) * 100 = 75% (expressed as a whole number). By default, Use maximum allowed speed variation is not selected. The run criteria become read-only when you have acquired a run.

What next?

Click >> Trial List in the bottom-right corner.

Figure 3.3 The Run Criteria in

the Experiment Settings screen. 3 - Set up an Experiment

3.5 Define The Trial List

The Trial List

In the Trial List you can enter a number of variables for the trials you plan to acquire.

Open the trial list

Do one of the following: Choose Setup > Trial List.

Click the Trial List icon

In the Experiment Tasks window, select Open Trial List. In the Experiment Explorer, under Setup, double-click Trial List.

Add trials

1. Click the Add Trial(s) button.
2. In the Add Trial(s) window, enter the Number of Trials you want to add for each time point and treatment group you defined in the Experiment Settings and click Add. We advice you not to add more than 500 trials per experiment. Repeat this step for each time point * treatment group combination.
3. If necessary, re-assign a treatment group to a trial/animal by selecting a treatment group from the list.
4. You can now define the following User Variables: Animal - Click a cell in the Animal ID column to change the animal ID. Time Point - Select a time point from the predefined list in the Time Point column (see time points on page 38 for details). Optionally, you can enter a Description. This description is also exported to an export file with the statistics and can be used as an independent variable. The Trial name Trial0001, Trial0002, etc. is used as an ID to identify individual trials. Therefore, trial names must be unique. You can edit trial names.

System variables

The Trial List also displays the following system variables for each trial: Acquisition Status - The shows the Acquisition Status of a trial. The status can be Planned, Partially acquired, Acquired. Total Runs - This shows the number of acquired runs. 3 - Set up an Experiment Compliant Runs - This shows the number of acquired runs that meet the run criteria (see page 39). Classification status - This shows Classification Status of the acquired runs of a trial. The status can be Not classified, Partially classified, Classified.

Delete a trial

Do one of the following: In the Trial List, select the trial you want to delete and click the Delete Trial(s) button. tip You can select multiple trials: select the first trial you want to remove, press and hold the Shift key and select the last trial you want to remove. if you want to select multiple, individual trials, press and hold the Ctrl key and select the trials. In the Experiment Explorer, right-click a trial and select Delete. important Deleting a trial cannot be undone. It is not possible to delete an 'active' trial.

Sort the trial list

You can sort each column of the Trial List by clicking its column header. Although you can sort the Trial List and/or edit trial names, in Acquisition, the order of trials is always the original order when the Trial List was created.

Copy and paste contents in the trial list

1. Select the contents of the cell, then right-click and select Copy (Ctrl+C).
2. Click the cell where you want to paste the text, right-click and select Paste or press Ctrl+V. Note that you cannot copy and paste multiple cells from Excel. Figure 3.4 The Trial List. In this example, six trials have been defined for six different animals from three different treatment groups. 3 - Set up an Experiment

3.6 Experiment Setup Profiles

You can save the current Experiment Settings, time points, treatment groups and Trial List to an Experiment Setup profile. You can have multiple Experiment Setup profiles. When you create a new experiment, you select an Experiment Setup profile, so those settings are copied to the new experiment without the trials.

Add an Experiment Setup profile

To create a new Experiment Setup profile that contains the current Experiment Settings and Trial List: 1. Do one of the following: In the Profiles Explorer, right-click Experiment Setup Profiles and select Add New Profile. Choose Profiles > Experiment Setup Profile > New. 2. Select 'Create an Experiment Setup Profile...from the current experiment'. When you select Create a blank Experiment Setup Profile, an Experiment Setup profile is created with default experiment settings and no time points, treatment groups or trials. 3. Enter a name and click Add. 4. If necessary, make adjustments and click OK to store the profile.

Open an Experiment Setup profile

Do one of the following: In the Profiles Explorer, right-click an Experiment Setup profile and select Open. Choose Profiles > Experiment Setup Profile > Open. Next, select a profile from the list and click Open.

Duplicate an Experiment Setup profile

1. In the Profiles Explorer, right-click an Experiment Setup profile and select Duplicate.
2. Enter a name and click OK.

Rename an Experiment Setup profile

1. In the Profiles Explorer, right-click an Experiment Setup profile and select Rename.
2. Type in a name and press Enter. 3 - Set up an Experiment

Delete an Experiment Setup profile

Do one of the following: In the Profiles Explorer, right-click an Experiment Setup profile, select Delete and click Yes. Choose Profiles > Experiment Setup Profile > Delete. Next, select a profile from the list and click Delete.

3.7 Set Your Preferences

Procedure

1. Choose File > Preferences or click the Preferences icon on the tool bar
2. Click the tab that applies and make the necessary changes. General - Choose the Distance Unit (Millimeters, Centimeters, or Inches) and the Number of Decimals shown for Numbers, Times and Percentages.

Folders and Auto Save - Optionally, change the default location of the new

experiments, new backup files and the export folder. Here you can also turn on/turn off Auto Save and set the auto save interval. Colors - You can choose the colors in which paws and other body parts are displayed in the Print and Timing View. For more details, see the below. Note that the default colors have changed in CatWalk XT 10.7 to make them better distinguishable to most users. Messages - We recommend to keep the option Regularly prompt for backup selected; every 10th time you save an experiment, a message appears reminding you to back up your experiment. 3. Click OK to apply the new preferences. 3 - Set up an Experiment

Colors

Paws / Limbs / Other

Select the colors that are used in the Timing View for Paws, Limbs and Other body parts. To change a color, click it and select a new color.

Classification

Select the colors of the rectangles and associated labels in the Print View. You can do this for Labeled, Unlabeled, Selected and Junk prints. To change a color, click it and select a new color.

Use individual colors for labeled prints

When you select this option, the labeled prints are displayed in the colors selected under Paws. When the option is not selected, all labeled prints are displayed in green.

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Source: CatWalk XT 10.7 - Reference Manual