Knowledge Base

5 - Carry out Data Acquisition 5.1 Prepare the walkway........................................................................... Make sure the walkway is clean, the corridor is put in place and the illuminated ceiling is lowered. 5.2 Carry out data acquisition................................................................... During acquisition an animal crosses the walkway and these runs are recorded. After acquisition you can play back runs for inspection and if necessary delete runs. In the Experiment Explorer, small Acquisition Status symbols allow you to check the Acquisition Status of trials and runs. 5 - Carry out Data Acquisition

5.1 Prepare The Walkway

Before you acquire data you need to make sure that: The glass plate is clean Lift the corridor. Use a soft cloth or tissue to remove droppings, urine or other dirt from the glass plate. You can use a propriety glass-cleaning fluid to further clean the glass plate. Experience from CatWalk users has shown that also water with some vinegar added or a70% alcohol solution are also effective in cleaning the glass plate. The camera is at the correct position The distance of the camera to the glass plate determines how much of the walkway is visible. In order to get 5-6 step cycles per run, you should see about 45 cm of the walkway for mice and about 70 cm for rats. Try this out with one or two animals to make sure you get the appropriate camera position. If you change the position of the camera, you need to redefine the walkway and re- calibrate the walkway (see Set up the walkway). Also make sure to focus the camera. The corridor is put in place Make sure the middle of the corridor is positioned in the middle of the glass plate. Adjust the width of the corridor to match the animal's size. The illuminated ceiling is lowered When you did not install the diffusion plate on top of the corridor walls, it is useful to leave a gap between the top of the corridor and the illuminated ceiling so you can put an animal into the corridor from the top. When you adjust the vertical position of the illuminated ceiling, always check in the Define Walkway window that the red LED lights of the illuminated ceiling completely cover the defined area. Optionally, you can use the Noldus goal box to let the animal run towards its home cage. 5 - Carry out Data Acquisition

5.2 Carry Out Data Acquisition

After you have prepared the walkway (see above), you are ready to start data acquisition. During acquisition, CatWalk XT uses the run criteria you have specified in the Experiment Settings (see page 39).

Procedure

Start data acquisition

1. Do one of the following: In the Experiment Tasks window, click Open Acquisition. Choose Acquire > Open Acquisition. In the Experiment Explorer, under Acquisition, right-click a trial and select Acquire Runs.
2. Under Trial Selection, select a trial from the list (see the figure below). When you have not defined one or more trials in the Trial List, select Create new trial from the list or go to the Trial List (see page 41) to define trials. Lower the illuminated ceiling gently; if you do this too roughly, it can make the corridor walls shake which can accidentally set off acquisition after you have clicked the Start Acquisition button. Do not lift the illuminated ceiling after you have clicked the Start Acquisition button; this results in the acquisition of a lot of data and a high processing load.
3. Click the Snap Background button to snap a background image of the empty, clean walkway. You cannot start acquisition before you have snapped a background image (see Acquisition Status on page 61). You can view the background image in the Acquisition Settings: Choose Setup > Acquisition Settings and click the View Background Image button. 5 - Carry out Data Acquisition
4. Click Start Acquisition or press Page-Up. The Status changes to 'waiting for run to start'.
5. Put the animal into the corridor from the side. Acquisition starts automatically as soon as the animal's contour is detected. The Status changes to 'recording Run#'. As soon as the animal disappears from view, the Status changes to 'waiting for run to start'.
6. If you have specified in the run criteria of the Experiment Settings to acquire more than 1 compliant run, now take the animal out of the corridor and put it back in on the other side or let it turn around for the next run (step 5).

Stop data acquisition

7. You can manually stop data acquisition by clicking the Stop Acquisition button or by pressing Page-Down.
8. Acquisition stops automatically as soon as the set number of compliant runs (run criteria on page 39) has been acquired. See also page 61.

What next?

When the set number of compliant runs has been acquired, the Acquisition Finished Tasks window opens (see Figure 5.2). You can now select: Acquire Next Trial - This is the trial that is listed next in the Trial List. Acquire New Trial - This creates a new trial that you can acquire. Classify Runs - This takes you to the Classification window where you can classify acquired runs. Figure 5.1 Part of the Acquisition screen. The background has been snapped and the Start Acquisition button has been clicked; acquisition starts when the animal is detected. 5 - Carry out Data Acquisition Review Runs - To inspect acquired runs (see below).

Notes

Acquired Run list

The Acquired Runs list (see Figure 5.3) shows the acquired runs with the following variables: Run - The run number. Start - The start data and time of the run. Duration - The total duration of the run. Compliant - A run is marked compliant or non-compliant with the run criteria. When you hover over the non-compliant icon, information is displayed about why the run is non- compliant with the run criteria. The run criteria become read-only when you have acquired a run. Direction - The walking direction of the animal. If the animal turns around the Direction cannot be determined. Run Average Speed - The speed of the recorded run.

Run Maximum Variation - The maximum variation in running speed (see the run

criteria) of the recorded run.

Figure 5.2 The Acquisition Finished Tasks

window. 5 - Carry out Data Acquisition Camera Gain - The Camera Gain value from the Detection Settings (see Configure the detection settings on page 48). Green Intensity Threshold - The Green Intensity Threshold value from the Detection Settings. Depending on your Run Settings in the Acquisition Settings, runs that are aborted or do not meet the run criteria are kept or discarded. A run stops automatically... When the run duration exceeds the maximum set in the run settings (page 53). In any case when run duration exceeds 60 seconds. This is indicated for that run in the Acquired Runs list. Acquisition stops automatically... When the set number of compliant runs (run criteria on page 39) has been acquired. When not enough internal memory is available. This can occur, for example, when you acquire a number of long runs (20-30 seconds) in a row, with short time between runs. In this case, CatWalk XT needs to both process and acquire (long) runs, which can cause the internal memory to 'overflow'.

Acquisition Status

The Status during acquisition can be:

Waiting for background snapshot of empty walkway to be taken - Press the Snap

Background button. You can view the snapped Background in the Acquisition Settings (see page 53). Ready for acquisition - Then press the Start Acquisition button. Figure 5.3 Part of the Acquired Runs list. In this example, two consecutive runs were acquired that both are compliant with the set run criteria. 5 - Carry out Data Acquisition Waiting for run to start - Recording starts automatically as soon as the animal appears in the video image. Recording Run[#] - A run is recorded and acquisition stops automatically as soon as the animal has completely disappeared from the video image. Camera connection lost, trying to restore the connection... - If the connection is lost, acquisition is stopped. Acquisition can only be resumed after the connection has been restored.

Waiting for animal to leave the walkway - This status message is shown in the

following cases: - The Maximum run duration (see page 39) has been exceeded while the animal is still on the walkway. - The animal has left the walkway but has left some faeces or urine so the run has not been stopped.

5.3 Acquired Runs

Review The Runs

Review a run

1. Under Video, from the View list, select a run.
2. To replay a run, press the Play button (see Figure 5.4 for a description of the playback buttons).

Options

Select a playback speed from the list. When you press the Pause button, the video pauses at its current position. You can move the video forward or backward one frame, by using the Play-forward-one- frame or Play-backward-one-frame button. You can keep them pressed to move through the run frame by frame. Note that the time between two subsequent frames is 1/100 s. When you press the Stop button, the video jumps to the beginning. When the run is paused or stopped, you can scroll through the video using the slider. 5 - Carry out Data Acquisition A run plays continuously, unless you turn off the Repeat button.

Delete Runs

important Deleting runs cannot be undone. We recommend to make a backup of your experiment (see page 149) before deleting runs.

Delete a single run

1. Select the run you want to delete in the Acquired Runs list at the bottom of the screen. The currently active run (indicated in bold and blue in the Experiment Explorer) cannot be deleted. From the View list, select Live video to 'in-activate' the run.
2. Click the Delete Run(s) button. Alternatively, right-click an 'inactive' run in the Experiment Explorer and select Delete.

Delete multiple runs

1. Select the runs you want to delete in the Acquired Runs list at the bottom of the screen: The currently active run (indicated in bold and blue in the Experiment Explorer) cannot be deleted. From the View list, select Live video to 'in-activate' all runs. To select multiple, consecutive runs, click the first run you want to delete, press and hold the Shift key and click the last run you want to delete. To delete multiple, individual runs, press and hold the Ctrl key and click the runs you want to delete.
2. Click the Delete Run(s) button. When you next acquire an additional run in this trial, the run number continues from the previous number of acquired runs. For example, you have three runs (Run1, Run2, Run3) in the list and you delete Run3. When you next acquire a new run, this run is labeled Run4.

Figure 5.4 The playback control buttons. From left to

right: Play button / Pause button, Stop button, Repeat button, Playback speed list, Play-back-one-frame button, Play-forward-one-frame button, Slider. 5 - Carry out Data Acquisition

5.4 Acquisition Status Icons

In the Experiment Explorer, the following symbols allow you to check the Acquisition status of trials and runs.

Trials

Runs

Data selection status

For each trial and run it is also indicated whether it contains steps which are included in the

currently active Data Segmentation profile (see Select the data on page 92):

Trial - The number of runs within the trial that contain steps which are included in the data selection is indicated behind the trial. The figure below shows an example of a trial

Trial#

Green check mark For this trial the minimum number of compliant runs (as set in the Experiment Settings, see page 39) have been acquired.

Trial#

Orange check mark For this trial the minimum number of compliant runs have NOT been acquired.

Run#

Green round icon This run meets the run criteria set in the Experiment Settings.

Run#

Orange round icon This run does NOT meet the run criteria. 5 - Carry out Data Acquisition with 3 runs which all contain steps included in the currently active Data Segmentation profile. Run - An asterisk (*) behind a run indicates that the run contains steps which are included in the data selection.

What next?

You can acquire another run for the current trial by selecting Live video from the View list under Video. You can acquire runs for another trial; go to step 2 on page 58. You can continue to Classification (see Classify Runs on page 66). Click >> Classify Runs in the bottom-right corner or choose Acquire > Classify Runs.

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Source: CatWalk XT 10.7 - Reference Manual