Knowledge Base

Setting up the experiment in EthoVision XT

Create the Experiment

1. Start EthoVision XT and choose File > New from template.
2. In the Select a template option window, select Apply a pre-defined template. Next, follow the instructions in the guided setup. For more information, see Set Up an Experiment in the EthoVision XT Help. For details on connecting the camera, see Camera Installation in the EthoVision XT Help, or watch the video tutorial Set Up the Camera (Help > Video Tutorial).
3. Enter the name of the experiment and click OK.
4. Before you can actually acquire data, check the settings listed in the rest of this section.

Experiment Settings

Choose Setup > Experiment Settings.

Under Video Source and Tracked Features, make sure that the options selected correspond to your needs. To adjust the camera settings, click the video icon in the camera row.

Note: The option Deep learning is only available if your PC has a graphic processor (GPU) that supports additional software (CUDA). See Deep learning: Requirements and Limitations in the EthoVision XT Help.

Arena Settings

Choose Setup > Arena Settings > Open Arena Settings 1.

1. Click Grab to grab an image of the empty enclosure from the camera image, or click Browse to select a video file and then click Grab.
2. Click 1. Draw Scale to calibrate your arena.
3. Click 2. Select Shape and Draw Arena. Check that the arena covers the whole area in which you want to track the animal. For open fields and other enclosures, remember to include enough of the walls so that the animal is still tracked when it rears, but exclude any bright reflective rims that might interfere with tracking. Make sure the label stays inside the arena.
   • If you need to rotate the outline of the arena, drag around all elements, then click the Rotation mode button and move the outline until it matches the arena in the video image.
   • If you need to reshape the outline of the arena, click the Point edit mode button and move the vertices of the outline.
4. To draw zones, click 3. Select Shape and Draw Zones. See more details in the chapter about your test.

For details, see Arena Settings in the EthoVision XT Help.

Trial Control Settings

In the Trial Control Settings you can define conditions for the start and stop of data acquisition. For details, see the EthoVision XT Help.

Choose Setup > Trial Control Settings.

Detection Settings

Choose Setup > Detection Settings > Detection Settings 1.

1. If you work with pre-recorded video, select a video file. If you work with the live camera image, release the animal in the arena.
2. Click Automated Setup.
3. Select:
   • Rodent for tracking rats and mice.
   • Adult fish for tracking fish from the top view.
   • Other for any other case such as tracking insects, crustaceans, or when tracking fish from the side view.
4. When the subject does not move a lot and is far from the enclosure walls and other objects, draw a rectangle around it. EthoVision XT detects the subject.
   • If the subject's body is well detected (marked in yellow), click Yes.
   • In other cases, move the Finetune slider or click No and adjust the Advanced detection settings.

Note: The Automated Setup may not work in all situations. If the subject is not detected correctly, see the Advanced detection settings below.

Advanced Detection Settings

1. Under Video, choose the sample rate.
2. Under Method, check that either Dynamic subtraction or Differencing is selected as the detection method. Differencing is the preferred option if other methods do not work well, or if you work with hooded animals.
3. Select the tracking method. The options here depend on your experiment settings, including the number of body points you want to track. The optimal method is automatically selected after choosing the type of animal in the Automated Setup. For more information, see Tracking methods in the EthoVision XT Help.
4. When using Dynamic subtraction, move the slider to define the animal's contrast. The animal must be fully detected in all parts of the arena and the noise must be minimal. When using Differencing, set the Sensitivity slider. The slider determines what difference in contrast from the background is seen as the animal.

For more information:

• Choose Help > EthoVision XT Help and search for Advanced Detection Settings.
• Choose Help > Video Tutorial and watch the videos under How Subject Detection Works.

Trial List

Choose Setup > Trial List.

Enter your independent variables such as rat ID, first or second phase of the experiment, treatment (with values drug vs. control), dose, type of object, name of the experimenter, etc. If you want, you can pre-define all your trials here, or you can enter the independent variable values as you carry out the trials. You can also prepare the trials in Excel, randomize them, and then paste the values into your Trial List.

Furthermore, you can define a list of trials for batch acquisition. See Acquire a series of trials in the EthoVision XT Help.

Protocols on the Web Featuring EthoVision XT

Researchers are encouraged to publish test protocols to improve reproducibility of animal experiments.

Browse to https://www.bio-protocol.org/en/searchlist?content=ethovision to find protocols created with or mentioning EthoVision XT.

Acquire the Data

Protocol

Each test described in this manual has one or more specific protocols. See the chapter that applies.

Important: Always record your video with EthoVision XT or MediaRecorder. Do not record video with Pylon Viewer or other software. The resulting video file may not be compatible with EthoVision XT.

Acquire the Tracks

1. Check that you have selected the correct Video Source in the Experiment Settings.
2. Choose Acquisition > Open Acquisition.
3. Optional: Skip this step if you have already entered the values of the independent variables in the Trial List. Open the Independent Variables tab of the Analysis Results and Scoring pane at the bottom of your screen and enter the values of the independent variables. You can also do this during acquisition.
4. If you did not plan any trials in the Trial List, click the New trial button in the Playback Control window (Ctrl+F3).
5. If you planned two or more trials, select in the Acquisition Settings window whether you want to track only the next planned trial or all planned trials. If you carry out batch acquisition and track live, also specify the Inter-trial interval.
6. Optional: In the Acquisition Settings window, select Auto-start data analysis. Do this to start calculation of analysis results immediately after acquisition. If you choose this option, first create an Analysis profile and optionally a Data profile and a Track Smoothing profile. Choose whether to carry out analysis only for the profiles highlighted in blue in the Experiment Explorer, or for all possible profile combinations. In the latter case, first delete all profiles you do not need for analysis.
7. Start the trial by choosing Acquisition > Start Trial, clicking the Start trial button in the Playback Control window, or pressing Ctrl+F5.
8. If you do live tracking, release the animal in the arena.
9. Data acquisition starts when the Start track condition in your Trial Control Settings becomes true.
10. The trial stops automatically when the Stop track condition specified in the Trial Control Settings becomes true.

Source: EthoVision XT 19 - Application Manual