Knowledge Base

Prerequisites

Before you can start working with the DanioVision system, you need to connect the DanioVision Observation Chamber to the EthoVision XT computer and, optionally, set up the water-flow system. After you have turned on the DanioVision Observation Chamber with the switch on the front panel, wait at least 15 minutes for the DanioVision chamber to 'start up'.

Also make sure to remove the lens cap from the camera.

Assign Treatments To Wells

To prevent systematic errors as a result of potential variation in temperature, light intensity or other unknown variable across a well-plate, it is recommended to either assign larvae from different treatments randomly to the wells or make sure that wells containing different treatments (that is, different solutions or different concentrations of the same solution) are evenly distributed across the well-plate (so, for example, one type of solution is not only put in the center wells).

Create A DanioVision Experiment

Preferred Method

With this method, all arenas are created automatically, but need to be manually adjusted, using the Arrange Arenas option. Unnecessary functionality like manual scoring is removed from the interface and detection settings are optimized for DanioVision.

If you select a template which contains more arenas than needed, you can exclude the unused arenas with Data Selection. After you have followed the steps below to create the new experiment, you must still check/adjust Experiment Settings, Arena Settings and Detection Settings before you can track any animal correctly.

1. Do one of the following:
   • In the EthoVision XT Startup window, under New experiment, click New from template.
   • Choose File > New from Template.
2. In the Select a template option window, click Apply a pre-defined template. Next, follow the instructions in the guided setup as described below.
3. Which video source will you use? Select the option Live tracking (and saving video files), click the Sources button and select the Basler camera. Click Next >.
4. Which subjects will you track? Select Fish and then Zebrafish larvae from the list. Click Next >.
5. How is the arena configured? Select an Arena template from the list, then click Next >.
   • DanioVision DVOC 004x, 24 round wells
   • DanioVision DVOC 004x, 48 round wells
   • DanioVision DVOC 004x, 48 square wells
   • DanioVision DVOC 004x, 96 round wells
   • DanioVision DVOC 004x/T, 24 round wells *
   • DanioVision DVOC 004x/T, 48 round wells
   • DanioVision DVOC 004x/T, 48 square wells
   • DanioVision DVOC 004x/T, 96 round wells
   • Open field, round
   • Open field, square
   • Well plate, round wells — Select this option if you have a different number of round wells
   • Well plate, square wells — Select this option if you have a different number of square wells

   * Select one of the options with /T when you have installed the DanioVision Tapping Device and you want to use it in this experiment.

   Tip: To know which DVOC version you have, see the serial number on the label located on the back panel.

   Note: Arena templates are also present for older DanioVision DVOC versions: DanioVision DVOC 001x–003x.

   Note: If you selected a template for an older DanioVision version, it is possible that the DanioVision detection settings method does not give optimal detection of the larvae with images from your camera. If that is the case, use another detection method in the Advanced section of the Detection Settings pane. Consult the DanioVision manual that came with your setup, or see Configure Detection Settings in the EthoVision XT Help.

6. Initialize template experiment. Check here that all settings are correct and, if so, click Finish.
7. Enter the name of the experiment and click OK. The EthoVision XT Overview window opens.
8. Follow all the next steps:
   • Experiment Settings
   • Arena Settings
   • Trial Control Settings
   • Detection Settings

Other Ways To Create A DanioVision Experiment

No matter which method you choose, when you create a DanioVision experiment unnecessary functionality like the Manual Scoring Settings is removed from the interface and detection settings are optimized for DanioVision.

• File > New from Template > Apply a custom template — Choose this method to create an experiment based on an existing one. For example, when you want to replicate an experiment with the same number of arenas, the same trial control procedures, etc. See Create a new experiment based on an existing experiment in the EthoVision XT Help.
• File > New — In the window that appears, select the option DanioVision experiment. In the Experiment Settings, next to Number of Arenas, enter the number of wells. With this option you have to draw the arenas manually. For more information on creating an experiment manually, see Set Up an Experiment in the EthoVision XT Help.

We advise creating an experiment with a predefined template (first method), because all arenas are then defined automatically.

Experiment Settings

Choose Setup > Experiment Settings.

Video Source

1. Under Video source, click the Video icon on the right side of the row of your camera.
2. In the Video Settings window that appears, click the Formats tab and select the Resolution and Frame rate. Default resolution is 1280 x 960 at 25 frames/s. If you create an experiment based on a template with the Tapping Device, set the frame rate to 60 fps and reduce the resolution according to your setup.

From the Color space list, choose Y800. This is the color space for a monochrome video image. The other options, suitable for color images, do not apply to DanioVision.

Tracked Features

Specify whether you want to track the center point of the fish (default) or the center point, the nose point and the tail base. Choose the latter option only if you track fish in a close-up image.

Body Point Detection Technique

The Contour-based technique is selected. The option Deep learning is not available for fish tracking.

Analysis Options

Specify whether you are interested in how long and how frequently your subjects have visited defined zones.

Source: DanioVision DVOC-0041 Reference Manual, Noldus Information Technology