Knowledge Base

5 Set Up EthoVision XT

Prerequisites

Before you can start working with the DanioVision system, you need to connect the DanioVision Observation Chamber to the EthoVision XT computer (see page 15) and, optionally, set up the water-flow system (see page 18). 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 (see page 106). 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, 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. DanioVision DVOC 004x/T, 96 round 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. For details see page 72.

tip To know which DVOC version you have,

see the serial number on the label located

on the back panel. 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.

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. See page 45. Arena Settings. See page 49. Trial Control Settings. See page 57. Detection Settings. See page 64.

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. For details,

see Create a new experiment based on an existing experiment in

the EthoVision XT Help.

File > New and 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. Instead, we advise to create 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 30 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 (see the table on page 29).

See also the guidelines in columns G, H and I in Table

1 on page 29.

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

If you are interested in how long and how frequent your subjects have been active vs. inactive, under Analysis Options select Activity analysis.

Make sure you also adjust the Activity settings in the Detection

Settings (see page 66).

For more information about setting up an experiment, see Set Up an

Experiment in the EthoVision XT Help.

Use Of Trial Control Hardware

Follow this section if you use stimulus devices like the white/color lights and the tapping stimulus device. 1. In the Experiment Settings, under Trial Control Hardware, make

sure that Use of Trial Control hardware is selected and click the

Settings button. 2. In the Hardware Interface window that opens, choose the type of system you have. If you have DanioVision DVOC-0041:

Choose DanioVision DVOC-004x/T if you use the Tapping Device

in this experiment. In all other cases choose DanioVision DVOC-004x.

The other options DanioVision DVOC-001x - 003x are meant for

older versions of the DanioVision Observation Chamber.

note The option Mini USB-IO Box only applies when you use a Mini

USB-IO box instead of DanioVision DVOC. 3. In the Device Configuration window, under Device features, the hardware devices activated for this experiment are listed. 4. optional The default status of the DanioVision White Light

Stimulus if Light off. This means that, when you start a trial, the

white light is switched off. To use the white light as a stimulus, program its activation with Trial Control. If, however, you want to use the white light as a default lighting condition, and use the darkness as a stimulus, do the following: Click the White Light Default button. b Under Default device state, select Light on. Choose a percentage of intensity (0-100) and click OK. Then in the Trial Control procedure you can program when to switch the light off. See Trial Control Settings on page 57. 5. optional If you connect additional hardware, under Plug-in devices,

select the devices in the corresponding rows for TTL Port 1-4, or

Expansion 1 / Port 1-4 depending on which port on the DanioVision

back panel you use. 6. Click OK. 7. optional If you set the default state of the White Light Stimulus to

Light on, open the Trial Control Settings. This will confirm your

selection.

Notes

The Tapping Stimulus is listed under Device features when you

select DanioVision DVOC-004x/T in step 2. If you upgraded from an older version of EthoVision XT, and you use an experiment created in the older version as a template for a new

one, the DanioVision detection method is not available. Therefore,

we recommend to create a new experiment with the newest

version, and use this as a template (File > New From Template > Use

a custom template). If you upgraded an experiment from an older EthoVision XT version, do not change the Trial Control Hardware Settings in the

Experiment Settings. Leave Noldus Mini USB-IO Box selected in the

Hardware Interface window. Otherwise the Trial Control rules, for

example to control the white light, may not work. When you change the default state of the White Light Stimulus to

Light on, note that the white light is only switched on in one of the

following cases: When you open the Trial Control screen. When you open the Arena - Hardware Mapping window. When you start a trial. For more information on Trial and Hardware Control, see the Reference Manual - Trial and Hardware Control in EthoVision XT.

---

Source: Reference Manual - DanioVision DVOC-0041