Knowledge Base

3 Set Up DanioVision

Connections

The back panel of the DanioVision Observation Chamber contains the following connections (see Figure 3 below): 1. Expansion 1. You can optionally use this connector to set up to 4 TTL out lines, to control external devices. For details, see page 127. 2. Temp. Connector for the temperature sensor. Use this in combination with the DanioVision Temperature Control Unit (TCU). 3. Cable grommet. If you install additional hardware inside the observation chamber, puncture the rubber membrane to let the cables pass through. For example, to connect the sensor of a digital thermometer placed in the water basin to a digital display outside the DanioVision Observation Chamber. 4. Gigabit Ethernet (GigE) camera connector. Use this output to connect the DanioVision camera to the EthoVision XT computer.

Figure 3 The back panel of the DanioVision Observation Chamber. See text for

explanation. The label with the CE marking contains the product version. 5. Expansion 2. This is a RJ45 type, 8-pin feed through connection. You can use it to connect future internal add-on hardware to get external signals in the DanioVision Observation Chamber. 6. Connector for water flow (see page 18 for details). 7. TTL1 to TTL4. You can optionally use these TTL input/output connections to control external devices such as a sound or shock generator, or the DanioVision Temperature Control Unit. 8. USB port (type Standard-B) to connect the DanioVision Observation Chamber to the EthoVision XT computer. 9. Connection for the 24 V power supply. 10.Connectors for water flow (see page 18 for details).

Connect Daniovision

Make sure the DanioVision Observation Chamber is placed on a level surface!

Power

Connect the DanioVision Observation Chamber's 24 V socket (9 in

Figure 3) to the power supply using the power cable and adaptor.

Video

Use the Ethernet cable with the large round connector to connect the

digital video output of the DanioVision Observation Chamber (4 in

Figure 3) to the Ethernet port labeled DanioVision camera on the

EthoVision XT computer. The DanioVision camera must be connected to a 1-Gb Ethernet card. See page 23 for how to install this card on your computer. If you have purchased a PC from Noldus together with DanioVision, this card is already installed. Contact Noldus if you need a new Ethernet card for the DanioVision camera.

White Light, Tapping Device, and other hardware

Use the USB cable that comes with DanioVision to connect the USB

port of the DanioVision Observation Chamber (8 in Figure 3) to a USB

port on the EthoVision XT computer. Do this only if: You want to control the White Light or the Tapping Device in the DanioVision Observation Chamber during data acquisition in EthoVision XT. You have the DanioVision Temperature Control Unit and you want EthoVision XT to take action if the water temperature gets too low or too high. You want to control any custom hardware connected to the DanioVision Mini USB-IO box.

Figure 4 Basic connections between the EthoVision XT computer and the

DanioVision Observation Chamber. For controlling other devices like the Toplight Unit and the Temperature Control Unit, see the corresponding sections.

Set Up A Water-flow System

If you require a temperature-controlled water flow underneath the well plate, the Noldus DVTCU Temperature Control Unit is the preferred method. The back panel of the DanioVision Observation Chamber contains three connections for controlling the water flow (see Figure 6): a water inlet (marked in green), a water outlet (marked in yellow) and a water overflow (marked in red). Figure 5 The DanioVision DVTCU Temperature Control Unit.

Figure 6 The back panel of the DanioVision Observation Chamber, with the

numbers indicating the connections of the water-flow system: 1 - water inlet; 2 - water outlet; 3 - water overflow. Connect the DanioVision Observation Chamber to the DVTCU using the tubes that match the color of the connectors. Please see the Reference Manual - DanioVision Temperature Control Unit DV-TCU for the complete instructions.

Suggested temperature

For Danio larvae, the temperature of the water flowing through the system is usually 28 degrees Celsius. You can set a different temperature when needed.

Figure 7 Tube connections between the DanioVision Observation Chamber and

the DanioVision Temperature Control Unit. Color dots represents colors on the tubes. Arrows indicate the water circulation.

Light And Switches

Main switch

The main switch is located on the front panel. After you switch on DanioVision, wait at least 15 minutes for it to 'start up' and to avoid condensation in the system.

Internal LED light

The DanioVision Observation Chamber is equipped with a LED light to illuminate the inside of the chamber while you set up your experiment.

Operate the Light switch at the left of the camera to turn the light on

and off.

Anti-Moisture switch

This switch is located at the right of the camera. Operate this switch to adjust the anti-condensation mechanism (page 35).

Low light switch

This switch is located on the Mini USB-IO box, behind the camera at the back of the observation chamber.

When the switch is set to H (default), the standard light levels are

activated, from ±20 to ±10000 lux.

Set this switch to L to allow very low light intensities, from 0 to ±20

lux. For details, see page 36.

Install Ethovision Xt

If you have purchased the DanioVision Observation Chamber including a computer from Noldus Information Technology, all software has been installed and tested. You can skip this section.

See Set up EthoVision XT on page 41

If you use your own computer (or a computer you bought from Noldus IT in the past; in that case, make sure it meets the EthoVision XT system requirements), see below. EthoVision XT 16 is supported with Windows 10 Pro, 64 bit. For more information about system requirements, press F1 in EthoVision XT.

Mini USB-IO box drivers

The Mini USB-IO box is the embedded electronics unit that communicates with EthoVision XT. The Mini USB-IO box makes it possible for EthoVision XT to control for example the white light stimulus. Before installing EthoVision XT, remove older versions of the drivers for the Mini USB-IO box. To do so: 1. In the Windows Control Panel select Programs and features. 2. Click each of the items whose name begins with Noldus_Hardware Interface.. and click Uninstall. 3. Insert the EthoVision XT Installation USB stick into your computer and follow the instructions to install EthoVision XT. When you install EthoVision XT, the drivers of the Noldus Mini USB-IO Box are automatically installed.

important When you open an experiment from EthoVision XT 12 or

lower, a warning appears, informing you that you cannot open upgraded experiments in the old version of the software anymore. Make a backup of your DanioVision experiment in the older version of EthoVision XT before opening it in EthoVision XT. To make a backup, choose File > Make Backup.

important If you uninstalled the older version of EthoVision XT, you

cannot use the Backup function. Instead, make a copy of your experiment using Windows Explorer before you open it in the newer EthoVision XT version. Always copy the complete experiment folder and not only the *.evxt file otherwise your experiment does not open.

For more information

See Installation in the EthoVision XT Help for instructions on how to

install EthoVision XT. For more information on the Mini USB-IO box, see the Reference

Manual - Trial and Hardware Control in EthoVision XT, which you can

find on your EthoVision XT computer, under Noldus > EthoVision XT 16

Other Documentation.

Install The Network Card For The

Daniovision Camera

DanioVision works with a Basler Gigabit Ethernet (GigE) video camera, connected via an Intel PRO/1000 CT 1-Gb Ethernet card installed on your computer. If you ordered a computer from Noldus Information Technology when you purchased DanioVision, it came with that Ethernet card. The card has already been installed and tested. In that case, skip the sections below and continue with Chapter 4 on page 32. If you bought your computer somewhere else, you will have to install the Ethernet card yourself. This involves a few steps (see below). Figure 8 The Intel PRO/1000 CT Ethernet card.

Step 1. Insert the Ethernet card in the DanioVision computer

1. Turn off your computer and all connected peripherals, such as the monitor and printer. Make sure that the computer is unplugged.
2. Remove the PC's casing according to the instructions provided in the PC's user manual.
3. Select a free PCIe expansion slot, and remove the corresponding extension cover. When possible, choose the slot that gives maximum performance. To estimate performance, take note of the slot version (2, 3, etc.) and compare it with the following values: PCIe v1.x: 250 MB/s PCIe v2.x: 500 MB/s PCIe v3.0: ~1 GB/s PCIe v4.0: ~2GB/s PCIe v5.0: ~ 4GB/s Note that values are given per lane; they should not be multiplied by the number of lanes in a slot (e.g. x4) since the card has a 1x connector). For example, SLOT1-PCIe3x4 means version 3.0, with four lanes. important Do not insert the PCIe board in the blue or white slots.
4. Unpack the Ethernet card, place it into the slot, and press it carefully into position. If the card does not fit into place easily, remove it and repeat the operation. When touching the board, its electronic components can be damaged by static electricity. To avoid any such risk, make sure that you are grounded. You can ground yourself by putting on an earthing wristlet, and attaching its clip to the metal frame of the computer. If an earthing wristlet is not available, you can hold the metal frame with one hand while holding the Ethernet card in your other hand. Ensure also that your clothing does not touch any components while handling the card.
5. Fix the card to the chassis and re-fit the computer's cover. For more information about installing the camera and the Ethernet board, see Camera Installation in the EthoVision XT Help.

Step 2. Install the camera drivers

1. Insert the EthoVision XT installation USB stick into your computer.
2. Double-click EthoVision XT Setup.exe. If you have already installed EthoVision XT, select Modify.
3. Under Drivers and tools, select Basler GigE camera driver.
4. Continue with installation. Under Profile, select Camera User, then click Next.
5. Under Interfaces, select GigE, then click Next.
6. Connect the DanioVision camera to the port of the Ethernet card using a network cable (see D in Figure 3 on page 15).

Step 3. Assign the IP address to the Ethernet card

tip Watch the video tutorial Set Up the Camera. In EthoVision XT,

choose Help > Video Tutorial. 1. In Windows (here version 10), search for Network Connections. 2. Right-click the Local Area Connection and click Properties. If your

computer has more than one Local Area Connection, choose Basler

GigE Vision Adapter. Write down the number of this connection. 3. Select Internet Protocol Version 4 (TCP/IPv4) and click Properties. 4. Select the options: Use the following IP address and Use the

following DNS server addresses and fill in the details as shown in the

next figure.

Also select the checkbox Validate settings upon exit. When done,

click OK and then Close.

Step 4. Set the IP address of the DanioVision camera

tip Watch the video tutorial Set Up the Camera. In EthoVision XT,

choose Help > Video Tutorial. 1. In Windows, search for IP Configurator and start this application. 2. Select the camera. 3. Fill in the details in the IP Address and Subnet Mask fields under Static IP Address as shown in the figure below. 4. Click Save and then Close. 5. Follow the instructions below to configure the DanioVision camera.

Configure The Daniovision Camera

Camera settings

The DanioVision camera that you received is already configured according to your setup. Noldus created three main settings profiles,

called User Sets, stored in the Pylon Viewer software which controls the

camera: User Set 1, User Set 2 and User Set 3. Only one User Set can be

active at a time. For each video resolution, you must use different camera settings and in some cases a different camera lens. For example, the video resolution determines the maximum frame rate. The higher the required resolution (in number of pixels), the lower the maximum frame rate (in frames per second). The three User Sets are specific for a combination of video resolution and frame rate (Table 1).

Which User Set is currently selected?

Make sure that EthoVision XT is closed. Start the Basler Pylon Viewer

software and in the Features panel (for details, see the procedure in the

next pages), under Configuration Sets, look for the item Default

Startup Set. This is the User Set that contains the current settings. Always check that the settings in Pylon Viewer for a particular User Set correspond to those in the table!

Note

EthoVision XT reads the settings from the camera driver software. For a specific EthoVision XT experiment you can override the values of video resolution and frame rate values that are stored in the driver, not other settings; see page 45. The maximum frame rates have been measured with a 96 well plate setup. Other values may be optimal in other setups.

1 User Set 1 is the default User Set in most applications. User Set 2 is pre-

selected if you purchased a 12-mm lens. User Set 3 is pre-selected if you purchased a 8-m lens.

2 For User Set 2, Binning mode must be Summing. For other User Sets

either option has no effect with binning equal to 1.

Table 1 Overview of predefined User Sets in the camera driver software and

associated video frame rate, video size and required camera lens.

Resolution and

maximum frame rate

1280 x 960, 30 fps 640 x 480, 60 fps 800 x 600, 60 fps

Camera lens

12 mm 12 mm 8 mm + 0.5 mm spacer ring Settings in Pylon Viewer

User Set1

User Set 1 User Set 2 User Set 3

Pixel Format

Mono 8 Mono 8 Mono 8

Analog Gain

Center X and Center Y

Horizontal binning,

Vertical binning2

1, 1 2, 2 1, 1

Exposure TIme (Abs)

in microseconds 3

4000 2000 4000 Settings in EthoVision XT

Resolution

1280 x 960 640 x 480 800 x 600

Frame rate (fps)

Color space

Y800 Y800 Y800 3 For all User Sets: Enable Acquisition Frame Rate must be selected.

Adjust the camera settings in EthoVision XT

In EthoVision XT, choose Setup > Experiment Settings and click the

camera button. Adjust the settings according to the table on the previous page.

For details, see Adjust camera Settings in EthoVision XT in the

EthoVision XT Help.

Adjust the camera settings in Pylon Viewer

You can also adjust the camera settings directly in the camera software Pylon Viewer. Adjust the settings according to the configuration you

want to use in Table

1. First, choose a video resolution and frame rate combination, then mount the recommended camera lens, and next make the appropriate settings in Pylon Viewer. Finally, adjust the appropriate settings in EthoVision XT.

For more information about Pylon Viewer, see the Configure the digital

camera in the EthoVision XT Help.

Pixel format (column B inTable

1).

Analog gain (column C in Table

1).

Center X and Center Y options (column D in Table

1).

Horizontal and Vertical binning (column E in Table

1).

Acquisition frame rate and Exposure time (column F in Table

1).

tip To preview the camera image, click the Continuous Shot

button on the toolbar.

tip You can increase the Analog gain to 2 if you need a brighter camera

image. However, the image noise will also increase, which may influence tracking.

To save the settings, click the Stop button and open the

Configuration Sets item. From the Configuration Set Selector

list, select the User Set you want to save the settings to. Next to User

Set Save, click Execute. Select the User Set you want to use at a daily

basis. From the Default Startup Set list, select the User Set of your

choice.

Camera view

Check that the camera view is correct by placing a wellplate in the DanioVision Observation Chamber. Make sure that: The well plate is in the middle of the field of view, not rotated or skewed. If not, see page 125. The well plate is in focus. If not, operate the focus ring of the camera lens. Fixation screws of all rings on the lens are tightened. The aperture is chosen such that the image appears slightly overexposed. With water in the well plate, the image is fine. When you create an EthoVision XT experiment, check that the video Resolution, Video frame rate and Color space are as in Table 1 (page 29) for the User Set you want to use. See the next chapter and also Fine camera adjustments on page 122.

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Source: Reference Manual - DanioVision DVOC-0041