Experimental setups#
Zebrafish (in the lab)#
Polavieja Lab setup for juvenile zebrafish (same as Supplementary Figure 3 of the paper)#
The main tank was placed inside a box built with matte white acrylic walls (a). The lighting was based on infrared and RGB LED strips. A cylindrical retractable light diffuser made of plastic ensured homogeneous illumination in the central part of the main tank. A 20 MP monochrome camera (Emergent Vision HT-20000M) with a 28 mm lens (ZEISS Distagon T* 28-mm f/2.0 Lens with ZF.2) was positioned approximately 70 cm from the surface of the arena. To prevent reflections of the room ceiling, we used black fabric to cover the top of the box (b). We used this setup to record zebrafish in groups and in isolation. Videos of groups of 10, 60 and 100 fish were recorded in a custom-made one-piece circular tank of 70-cm diameter, designed in-house. The tank was filled with fish system water to a depth of 2.5 cm. The circular tank was held in contact with the water of the main tank approximately 10 cm above a white background to improve the contrast between animals and background (c). A water-recirculating system equipped with a filter and a chiller ensured a constant water temperature of 28 °C.
In this link you can find the list of the different parts needed to build the experimental box, with its dimensions, and links to the Thorlabs webpage.
A simple and cheap way to build a cylindrical light diffuser is with two plastic gymnastic hoops and a white translucent plastic shower curtain, joined with plastic zip ties.
The Scientific Hardware Platform at the Champalimaud Foundation helped us design several parts of the setup. A key piece is the circular tank: it is made from a single piece of acrylic, so it has no straight edges or corners. This prevents the fish from gathering in the corners, which is common in rectangular tanks.
The tank models we have used in the lab:
We always place the transparent tank inside a white matte acrylic copy of the same tank. The white tank acts as the background and increases the contrast with the animals. The two tanks are 2 to 5 cm apart vertically, and the white tank is also filled with water, which prevents reflections of the animals on the walls of the tank.
Zebrafish (in internal summer courses)#
For the course of the INPDP PhD programme in the Champalimaud and for the CAJAL behavior summer courses we designed an easy-to-replicate setup, so that 10 of them could run in parallel in the teaching lab.
INPDP and CAJAL sessions setup#
The setup consists of an experimental box of 80 x 110 x 70 cm with white matte walls and a white blackout curtain (see panel above). Unlike the lab setup above, which uses a diffuser, this setup uses indirect light from 4 white LED spotlights reflected on the white walls (see panel b above).
The arena is a custom-made 30 cm circular tank made of transparent acrylic (see panels b, d and e above). To improve the contrast between the animals and the background, it sits inside a custom-made 30 cm circular bowl of white matte acrylic (see panels d and e above). Both are held inside a rectangular plastic tank by a custom-made white acrylic holder. For long recordings, the rectangular tank can also hold water with an aquarium heater and a pump to keep the temperature stable (after some time, convection brings the water in all containers to the same temperature).
To hold the experimental tank on a stable surface, we built a custom-made acrylic platform that fits on top of the Thorlabs breadboard (see panel c above, see also the models here and here).
The arena is recorded from above with a PointGrey Chameleon 3 camera and a Fujinon 2.8-8 mm f/1.2 lens, connected to a computer outside the box (see panel a above). The camera is mounted on a Thorlabs pole fixed to a 30x30 cm Thorlabs breadboard (see panel c above).
Zebrafish (in external summer courses)#
For the 2018 QBIO Summer research course @KITP, UCSB we designed a portable setup that fits in a protective flight case:
QBIO course setup#
Download the model, the dimensions of the aluminum rails structure, the 300mm circular tank model, and the tank holder and light diffuser frame models.