Camera calibration and reconstruction for fish experiments

The last few months I have been working hard on the sophisticated new experimental set-ups in the lab with which we will be able to get high spatial and temporal resolution tracking of large schools of fish, in tanks that are up to 3x3m in size!

To get highly accurate spatial data of the fish we need to correct for the distortion of the camera lens, which almost all lenses have to some extent. I just finished the script (in Python) that enables us to undistort the image from a camera using functions in opencv based on a video of a moving checkerboard.

Me calibrating a camera with a checkerboard pattern, with colours showing the output of my python script, with a school of 1000 moderlieschen in the background :)

Me calibrating a camera with a checkerboard pattern, with colours showing the output of my python script, with a school of 1000 moderlieschen in the background :)

It works pretty well already, even with non-optimal videos. Next step will be to stitch the videos of multiple linked camera’s.

Stickleback experiments with Schistocephalus

Recently I started a couple experiments related to parasite infection of Sticklebacks with Schistocephalus, a tapeworm with a fascinating life cycle that requires three separate host species. Our experiments focus on how the parasite affect the fish’s movements, its social interactions and positioning, collective behaviour, and survival in the context of predation.

Today, when moving fish around for experiments, I noticed one particularly bulged individual that, instead of a the smooth elongated body had the body shape of a brick! A clear sign of Schistocephalus infection. We put it down and measured its body weight, both before and after opening up its stomach cavity. What we found was not one, not two, not three, but four individual flatworms with a total weight of 55% of that of the fish! Incredibly how the fish could actually survive with such an immense parasite load.

Three-spined stickleback before and after removing four Schistocephalus worms

Three-spined stickleback before and after removing four Schistocephalus worms