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.

Last experimental work of PhD finished!

stickleback-testing-JollesToday I finished my last experiment that will be part of my PhD! I have been locked away in the lab for a couple weeks, testing hundreds of fish on their personality and collective behaviour, but now analysis and writing can fully start. I must have tested close to a thousand fish in the two and a half year since the start of my PhD, most of which are now enjoying a happy end of their lives back in the wild. I have all the data of a number of exciting projects that will not need me to go back to the lab for at least half a year but I can actually not wait to test my next hypothesis! The three-spine stickleback is an amazing species to work with and I will definitely continue working with them after my PhD.

New video of three-spine stickleback in my lab

Today I took a new video of the stickleback in my lab to use to talk about my work and these amazing fish during public lectures and conference presentations!

What you can see really well in this short little video is the large morphological and behavioural variation of the fish. Despite being similar in age the fish are quite different in body size as well as their colouration. Also pay attention to the spines, you can see individual fish often raising their spines at the moment they feel threatened by my presence.

One of the social housing tanks I use to house some of my hundreds of little stickebacks

One of the social housing tanks I use to house some of my hundreds of little stickebacks

Renovating my lab

IMG_0635I have been locked away in my lab for most days in January/February this year for a total lab renovation to have a fully automated testing set-up that enables me to test large numbers of fish in very little time.

Now everything is in full working order I will write some more detailed blog posts about it in the near future! My first two student projects that used the new set-up worked out great and I am excited to go large scale soon!

Timelapse video of a boldness session

Continuing on from yesterday’s post about the personality testing for boldness, today I made a time-lapse video from one of the sessions to get a quick overview of the actual running of the experiment. For most experiments I work with 40-64 fish per batch and potentially run multiple batches. Therefore, to be able to test all fish on the same day I test 8 fish simultaneously in 8 separate lanes for one hour and run 8 consecutive sessions in a row.
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Home to work at my Cambridge lab

I am working on a short film about my research at the University of Cambridge that will showcase the fascinating aspects of animal personality as well as depict a day in the life of a behavioural scientist, from wading through wild streams catching sticklebacks to doing experiments in my underground lab in the centre of Cambridge. As inspirations for the short, I will be posting short clips here on my blog. This first one shows my daily commute from my house out in the west of Cambridge to my basement laboratory at the department of Zoology.

Just another (cold, 12 hour) day in the lab

Often I wear a thick winter coat when working in my lab but today I forgot it.. Just on a day when I have to spent 12 hours in the lab..

Often I wear a thick winter coat when working in my lab but today I forgot it.. Just on a day when I have to spent 12 hours in the lab..

Although most people will probably be enjoying another warm and sunny summer day (unless you live in Britain), I will be in my underground fish lab for 12 consecutive hours. It is about 11 degrees Celsius down here to keep the water housing the hundreds of sticklebacks nice and cool so they won’t get into breeding state and show the associated changes in territorial/mating behaviour. I am however feeling a bit chilly as well as I forgot my coat today.. By typing this I hope at least my hands and fingers will warm-up a bit.

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