We release individual fish in the center of arena and videotype its moton until it reaches a wall of arena. We need a software to calculate an angular orientation of fish track relative to North-South axis, especially at the moment when fish reaches the wall.
I may not have understand the question perfectly and I am not aware of a software package capable of doing this automatically, but in case you can manually obtain the angle data you will only need to use circular statistics to analyze your experiment. I know that that is possible with PAST and R for instance.
But, something to obtain the data automatically I do not know whether it exists.
Thank a lot for suggesting PAST, we certainly will try it!
If you were asking about tracking. Here is something you might want to look into: http://canmove.lu.se/birdoritrack/download
Hi Valentin, have a look at the work done by both P. Domenici and R. Blake on fish kinematics and locomotion in the Jounal of Exp. Biology, links here:
http://jeb.biologists.org/search?author1=R+Blake&sortspec=date&submit=Submit
http://jeb.biologists.org/search?author1=P+Domenici&sortspec=date&submit=Submit
The methods in these papers might be able to help you out. I used circular statistics in Matlab to calculate radius from the "Circle by Pratt" function as a proxy for angle in my work measuring maneuverability (not published yet sorry).
Good luck.
Hi Valentin,
Do you need a software to track the fish from the video, or you already have the trajectory and you only need to analyze it? For the tracking part we have recently developed multiwelltracker:
http://www.multiwelltracker.es/
Alfonso, we have a tracking program with a trajectory as an output. What we need is a program which automatically divides the trajectory into user-defined number of fragments and calculate a mean direction of each fragment.
For the analysis I'm afraid I do not know any open-source tool. My former laboratory (http://www.neural-circuits.org/) is developing one, idSocial. It is centered on social behavior, but might incorporate what you need. But it is not released yet, it will probably take a couple of months to have it ready. You may contact Gonzalo Polavieja and/or Robert Hinz to get more details about it.
Good luck!
Valentin,
There are a few libraries in the statistical programming language R that can do a variety of circular statistics. The two most common ones are CircStats and circular. An example of some circular statistical analysis can be found for example in these two papers:
http://www.ncbi.nlm.nih.gov/pubmed/18051648
http://dx.plos.org/10.1371/journal.pone.0051100
Hope this helps
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