Chena River Chinook Salmon Study

Four members of the Chena Project (Mark Wipfli, Elizabeth Green, Megan Perry, and me, Jason Neuswanger) all gave talks at the national American Fisheries Society conference in Nashville from August 30th – September 3rd, 2009.  Below are some videos and software downloads related to my talk, Accessible 3-D video methods for in situ fish measurement and behavioral analysis.  My coauthors include the late Nick Hughes, and also Mark Wipfli and Lon Kelly.  Nick and Lon pioneered the application of 3-D video techniques to fish behavior several years ago, and this talk concerned recent advances to the method that make it more useful to many other researchers.  It now allows us to measure the lengths and locations of fish in 3D with sub-millimeter precision under ideal conditions, and close to that under most conditions.  People can use this software to do it without knowing the underlying mathematics or computer programming (although knowledge of those topics gives anyone more power to customize their work).

Fish Video Highlights

These are some of the prettiest moments from my two years filming the foraging behavior of juvenile Chinook salmon.  They include a variety of revealing situations that show how the fish react to important elements of their environment such as food and predators.

Here’s a recording of the VidSync software, with a yellow arrow (part of VidSync’s built-in annotation features) following one fish through the course of a feeding maneuver.  It rises up from its “focal point” where it watches for prey, grabs something tasty, then sees a big piece of debris and scoots over to try it out.  It spits out the debris and goes back to its focal point.

Here’s the 3D digitization of that maneuver:

This is the same thing, viewed from 4 different angles:

Here’s a different prey capture maneuver, from the 2010 symposium on salmonids in Luarca, added to this post on 5/23/2010:

Of course, we don’t study maneuvers like that just to generate slick animations for PowerPoint shows.  The real point is to look at how far fish are moving for prey, which can be combined with information about water velocity and what the other fish are doing to help answer some important scientific questions.  For example, how much energy are they expending to capture prey — energy that could otherwise go toward growth?  Who gets more food for less energy, fish in fast water or fish in slow water?

Another important topic for our Chena research is territoriality.  The upper limit to how many fish a habitat can support depends on how much food there is and how the fish use that food.  When there’s a group of fish, there are millions of ways a limited supply of food could be divided between them.  Studying territoriality tells us something about how many fish are likely to do well in a given situation, and how many might be left out and risk starvation.

For a simple sense of territories, you can see the fairly uniform spacing among the fish in this 3D snapshot of a school of fish as the movie circles around it:

However, one moment in time can’t tell us much.  It gets much more interesting when we look at where the fish are relative to one another over a longer period of time.  The video below, from the VidSync software, shows part of 10 minutes of footage I analyzed to see the feeding territories of 4 fish in this video.  Each arrow marks a prey capture, and fish has different-colored arrows.

Here are the 3D territories.  At first glance on the original video it seems like the fish are just in sort of a mixed-up mess, chasing whatever tasty thing they see.  Watching them carefully and mapping their feeding in 3D immediately reveals some very interesting biological information: they’re respecting each other’s personal space remarkably well, with no intrusions during these 10 minutes.  It’s exciting to see a method reveal such interesting information even without the benefit of the large sample size and statistical rigor that will accompany this video method in practice.

FishDLT and VidSync Software for Scientists

This software is a work in progress: lots of work, and lots of progress.  It works well enough that we’re using it to process real data right now, but the current version of FishDLT has some personality (i.e. glitches) related to flaky behavior of Mathematica’s variable scoping in DynamicModules.  I’m planning to shift most if not all of the user interface stuff (buttons and picture-clicking) form FishDLT into VidSync, which will solve that problem and double (or better) the speed with which most things can be done.  That upgrade will probably be done by the time any other users begin to apply it to their data.  However, if you want to get started right away using the demo video, and you run into problems, contact me and I’ll be happy to help.

Hardware and Software Information/Downloads

Contact

Feel free to email me (Jason Neuswanger) about anything related to this method or these programs.  My address is my first initial dot my last name at sfos.uaf.edu, all lower-case.  (I can’t just write out my email address online, or spam robots will flood my inbox.)