The research software on this page is under ongoing development by Jason Neuswanger. VidSync requires Mac OS X 10.5 or 10.6, and FishDLT requires Mathematica 7.
Both programs were created as a tool for Jason’s Ph.D. work and Megan Perry’s M.S. work on juvenile Chinook salmon in the Chena River in central Alaska. Megan uses them to measure fish, while Jason is using them to analyze foraging behavior and competition in a manner similar to the work of Hughes & Kelly (1996) and Hughes et al. (2003). However, the methods are applicable for making precise 3D measurements in general, provided the target is visible in both cameras and the cameras have been calibrated. Under ideal conditions, the system can measure fish close to the cameras to the nearest millimeter, and can usually get within a few millimeters on fish close enough to see well. Users viewing larger fish far away in extremely clear water (or those studying things on land) could expect slightly larger absolute errors, although the errors as a percentage of body length should remain comparable to ours.
VidSync Details
VidSync is an application for Mac OS X 10.5+. It’s used to synchronize the left and right videos, play them back in sync, mark them up with symbols to annotate the things you want to measure, and output synced screenshots for analysis in FishDLT.
Most applications of this form would be Mathematica “libraries,” files with a .m extension, but using a library worsened some quirky malfunctions related to the user interface. Instead, there’s a Mathematica notebook file, FishDLTEnvironment.nb, which you can open, choose “Evaluate Initialization Cells,” and close. Then you perform your analysis using FishDLTUsage, which has a few simple commands to launch the relevant graphical interfaces.
FishDLT Details
FishDLT is a Mathematica 7 notebook used to calibrate and analyze the video stills captured by VidSync, then format the output in a presentable way.
Demo Download and Directions
The documentation for this software will be very much improved soon.
This download includes both VidSync, which you can just drag into your Applications folder on a Mac, and two FishDLT files, FishDLTEnvironment and FishDLTUsage. It also includes two small example video files. Normal videos don’t come out of the two cameras synchronized, so the user has to do it manually based on some event visible simultaneously in both cameras (flicking on an LED light works well). However, the demo videos start at the same point from already-synchronized files, so you just need to load them (File -> Load Left Video, etc) and check the “Lock Synchronization” button and you can use the simultaneous playback features properly.
Hardware Description and Tips
We’ll be updating this section shortly with much more detail and many more pictures. This is a sample of the kind of information we’ll provide.
The High-Definition (HD) Camera System
We use two Sony HDR-SR12 video cameras that record 1920×1080i video directly to the hard drive. They’re in Ikelite housings fitted to that camera model, which have space for a battery that lasts about 2 hours in each camera. They use special Zen Underwater wide angle lenses, which replace the standard flat Ikelite ports with a wide-angle lens with excellent optical quality. We use one of the “lipstick cameras” described below as a viewfinder.
The trickiest part about this camera system is focusing, because in our system we can’t look down through the camera housing to see how it’s worked out. We’ve got to manually focus it, but the manual focus distance displayed on the cameras isn’t the real focused distance of the system, because there are some major changes going through the wide-angle lens and the air-water interface. We’ve worked out a relationship for our system in which fish at about 0.5m need to be focused at about 2m, fish at 1m should be focused at 4m, etc. We can share this with interested users of an identical system, or share advice about deriving your own focus relationship.
The Standard-Definition (SD) “Lipstick” Camera System
For the standard-definition system, we contacted the Xtreme Recall company, and they sent us the wiring for a custom dual “lipstick camera” system for a reasonable price. More details soon.
The Quadrat
This is a cube made of Lexan polycarbonate, with black silicone points embedded on a carefully spaced grid generated by a computer graphics program and printed out on transparency paper during the construction. More details soon.