Example field protocol

The following is just one example of a field protocol for collecting VidSync data. This protocol was used to collect footage of juvenile Chinook salmon feeding behavior in the Chena River, Alaska, during Jason Neuswanger’s Ph.D. research. Everybody’s protocol will differ based on study needs and equipment, but it is definitely useful to write down all your planned steps to avoid forgetting things, at least on the first few field excursions.

Evaluate site suitability. Individual protocols should list study-specific biological criteria as well as video quality criteria (e.g., lighting, field of view, background, contrast, obstructions between cameras and fish).
Verify lenses are clean of debris or residue.
Clean and re-grease the waterproof housing O-rings.
Turn the cameras on.
Write down the current time and remaining battery life if the cameras are to be deployed until batteries die.
Manually focus both cameras for the intended subject distance. A camera’s displayed focus distances aren’t correct for shooting through a housing into water; develop custom focus distances by testing beforehand.
Place cameras in housings and double-check fasteners.
Place a desiccant packet in the housings to prevent condensation-caused fogging in cold water.
Verify the zoom setting on both cameras (usually, widest angle). Keep zoom and focus fixed hereafter.
Start recording. Write down the time, so video timecodes can be linked to real times and noteworthy observations (e.g., a loud boat passing by).
Videotape a whiteboard with site name & date. This prevents confusion when naming or reorganizing video files. Site name may correspond to a GPS waypoint name.
Blink an LED light once, in view of all cameras, for synchronizing video clips in VidSync.
Videotape the checkerboard in each camera separately with both board and cameras submerged. It should face each camera as flatly as possible, and be far enough away to be in focus, but close enough to fill the screen. Avoid the uneven lighting of bright sunlight under a wavy surface, and seek to film in bright shade.
Videotape the calibration frame with similar lighting, with both frame and cameras as still as possible, making sure both faces are close enough to the cameras to take up a reasonably large portion of the screen. Only one ideal shot is needed, but try many poses to assure a good view. Allow time for settling of any disturbed detritus that might block the view of the frame nodes.
Verify that the cameras are still set properly, double-checking recording status, zoom, and focus.
Deploy the cameras to observe fish, securing the system as needed.
Individual protocols should describe additional measurements (e.g., drift net samples, temperature measurements, above-water site photographs) to be taken during filming at each video site.

Fancier example

This was the protocol my team use during my postdoctoral research in Alaska through the University of Georgia, studying the behavior of 3 different species of drift-feeding fish using VidSync. If the reference to cous cous in step 1 takes you by surprise, it’s because we tested many materials and found that Israeli cous cous (a totally different substance from regular cous cous) after soaking in water made for exceptionally good, near-neutral-buoyancy, highly visible tracers for computing water velocity fields in VidSync. In this study, we were using two Nikon D5300 DSLR cameras wired to Atomos Ninja HDMI recorders on shore. I would not recommend that specific setup to my worst enemy, but we collected great data. As in the first example, this protocol is not directly useful to anyone else on its own, but it might serve as a good example of the kinds of details to think about and write down before going into the field (and throughout pilot work in the field) on your own studies.

  1. Start soaking Israeli cous cous and chopped marabou velocity tracers at least an hour in advance of when they’ll be used.
  2. Find a good fish to film (or Chinook school) and remember its exact location.
    1. If necessary, use the GoPro on carbon fiber rod to find feeding fish and identify their exact focal point in relation to underwater landmarks.
    1. Unless filming Chinook, try to find a fish is feeding by itself with minimal visible influence from nearby competitors.
  3. Prepare drift nets:
    1. Find a representative location and pound in the rebar for it, somewhere the net(s) can be handled without scaring the fish.
    1. Use the PVC pole to measure depth at the drift net site. Record it now and use it later to determine where to place the net(s) on the pole.
    1. Fix the drift nets to the pole, but don’t place them yet. Write down the position of the top of each net (middle of the top tube) on the pole.
  4. Prepare the cameras (starting outside their housings). The order of some of these steps (power / live view / connections) is very important for the cameras to run properly.
    1. Fix the cameras tightly onto their crossbar and verify that the joints are tightened so they won’t wobble (but don’t fix the crossbar to the main mount yet).
    1. Make sure the housing O-rings are clean.
    1. Make sure the camera lenses are really, really clean. Smudges really show up with short-focused fisheye lenses.
    1. Electrical tape a desiccant packet inside the right wall of the housing.
    1. Connect the power and HDMI cables to the housing and generator.
    1. Turn on Atomos units and connect them to the HDMI cables.
    1. Power the cameras on. Settings as follows:
      1. 1080p30
      1. Movie quality: High
      1. Manual movie settings: On
      1. HDMI: Output resolution 1080p, device control Off
      1. If using Samyang lenses with ‘A’ mode, set aperture to f/22, which gives the camera electronic control of the real aperture.
      1. Lens and focal length strategy:
        1. Chena – Try to place the cameras 20-35 cm from the fish, with the 8 mm Samyang lenses focused at 1’. If required subject distances are 40+ cm, use the Tokina at 17 mm. Try to avoid distances of 60+ cm, although 60-80 might be okay with excellent lighting and backdrop.
        1. Panguingue – When bathymetry and focal points allow, try for subject distances in the 30-60 cm range with the Samyang lenses. For 60-100, use 17 mm, or maybe 13 on the low end of the range if there are field-of-view concerns. Try to avoid distances of 100+ cm, although 100-130 should be workable at 17 mm.
        1. Clearwater – For fish with very predictable focal points, try for subject distances in the 40-80 cm range with the Samyang lenses. In the 80-120 range, use the Tokina at 13 mm. Beyond that, use 17 mm. Try to avoid distances of 200+ cm, although 200-250 is workable at 17 mm.
        1. All sites – Use electrical tape to secure the focus and focal length rings so they can’t accidentally slide.
      1. Focus strategy:
        1. If using the Samyang 8 mm, focus at 1.2’ for Dollies and Grayling, or 1’ for Chinook.
        1. Always focus the Tokina lens on the “1” in “1.25,” regardless of focal length.
      1. Exposure strategy:
        1. Inconsistent lighting, such as thick passing clouds or deep, moving tree shadows: Use ‘A’ mode, f/11. Otherwise, use manual exposure as described below.
        1. Consistent, direct sunlight: f/11, 1/500 s, ISO 1250
        1. Consistent, brightly overcast: f/11, 1/320 s, ISO 1600
        1. Consistent, shaded from direct sun but 50%+ bright skylight: f/11, 1/250 s, ISO 1600
        1. Consistent, heavy shadows: f/8, 1/60 s, ISO 6400
        1. In general, be willing to go up to ISO 6400 before dropping shutter speed below 1/200 s. But be willing to drop down to (and not below) 1/200 s before taking ISO above 3200.
        1. Remember aperture cannot be set while live view is on. Toggle it off, set the aperture, then toggle it back on.
    1. Electrical tape the focus (and zoom, for Tokina) sliders in place.
    1. Turn on live view.
    1. Verify that the cameras are sending the HDMI feed plain video without a bunch of stats; cycle the ‘Info’ button to fix if necessary.
    1. Plug in the red override cable stub.
    1. Seal the camera housing, being careful of the cables and making sure the bottom one is in its holder.
    1. Fix the crossbar to the main mount using a 9/16” wrench and lock washer.
  5. Position the cameras to record the fish.
  6. Make sure the fish come back into position and the camera’s pointed well. If manually exposing, double check exposure and adjust shutter speed with housing knobs if needed.
  7. Press record on both Atomos Ninjas at the exact same time (makes syncing easier).
  8. Write down the time the cameras started recording.
  9. After the fish have settled into normal feeding, place the drift nets:
    1. Drop them over the pole.
    1. Record the time they were dropped in.
    1. Record the velocity of the water entering each net, in the horizontal and vertical center of either the left or the right half of the net.
  10. From this point on, avoid walking around at all upstream of the filming site / nets / fish so as to avoid artificially raising the amount of debris in the water.
  11. Leave cameras alone for about 2 hours to record the fish. Based on the 2015 videos we had processed by May 10, 2016, hitting our target of 100 foraging attempts per fish observed took anywhere from 4 to 8 minutes (Chinook), from 6 to 30 minutes (Dollies), and from 17 to 51 minutes (Grayling).
  12. Pull and process the drift nets before they begin to clog and back up significantly (typically about 30 minutes, dependent on velocity/debris).
    1. Record the time and velocity as before.
    1. Label Whirl-paks with the site code, YYYY-MM-DD-Nsite on the outside in permanent marker and in pencil on a piece of paper inside the bag.
  13. When finished, record post-observation water temperature and time.
  14. Try to catch the main fish we clearly observed on camera, for gastric lavage. While the fish are being caught:
    1. Write down the time each fish was caught (Panguingue/Clearwater), or the single time the trap was pulled or netting was done (Chena). If the fish was definitely caught off-camera, write ‘oc’ next to the time.
    1. Store the fish together in a safe container.
    1. Label Whirl-paks for each fish, both on the outside in sharpie and in pencil on a piece of paper inside the bag.
    1. Labels use the form “YYYY-MM-DD-Nsite Fish Nfish”
  15. Before processing fish, finish the video site and calibration data on-camera. Do not move the cameras at all until if/when it’s necessary for calibration:
    1. Get surface/depth data:
      1. If the surface is visible on camera, poke a twig down through the surface (or a branch full of twigs) throughout the visible part of the surface. Record the “surface-point” time.
      1. If the surface isn’t visible, or only barely so off in the distance, measure the depth at the fish location with a drift net PVC pole. Take the measurement, then use the bubble level to get the pole perfectly vertical. Right when it’s perfectly vertical, yank it up fast. Record “vertical-pole” time.
    1. Throw the cous cous and/or marabou velocity tracers such that they drift throughout the area the fish was using. Throwing cous cous far upstream helps filter out the less neutrally buoyant pieces. Try to release a small number (5-15) of particles at a time, and reach in or use a pipe to release some down near the bottom.
    1. Do the 3-D (checkered dot calibration), with minimal or no movement of the cameras from the observation position if possible.
    1. Do the checkerboard calibration for distortion.
  16. For each fish captured:
    1. Anesthetize it with Aqui-S (0.5 to 1 ml, i.e. cm3, per gallon H20). That equals about 1 mm in the bottom of the cap of our bottle, per gallon.
    1. Perform gastric lavage with the syringe (Chinook) or sprayer (Grayling/Dollies). Flush stomach contents directly into Whirl-paks (Chinook), into the drift net processing screen (Dollies), or into the big screen (Grayling), and transfer to Whirl-paks from there.
    1. Photograph the whiteboard with the fish code.
    1. Photograph it from both sides in a Lexan holding tube to measure length and match samples with fish on video. Find uniform lighting, and keep the face of the photo tank clean of water droplets and fog.
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