Training Log: Oculina Imaging & Sampling Protocols

Purpose:

The goal of this training was to provide me with the tools to build a pipeline to collect chlorophyll from image data. On this dive, we took images of Oculina off the coast of Sdot Yam. Once the images were collected, we also collected physical samples. The goal is to build an image processing pipeline that has the same results as lab chlorophyll processing techniques.

1. Camera & Strobe Settings

Instructions from Hagai Nativ

Equipment:

Camera: Canon G7 X MK III, Nauticam Housing

Strobe: Sea&Sea YS-D3 DUO DS-TTL RC

Camera Imaging Settings

  • Mode: Manual
  • ISO: 200 (do not use Auto)
  • White Balance (K): 5400 (matches the color of the strobe)
  • Shutter Speed: 1/200
  • Aperture: f/11

Strobe Setup & Mechanics

  • Positioning: The strobe will be set in the water. Power depends on distance, but usually starts at half power.
  • Connection: The strobe cable connects to the port on top of the housing lens.
  • Batteries:
    • Requires 4 AA batteries (loaded via the back).
    • Note: Make sure to lock the seal when replacing the cover.
    • Capacity: ~300 images at full power.
    • Use fresh batteries.
  • Activation:
    • Housing: Use the switch on the left side of the housing to flip up the built-in flash.
    • Note: The flash can be turned on underwater, but cannot be retracted once submerged.
    • Software: The strobe can be turned off via the camera’s flash button if needed.

Flash Settings (In Camera)

  • Flash Mode: Manual
  • Shutter Sync: 1st Curtain
    • (1st curtain = flash fires when curtain fully opens. 2nd curtain = flash fires as curtain begins to close).
  • Flash Output: Minimum (Important)
  • Red-eye Lamp: Off (Important)

Shooting Technique

  1. Strobe Angle: Angle the strobe to be parallel to the camera. Do NOT angle it directly at the sample. This allows light to bounce away from the sensor and reduces backscatter.
  2. Strobe Controls:
    • Right Wheel: Exposure value / Strobe power.
    • Left Wheel: Mode.
    • Center Light: Red indicates ready to fire.
  3. Standard Settings Used:
    • Power: 5.6 (Right wheel, top center, green light).
    • Mode: Flash mode (Left wheel, bottom center, green light).
    • Note: Use the same strobe power across all images.
  4. Quality Control:
    • Use the Info button to inspect the histogram after shooting.
    • Blinking pixels = Overexposed (Unusable/Unrecoverable).
    • Rule of Thumb: It is better to be underexposed than overexposed. The histogram should be weighted to the left.
    • Focus Warning: Zooming in can disrupt the autofocus on this camera.

2. Coral Imaging

Instructions from Dr. Derya Akkaynak (Performed on January 4th 2026)

  1. Take good enough photos to make a 3D model of the coral colony. There should be a color chart (it can be any chart for now) that appears in at least 2 frames. Get as close as needed, since it’s a single colony, we only care about the coral and none of the background.

  2. In the field, repeat the same task with strobes, and then turn off the strobes and use just natural light (note the depth you are at).
  3. Repeat the same thing in the lab (with the same color chart).
  4. In all sessions, the color chart should be the same one. It should be uniformly illuminated, not under shadow or glare.

Data Access: Photos captured of the two Oculina samples can be accessed here: https://drive.google.com/drive/folders/1ISvIgQ05h-ayrNQD3o1Le3rE7a913BmA?usp=sharing

3. Physical Sample Collection

(Performed on January 4th 2026)

Protocol

  1. Collection:
    • Collect chlorophyll samples from the field using a hammer and chisel.
    • Place each sample in its own labeled bag.
  2. Transport:
    • Preferred Method: Use a dry shipper to flash freeze the samples and transport them frozen.
    • Alternative: Transport to the lab while submerged in seawater.
    • Ensure every individual coral sample is in a small plastic bag with relevant details written directly on the bag.
  3. Storage:
    • If present, drain the water out of the bag,
    • Place samples in the -80°C freezer.
    • Consolidate the individual bags into a larger labeled box or bag.
    • Label the outer container with: Your Name, Date, and Sample Information.
    • Action Item: Inform the Lab Manager of the specific location of your samples in the freezer.

Author: Boaz Abramson

Laboratory: Mass Lab

Last Edited: February 5th 2026

Written on January 4, 2026