PHOTOGRAMMETRY & CORAL COLLECTION IN THE SOLOMON ISLANDS | EXPEDITION RE-CAP
- scuba_franny
- Nov 17
- 7 min read
Studying unexplored coral reefs from the shallow down to the mesophotic with Reefscape Genomics lab + Inkfish Expeditions in the Solomon Islands
SCUBA-DIVING FOR CONSERVATION SCIENCE IN THE SOLOMONS
Since the 1960s, scuba-diving has enabled scientists to study marine life in its natural habitats, leading to greater knowledge of ecosystems from the poles to the tropics[1]. In 2025, diving continues to be a valuable tool for marine conservation[2]. Advancements in technology, including rebreathers and submersibles, have increased access to fragile deep reef habitats and enable data collection with minimal disturbance. Other innovative monitoring methods—like 3D photogrammetry and genomic analysis, continue to support the evolution of marine science.
[1] Lang, Michael A.; Marinelli, Roberta L.; Roberts, Susan J.; Taylor, Phillip R. (2013). Research and Discoveries: The Revolution of Science through Scuba. Smithsonian Institution Scholarly Press. Book. https://doi.org/10.5479/si.1943667X.39
[2] Marques, S. D. (2025). Scientific diving is a valuable tool for research into the underwater world. Jornal da Universidade, n. 230.
This summer, Francheska ‘Scuba Franny’ Krysiak conducted scientific dives to study marine ecosystems both at home in Canada and abroad in the Solomon Islands. During the Solomons expedition, I volunteered with the Reefscape Genomics lab at the California Academy of Sciences to collect samples of over 200 individual corals from the upper mesophotic zone, between 40 to 60 meters. Along with the other divers, I gathered data on coral recruitment using fluorescence videography and captured thousands of photos for 3D modelling through photogrammetry. Lastly, my photography was used for science communication in daily expedition logs, and engagement with online audiences through weekly expedition updates on social media.
After 42 hours of travel from Canada to Honiara, the capital of the Solomon Islands, I joined the Reefscape Genomics (RG) lab aboard the R/V Hydra for Leg 3 of Inkfish Expeditions’ 4-month scientific endeavor in the South Pacific to document never-before-explored coral reefs. Leg 3 of the expedition, led by lead scientist Dr. Pim Bongaerts of the RG lab, focused on characterizing the biodiversity and ecology of shallow and mesophotic coral reefs across 5 distinct study sites.
NATURE’S LIVING LABORATORIES
RENNELL ISLAND AND THE INDISPENSABLE REEFS
Three of the five study sites were at Rennell Island, the world’s largest raised coral atoll. It was designated as a UNESCO World Heritage Site in 1998, as it encompasses marine, coastal and forest ecosystems. In 2013, it became the only site in the Pacific on UNESCO’s Danger List due to commercial logging and mining, as well as invasive rats. Then, in 2019, a bulk carrier carrying bauxite ore ran aground in Kangava Bay, causing an oil spill. During this expedition, we conducted several dives in Kangava Bay but we did not observe any signs of the lingering oil spill on the reef.
The Reefscape Genomics Lab uses underwater 3D imaging and genome sequencing to advance the understanding of coral reef biodiversity. The lab also aims to address critical knowledge gaps for conservation and restoration efforts, and inspire the next generation of environmental stewards. It is based at the California Academy of Sciences, a non-profit natural history museum and aquarium with a mission to “regenerate the natural world through science, learning and collaboration”. The Academy has one of the largest scientific dive programs in the world with approximately a hundred divers, including local volunteers, aquarium biologists, and a team of highly specialized rebreather divers documenting biodiversity in remote locations.
In addition to our dives at Rennell, we undertook a 24-hour crossing to the Indispensable Reefs — an even more remote location located more than 50 km from the nearest landmass. These reefs are comprised of three consecutive atolls stretching over 100 km in the Coral Sea. They are exceptionally isolated and biologically rich, making them a valuable natural laboratory for scientific research. Despite their ecological importance and pristine condition, they currently lack formal protection as a designated marine protected area, though they are included in broader regional conservation initiatives across several nations around the Coral Sea.
DIVING DEEP WITH CUTTING-EDGE TECH
REBREATHERS, ROVs, AUVs, and SUBMERSIBLES
The exploration and study of mesophotic and deeper reef zones would not be possible without the advanced diving technology that allows scientists to push the boundaries. During this expedition, 4 scientific rebreather divers conducted research activities in the mesophotic zone - a deeper part of the coral reef, typically between 30-150 meters. This zone is home to some of the most unexplored and understudied reefs around the world, and it is featured in the world’s only mesophotic exhibit: ‘The Twilight Zone’ at the California Academy of Sciences. Mesophotic coral reefs have both sunlight-dependent (photoautotrophic) stony corals (Scleractinia) as well as heterotrophic organisms like gorgonians and octocorals (Octocorallia), black corals (Antipatharia), sponges (Porifera) and algae. These reefs hold an immense wealth of unique biodiversity, but they remain largely unexplored due to the complexity of accessing them – scientific rebreather divers are changing that!
What is a rebreather? Rebreathers are a technical type of SCUBA gear that recycles each exhalation, allowing the diver to re-breathe the gas. They are more efficient than traditional open-circuit SCUBA for deep, long dives. This technology extends dive times and depths, reduces risk of decompression illness, and minimizes impacts as bubbles/ noise from open-circuit SCUBA can disturb marine life.
During the expedition, lead scientist Pim joined sub team leader Marc and media expert Julz Braatvedt in an Inkfish Expeditions’ submersible to dive to 300 meters. They collected data and samples from deep reef zones beyond the reach of standard scientific diving. The ecosystem at these depths was strikingly different, with photosynthetic coral observed as deep as 90 meters. Submersibles play a key role in advancing our understanding of the ocean's most mysterious deep-sea habitats because they are specially designed vehicles that provide a safe, pressurized environment for scientists to explore the ocean’s depths.
PIXELS AND PATTERNS
INNOVATIVE IMAGING TO MAP THE CORAL REEF IN 3D
Scientific divers used Sony A7RV cameras in Nauticam housings to take up to 5,000 photos per dive, following a ‘mow-the-lawn’ pattern to ensure image overlap for high-resolution 3D reef reconstructions. The camera, mounted on an aluminum frame attached to an underwater scooter, was equipped with strobes, video lights, and custom electronics to record and get feedback on positioning (depth and sonar). This setup was used along five 25-meter transects at depths of 5, 10, 20, 40, and 60 meters across five study sites—resulting in approximately 25,000 images!
In addition, we used fluorescence videography at 40 and 60 meters to scan the benthos for juvenile corals to investigate coral recruitment at depth. This technique enhances visibility of early-stage coral recruits that are otherwise difficult to detect under natural light, allowing us to assess settlement patterns and potential regeneration in the mesophotic zone.
An underwater robotics team led by Dr. Oscar Pizzaro from the Australian Centre for Robotics conducted benthic imaging surveys using a Seeker-class Autonomous Underwater Vehicle (AUV) to complement diver-based photogrammetry. The AUV was equipped with high-resolution stereo cameras and a precise localization system integrating Doppler Velocity Log, UltraShort BaseLine, and Inertial Measurement Unit technologies.
This enabled accurate navigation along both pre-planned and adaptive survey paths. The AUV provided broader spatial context to the 25m x 4m diver-surveyed “boxes,” allowing the team to assess trade-offs between spatial resolution, coverage rate, and image quality. Additionally, the team used a Remotely Operated Vehicle (ROV) to help select study sites based on a rapid assessment of coral coverage at depth, prior to divers entering the water to deploy transects and outline the “boxes” at each study site.
GENES FROM THE SEA
TINY SAMPLES, BIG IMPACT
In addition to creating 3D maps of the reef, we collected minimally invasive samples of stony corals from both shallow and mesophotic zones. Scientific divers collected small coral fragments (<1 cm2) along transects from the surface down to 60 meters, placing each sample in its own individually numbered 1.5ml tube. Post-dive, samples were preserved in ethanol, with exchanges tracked over several subsequent days. While the sample processing involves meticulous work, these steps are essential for later genomic analysis which lays the foundation for research that follows.
To link the genomic data from the samples to spatial imagery in the 3D maps, each diver used both POV (point of view) and BEV (bird’s-eye view) cameras to record the locations of each coral sample collected. This supports the evaluation of the genomic data spatially and can also gather phenotypic information (e.g., growth, bleaching, etc.) of the individual corals. Each sample tells a different part of the story about the reef and the individual corals that inhabit it. By studying these corals, insights into the biodiversity of the ecosystem can be gained, and the information can be used to inform future conservation efforts.
FIELDWORK REFLECTIONS
During this expedition, I had the incredible opportunity to dive some of the most remote coral reefs I’ve ever visited— it was my furthest journey yet, and one I’m deeply grateful for. I learned new science diving techniques like photogrammetry, and I saw several species of reef fish that I had wanted to observe for many years.
For the first time in my professional diving career, I got to conduct working dives in the mesophotic zone alongside another woman, marine scientist and rebreather diver (and new mom!) Dr. Ale Hernandez — an experience that was both empowering and memorable. The whole RG lab team was amazing to learn from, and it was a great opportunity to help out with research I admire and am truly happy to support as a science diver!
I also had the amazing opportunity to meet and connect with the crew and personnel from Inkfish Expeditions. It was a joy to be surrounded by knowledgeable, hard-working, and fun individuals and I am grateful for the chance to be a part of the team for a few weeks!
While the fieldwork was rewarding, the journey continues for the RG lab team to analyze the data to better understand these unique marine environments. As for me, I’m excited for future expeditions and the discoveries still to come!
Comments