LARGE-AREA IMAGING

Photography and other forms of imaging offer powerful ways for us all to learn about the world around us. We often use photography to provide a snapshot of one location, at one point in time, for us to return to again in the future. And enhanced forms of imaging, like microscopy or satellite photography, provide means of seeing nature at scales or from perspectives that are not possible with the human eye alone. As we seek to learn more about how coastal marine ecosystems are structured and are changing, we have been able to leverage new imaging technologies to widen our perspectives in both space and time.

Large-area imaging is the approach of creating virtual 3-dimensional replicas of natural landscapes using digital photography. By collecting large numbers of images taken from multiple perspectives, modern computational workflows assist in creating accurate and precise representations of the landscape (or in the case of coral reefs, of the seascape). These representations are sometimes called ‘digital twins’, as they provide a model of the surveyed landscape that can be explored within the digital environment for years to come. 

Our team has been working closely with partners in the Jacobs School of Engineering at UC San Diego, along with collaborators worldwide, to build a productive and accessible workflow for using large-area imaging to study the ecology of coral reefs. We recognize that there are multiple steps in the reliable and repeatable use of large-area imaging, which we generalize into four steps: (i) image acquisition, (ii) model construction, (iii) data visualization and analysis, and (iv) data curation and access. Each step offers unique challenges as well as unique opportunities for innovation. 

While our team’s expertise lies in the use of large-area imaging to explore fundamental and applied questions about marine ecology, we remain active in advancing the technology and increasing access to the world of colleagues interested in using these approaches for science and stewardship of reefs globally.

LARGE AREA IMAGERY COLLECTION + PROCESSING

STANDARD OPERATING PROCEDURES

Our team has been working to build a pipeline for employing large-area imaging to improve the quality and volume of coral reef demographic data. This effort has involved R&D efforts of ecologists, engineers, and field practitioners. 

Image

  • Sandin, Stuart A., Zgliczynski, Brian J., Bonito, Lindsay T., Edwards, Clinton B., Pedersen, Nicole E., Sullivan, Christopher J., Eyanud, Yoan, Petrovic, Vid (2023). Large Area Imagery Collection & Processing Standard Operating Procedures - Version 3.0 (2021). In Standard Operating Procedure Documents for Coral Reef Ecological Monitoring Collection. UC San Diego Library Digital Collections. https://doi.org/10.6075/J09C6XMJ.

The webinar covers the motivation and rationale of photomosaics, the steps involved with collecting the data and creating the product, and examples of how the technology has been used by restoration practitioners. Guest speakers include Art Gleason, Stuart Sandin, Nicole Pedersen, Alex Neufeld and Lisa Carne.

Field imagery collection, processing, and samples of 3D coral reef models from a few islands. 

A demonstration of annotated coral genera using a coral reef orthomosaic from Palmyra Atoll (Site FR3, 2014).

Select Publications in Large-Area Imaging

  • McCarthy, O. S., Contractor, K., Figueira, W. F., Gleason, A. C. R., Viehman, T. S., Edwards, C. B., & Sandin, S. A. (2023). Closing the gap between existing large‐area imaging research and marine conservation needs. Conservation Biology. https://doi.org/10.1111/cobi.14145. 

  • Edwards, C. B., Viehman, T. S., Battista, T., Bollinger, M. A., Charendoff, J., Cook, S., Combs, I., Couch, C., Ferrari, R., Figueira, W., Gleason, A. C. R., Gordon, S., Greene, W., Kuester, F., McCarthy, O., Oliver, T., Pedersen, N. E., Petrovic, V., Rojano, S., Runyan, H., Sandin, S. A., & Zgliczynski, B. J. (2023). Large-area imaging in tropical shallow water coral reef monitoring, research, and restoration: A practical guide to survey planning, execution, and data extraction. NOAA National Ocean Service, National Centers for Coastal Ocean Science. NOAA Technical Memorandum NOS NCCOS 313. https://doi.org/10.25923/5n6d-kx34.

  • Runyan, H., Petrovic, V., Edwards, C. B., Pedersen, N., Alcantar, E., Kuester, F., & Sandin, S. A. (2022). Automated 2D, 2.5D, and 3D segmentation of coral reef pointclouds and orthoprojections. Frontiers in Robotics and AI. https://doi.org/10.3389/frobt.2022.884317. 

  • Sandin, S. A., Edwards, C. B., Zgliczynski, B. J., Pedersen, N. E., Smith, J. E., & McNamara, D. E. (2022). Evidence of biological self-organization in spatial patterns of a common tropical alga. The American Naturalist. https://doi.org/10.1086/721323.

  • Sandin, S. A., Edwards, C. B., Pedersen, N. E., Petrovic, V., Pavoni, G., Alcantar, E., Chancellor, K. S., Fox, M. D., Stallings, B., Sullivan, C. J., Rotjan, R. D., Ponchio, F., & Zgliczynski, B. J. (2020). Considering the rates of growth in two taxa of coral across Pacific islands. Advances in Marine Biology. https://doi.org/10.1016/bs.amb.2020.08.006.

  • Kodera, S. M., Edwards, C. B., Petrovic, V., Pedersen, N. E., Eynaud, Y., & Sandin, S. A. (2020). Quantifying life history demographics of the scleractinian coral genus Pocillopora at Palmyra Atoll. Coral Reefs. https://doi.org/10.1007/s00338-020-01940-8

  • Pedersen, N. E., Edwards, C. B., Eynaud, Y., Gleason, A. C. R., Smith, J. E., & Sandin, S. A. (2019). The influence of habitat and adults on the spatial distribution of juvenile corals. Ecography. https://doi.org/10.1111/ecog.04520

  • Edwards, C. B., Eynaud, Y., Williams, G. J., Pedersen, N. E., Zgliczynski, B. J., Gleason, A. C. R., Smith, J. E., & Sandin, S. A. (2017). Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef. Coral Reefs. https://doi.org/10.1007/s00338-017-1624-3.

Keywords: Structure from Motion; SfM; photogrammetry; orthomosaic; photomosaic; artificial intelligence; TagLab; Viscore