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Methods and measurement variance for field estimations of coral colony planar area using underwater photographs and semi-automated image segmentation

Abstract

Size and growth rates for individual colonies are some of the most essential descriptive parameters for understanding coral communities, which are currently experiencing worldwide declines in health and extent. Accurately measuring coral colony size and changes over multiple years can reveal demographic, growth, or mortality patterns often not apparent from short-term observations and can expose environmental stress responses that may take years to manifest. Describing community size structure can reveal population dynamics patterns, such as periods of failed recruitment or patterns of colony fission, which have implications for the future sustainability of these ecosystems. However, rapidly and non-invasively measuring coral colony sizes in situ remains a difficult task, as three-dimensional underwater digital reconstruction methods are currently not practical for large numbers of colonies. Two-dimensional (2D) planar area measurements from projection of underwater photographs are a practical size proxy, although this method presents operational difficulties in obtaining well-controlled photographs in the highly rugose environment of the coral reef, and requires extensive time for image processing. Here, we present and test the measurement variance for a method of making rapid planar area estimates of small to medium-sized coral colonies using a lightweight monopod image-framing system and a custom semi-automated image segmentation analysis program. This method demonstrated a coefficient of variation of 2.26 % for repeated measurements in realistic ocean conditions, a level of error appropriate for rapid, inexpensive field studies of coral size structure, inferring change in colony size over time, or measuring bleaching or disease extent of large numbers of individual colonies.

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References

  1. Bak, R. P. M., & Meesters, E. H. (1998). Coral population structure: the hidden information of colony size-frequency distributions. Marine Ecology Progress Series, 162, 301–306.

    Article  Google Scholar 

  2. Barott, K., Smith, J., Dinsdale, E., Hatay, M., Sandin, S., & Rohwer, F. (2009). Hyperspectral and physiological analyses of coral-algal interactions. [Research Support, Non-U.S. Gov’t]. PloS One, 4(11), e8043. doi:10.1371/journal.pone.0008043.

    Article  Google Scholar 

  3. Bongiorni, L., Shafir, S., Angel, D., & Rinkevich, B. (2003). Survival, growth and gonad development of two hermatypic corals subjected to in situ fish-farm nutrient enrichment (Vol. 253). Oldendorf, Allemagne:Inter-Research.

    Google Scholar 

  4. Bythell, J., Pan, P., & Lee, J. (2001). Three-dimensional morphometric measurements of reef corals using underwater photogrammetry techniques. Coral Reefs, 20(3), 193–199.

  5. Cesar, H., Burke, L., & Pet-Soede, L. (2003). The economics of worldwide coral reef degradation.

  6. Cohen, A. C., & Holcomb, M. (2009). Why corals care about ocean acidification: uncovering the mechanism. Oceanography, 22(4), 118–127.

    Article  Google Scholar 

  7. De’ath, G., Lough, J. M., & Fabricius, K. E. (2009). Declining coral calcification on the Great Barrier Reef. Science, 323(5910), 116–119. doi:10.1126/science.1165283.

    Article  Google Scholar 

  8. Edmunds, P. J., & Elahi, R. (2007). The demographics of a 15-year decline in cover of the Caribbean reef coral Montastraea annularis. Ecological Monographs, 77(1), 3–18.

    Article  Google Scholar 

  9. Elahi, R., & Edmunds, P. J. (2007). Consequences of fission in the coral Siderastrea siderea: growth rates of small colonies and clonal input to population structure. Coral Reefs, 26(2), 271–276. doi:10.1007/s00338-006-0190-x.

    Article  Google Scholar 

  10. Gulshan, V., Rother, C., Criminisi, A., Blake, A., & Zisserman, A. Geodesic star convexity for interactive image segmentation. In Computer Vision and Pattern Recognition (CVPR), 2010 I.E. Conference on, 2010 (pp. 3129–3136): IEEE.

  11. Herlan, J., & Lirman, D. Development of a coral nursery program for the threatened coral Acropora cervicornis in Florida. In Proc 11th Int Coral Reef Symp, 2008 (Vol. 24, pp. 1244–1247).

  12. Hill, J., & Wilkinson, C. (2004). Methods for ecological monitoring of coral reefs, a resource for managers. Australian Institute of Marine Science.

  13. Hoegh-Guldberg, O. (1988). A method for determining the surface area of corals. Coral Reefs, 7(3), 113–116. doi:10.1007/bf00300970.

    Article  Google Scholar 

  14. Hoegh-Guldberg, O., Mumby, P. J., Hooten, A. J., Steneck, R. S., Greenfield, P., Gomez, E., et al. (2007). Coral reefs under rapid climate change and ocean acidification. Science, 318(5857), 1737–1742. doi:10.1126/science.1152509.

    CAS  Article  Google Scholar 

  15. Holmes, G. (2008). Estimating three-dimensional surface areas on coral reefs. Journal of Experimental Marine Biology and Ecology, 365(1), 67–73. doi:10.1016/j.jembe.2008.07.045.

    Article  Google Scholar 

  16. Hughes, T. P. (1984). Population dynamics based on individual size rather than age: a general model with a reef coral example. American Naturalist, 123, 778–795.

  17. Jones, A. M., Cantin, N. E., Berkelmans, R., Sinclair, B., & Negri, A. P. (2008). A 3D modeling method to calculate the surface areas of coral branches. Coral Reefs, 27(3), 521–526.

  18. Knowlton, N., & Jackson, J. B. C. (2008). Shifting baselines, local impacts, and global change on coral reefs. PLoS Biology, 6(2), e54. doi:10.1371/journal.pbio.0060054.

    Article  Google Scholar 

  19. Laforsch, C., Christoph, E., Glaser, C., Naumann, M., Wild, C., & Niggl, W. (2008). A precise and non-destructive method to calculate the surface area in living scleractinian corals using X-ray computed tomography and 3D modeling. Coral Reefs, 27(4), 811–820. doi:10.1007/s00338-008-0405-4.

    Article  Google Scholar 

  20. Leujak, W., & Ormond, R. F. G. (2007). Comparative accuracy and efficiency of six coral community survey methods. Journal of Experimental Marine Biology and Ecology, 351(1–2), 168–187. doi:10.1016/j.jembe.2007.06.028.

    Article  Google Scholar 

  21. Lirman, D., Thyberg, T., Herlan, J., Hill, C., Young-Lahiff, C., Schopmeyer, S., et al. (2010). Propagation of the threatened staghorn coral Acropora cervicornis: methods to minimize the impacts of fragment collection and maximize production. Coral Reefs, 29(3), 729–735.

    Article  Google Scholar 

  22. Lirman, D., Schopmeyer, S., Galvan, V., Drury, C., Baker, A. C., & Baums, I. B. (2014). Growth dynamics of the threatened Caribbean staghorn coral Acropora cervicornis: influence of host genotype, symbiont identity, colony size, and environmental setting. PloS One. doi:10.1371/journal.pone.0107253.

    Google Scholar 

  23. Marsh, J. A. (1970). Primary productivity of reef-building calcareous red algae. Ecology, 51(2), 255–263. doi:10.2307/1933661.

    Article  Google Scholar 

  24. Miller, M. W., Weil, E., & Szmant, A. M. (2000). Coral recruitment and juvenile mortality as structuring factors for reef benthic communities in Biscayne National Park, USA. Coral Reefs, 19(2), 115–123. doi:10.1007/s003380000079.

    Article  Google Scholar 

  25. Naumann, M., Niggl, W., Laforsch, C., Glaser, C., & Wild, C. (2009). Coral surface area quantification–evaluation of established techniques by comparison with computer tomography. Coral Reefs, 28(1), 109–117. doi:10.1007/s00338-008-0459-3.

    Article  Google Scholar 

  26. Pandolfi, J. M., Bradbury, R. H., Sala, E., Hughes, T. P., Bjorndal, K. A., Cooke, R. G., et al. (2003). Global trajectories of the long-term decline of coral reef ecosystems. Science, 301(5635), 955–958. doi:10.1126/science.1085706.

    CAS  Article  Google Scholar 

  27. Rahav, O., Ben-Zion, M., Achituv, Y., & Dubinsky, Z. (1991). A photographic, computerized method for in situ growth measurements in reef-building cnidarians. Coral Reefs, 9(4), 204–204. doi:10.1007/bf00290422.

    Article  Google Scholar 

  28. Spencer Davies, P. (1989). Short-term growth measurements of corals using an accurate buoyant weighing technique. Marine Biology, 101(3), 389–395. doi:10.1007/bf00428135.

    Article  Google Scholar 

  29. Stimson, J., & Kinzie, R. A. (1991). The temporal pattern and rate of release of zooxanthellae from the reef coral Pocillopora damicornis (Linnaeus) under nitrogen-enrichment and control conditions. Journal of Experimental Marine Biology and Ecology, 153(1), 63–74. doi:10.1016/s0022-0981(05)80006-1.

    Article  Google Scholar 

  30. Treibitz, T., Schechner, Y. Y., Kunz, C., & Singh, H. (2012). Flat refractive geometry. IEEE Transactions on Pattern Analysis and Machine Intelligence, 34(1), 51–65. doi:10.1109/tpami.2011.105.

    Article  Google Scholar 

  31. Veal, C. J., Holmes, G., Nunez, M., Hoegh-Guldberg, O., & Osborn, J. (2010). A comparative study of methods for surface area and three- dimensional shape measurement of coral skeletons. Limnology and Oceanography: Methods, 8, 241–253.

    Google Scholar 

  32. Young, C., Schopmeyer, S., & Lirman, D. (2012). A review of reef restoration and coral propagation using the threatened genus Acropora in the Caribbean and Western Atlantic. Bulletin of Marine Science, 88(4), 1075–1098.

    Article  Google Scholar 

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Acknowledgments

This study was supported by a funding from National Science Foundation Cyber Enabled Discovery and Innovation Award # 0941760. We wish to thank the Smithsonian Tropical Research Institute and the staff of the Bocas del Toro field station.

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Correspondence to Benjamin P. Neal.

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Neal, B.P., Lin, TH., Winter, R.N. et al. Methods and measurement variance for field estimations of coral colony planar area using underwater photographs and semi-automated image segmentation. Environ Monit Assess 187, 496 (2015). https://doi.org/10.1007/s10661-015-4690-4

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Keywords

  • Coral reefs
  • Colony size
  • Colony growth
  • Size structure
  • Planar area
  • Image segmentation