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UCSD Computer Vision

Coral Colony Segmentation And Area Measurement Tools

Related Projects: Computer Vision Methods For Coral Reef Assessment


Size and growth of individual coral colonies underlies community population dynamics on the reef. However, non-invasively measuring three-dimensional surface areas of in-situ colonies is currently not practical. Two-dimensional planar area measurements from photographic projection can be a practical proxy for surface area, but this method often has significant methodological errors, reducing accuracy and replicability. Here, we present improvements in both hardware and software to improve accuracy for obtaining planar area from digital photographs. Using a monopod support with adjustable length reference positioning and a semi-automated image segmentation program, we achieved a coefficient of variation of 2.26% for repeated measurements of coral planar area in realistic ocean field conditions. This level of error is appropriate for rapid, inexpensive field studies of coral colony community size structure, tracking growth over time, and measuring the areal extent of coral bleaching or disease on individual colonies.


Supplementary information for:
"Improved estimation of two-dimensional area of coral colonies from underwater photographs"
Neal, BP; Lin, TH; Winter, RN; Treibitz, T; Beijbom, O; Kriegman, D; Kline, DI; Mitchell, BG.
Corresponding author:
Neal, BP, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA,


These files contain instructions for construction and use of the monopod camera support and for the use of the semi-automated image segmentation program, as described in the paper above.

1. All files relating to construction and use of the monopod camera support are compressed for download in Construction drawings for the monopod were created with 2011-2012 Solidworks 3D by Dessault Systemes Solidworks Corp. All SLDPRT files in the folder "Solidworks construction schematic" can be assembled with "monopod_assembly.SLDASM". Users without Solidworks can also assemble and view the schematic with the freeware program eDrawings, opening the file "Monopod Assembly.EASM". Two-dimensional renderings of the device are also in "Monopod Camera Support Instructions.pdf", along with instructions for use.

2. All files relating to installation and use of the semi-automated image segmentation program are compressed for download in The semi-automated image segmentation program was created with Matlab R2013a, and will run on Matlab R2006a and later versions. The folder "growcut_GeoStarConvex" contains all program files, and these files are all compressed for download in "". Instructions for construction and use are in "Image Segmenting Procedure.PDF".