Integration of close‐range underwater photogrammetry with inspection and mesh processing software: a novel approach for quantifying ecological dynamics of temperate biogenic reefs

Type Article
Date 2021-06
Language English
Author(s) Ventura Daniele1, Dubois StanislasORCID2, Bonifazi Andrea3, Jona Lasinio Giovanna4, Seminara Marco1, Gravina Maria F.3, 4, 5, Ardizzone Giandomenico1, Scales Kylie, Rowlands Gwilym
Affiliation(s) 1 : Department of Environmental Biology University of Rome “la Sapienza” V. le dell’Università 32 Rome 00185,Italy
2 : IFREMER, DYNECO‐LEBCO, Centre de Bretagne, Technopole Brest‐Iroise, 1625 route de Sainte‐Anne, CS 10070 Plouzané 29280, France
3 : Laboratory of Experimental Ecology and Aquaculture Tor Vergata University Via della Ricerca Scientifica Rome 00133,Italy
4 : Department of Statistic, Sciences University of Rome “la Sapienza”‐ V. le dell’Università 32 Rome 00185,Italy
5 : CoNISMa Consorzio Nazionale Interuniversitario per le Scienze del Mare Rome, Italy
Source Remote Sensing In Ecology And Conservation (2056-3485) (Wiley), 2021-06 , Vol. 7 , N. 2 , P. 169-186
DOI 10.1002/rse2.178
WOS© Times Cited 19
Keyword(s) 3D modelling, biogenic temperate reefs, computer vision, mesh analysis, surface rugosity evaluation, volumetric estimates

Characterizing and monitoring changes in biogenic 3‐dimensional (3D) structures at multiple scales over time is challenging within the practical constraints of conventional ecological tools. Therefore, we developed a structure‐from‐motion (SfM)‐based photogrammetry method, coupled with inspection and mesh processing software, to estimate important ecological parameters of underwater worm colonies (hummocks) constructed by the sabellariid polychaete Sabellaria alveolata, using non‐destructive, 3D modeling and mesh analysis. High resolution digital images of bioconstructions (hummocks) were taken in situ under natural conditions to generate digital 3D models over different sampling periods to analyse the morphological evolution of four targeted hummocks. 3D models were analysed in GOM Inspect software, a powerful and freely available mesh processing software to follow growth as well as morphology changes over time of each hummock. Linear regressions showed 3D models only slightly overestimated the real dimensions of the reference objects with an average error < 5% between measured and model‐estimated dimensions for both length and volume. Manual inspection of models and semi‐automated surface‐to‐surface comparison allowed the computation of important metrics linked to the ecology of temperate reefs such as volume, surface area, surface complexity/rugosity, number and size of holes and creeks and the mean density of living worms per colony. Moreover we demonstrated the reliability of 3D surface complexity estimates against two linear rugosity measures: a traditional and a virtual variant of the ‘chain‐and‐tape’ method. Finally, besides 3D models deviation analysis via surface comparison, a Bayesian latent variable model approach was adopted to highlight the significative effects of sea state conditions on S. alveolata hummocks metrics. We demonstrated without damaging the benthic organisms that SfM approach allow continuous study of temperate bioconstruction leading to a fine description of short‐term structural modification mediated by hydrodynamics, making this technique accessible and repeatable to many other areas of ecological research.

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Ventura Daniele, Dubois Stanislas, Bonifazi Andrea, Jona Lasinio Giovanna, Seminara Marco, Gravina Maria F., Ardizzone Giandomenico, Scales Kylie, Rowlands Gwilym (2021). Integration of close‐range underwater photogrammetry with inspection and mesh processing software: a novel approach for quantifying ecological dynamics of temperate biogenic reefs. Remote Sensing In Ecology And Conservation, 7(2), 169-186. Publisher's official version : , Open Access version :