Creating 3-dimensional (3D) models of underwater scenes has become a common approach for monitoring coral reef changes and its structural complexity. Also in underwater archeology, 3D models are often created using underwater optical imagery. In this paper, we focus on the aspect of detecting small changes in the coral reef using a multi-temporal photogrammetric modelling approach, which requires a high quality control network. We show that the quality of a good geodetic network limits the direct change detection, i.e., without any further registration process. As the photogrammetric accuracy is expected to exceed the geodetic network accuracy by at least one order of magnitude, we suggest to do a fine registration based on a number of signalized points. This work is part of the Moorea Island Digital Ecosystem Avatar (IDEA) project that has been initiated in 2013 by a group of international researchers (https://mooreaidea.ethz.ch/).
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Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying
Underwater photogrammetry is increasingly being used by marine ecologists because of its ability to produce accurate, spatially detailed, non-destructive measurements of benthic communities, coupled with affordability and ease of use. However, independent quality control, rigorous imaging system set-up, optimal geometry design and a strict modeling of the imaging process are essential to achieving a high degree of measurable accuracy and resolution. If a proper photogrammetric approach that enables the formal description of the propagation of measurement error and modeling uncertainties is not undertaken, statements regarding the statistical significance of the results are limited. In this paper, we tackle these critical topics, based on the experience gained in the Moorea Island Digital Ecosystem Avatar (IDEA) project, where we have developed a rigorous underwater photogrammetric pipeline for coral reef monitoring and change detection. Here, we discuss the need for a permanent, underwater geodetic network, which serves to define a temporally stable reference datum and a check for the time series of photogrammetrically derived three-dimensional (3D) models of the reef structure. We present a methodology to evaluate the suitability of several underwater camera systems for photogrammetric and multi-temporal monitoring purposes and stress the importance of camera network geometry to minimize the deformations of photogrammetrically derived 3D reef models. Finally, we incorporate the measurement and modeling uncertainties of the full photogrammetric process into a simple and flexible framework for detecting statistically significant changes among a time series of models.
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- Award ID(s):
- 1637396
- NSF-PAR ID:
- 10235112
- Date Published:
- Journal Name:
- Remote Sensing
- Volume:
- 12
- Issue:
- 18
- ISSN:
- 2072-4292
- Page Range / eLocation ID:
- 3036
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Synopsis Acquiring accurate 3D biological models efficiently and economically is important for morphological data collection and analysis in organismal biology. In recent years, structure-from-motion (SFM) photogrammetry has become increasingly popular in biological research due to its flexibility and being relatively low cost. SFM photogrammetry registers 2D images for reconstructing camera positions as the basis for 3D modeling and texturing. However, most studies of organismal biology still relied on commercial software to reconstruct the 3D model from photographs, which impeded the adoption of this workflow in our field due the blocking issues such as cost and affordability. Also, prior investigations in photogrammetry did not sufficiently assess the geometric accuracy of the models reconstructed. Consequently, this study has two goals. First, we presented an affordable and highly flexible SFM photogrammetry pipeline based on the open-source package OpenDroneMap (ODM) and its user interface WebODM. Second, we assessed the geometric accuracy of the photogrammetric models acquired from the ODM pipeline by comparing them to the models acquired via microCT scanning, the de facto method to image skeleton. Our sample comprised 15 Aplodontia rufa (mountain beaver) skulls. Using models derived from microCT scans of the samples as reference, our results showed that the geometry of the models derived from ODM was sufficiently accurate for gross metric and morphometric analysis as the measurement errors are usually around or below 2%, and morphometric analysis captured consistent patterns of shape variations in both modalities. However, subtle but distinct differences between the photogrammetric and microCT-derived 3D models could affect the landmark placement, which in return affected the downstream shape analysis, especially when the variance within a sample is relatively small. At the minimum, we strongly advise not combining 3D models derived from these two modalities for geometric morphometric analysis. Our findings can be indictive of similar issues in other SFM photogrammetry tools since the underlying pipelines are similar. We recommend that users run a pilot test of geometric accuracy before using photogrammetric models for morphometric analysis. For the research community, we provide detailed guidance on using our pipeline for building 3D models from photographs.
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The evolution of underwater photogrammetry allows to realize 3D models of submerged object and structures throughout the use of rapid and efficient procedures either in terms of data acquisition and data processing. These procedures are based on solutions that are applied using natural control points, signalized markers and tie points; the most common algorithms are based on Structure from Motion (SfM) approach. The limit of these applications is sometimes due to the final accuracy, especially when the goal is a centimeter level of accuracy. This accuracy should be necessary when dealing with a survey devoted to deformation control purposes. An example is the underwater photogrammetry for the determination of coral growth; it is effectively a movement or a deformation detection issue where the geometric change is almost at centimeter or few centimeters accuracy level. When dealing with deformation control applications, a geodetic network is essential to realize a stable and unambiguous reference frame through the accurate and permanent installation of Ground Control Points (GCPs). Such a network, indeed, permits a robust reference frame for the georeferencing of images blocks in the different époques of data acquisition. Therefore, the comparison among subsequent photogrammetric restitutions is based on homogeneous 3D models that have been oriented in the same absolute reference system. The photogrammetric survey is based on a methodological approach especially adapted to underwater biometry (like coral growth determination) and to underwater archaeology. The approach is suitable both for modeling objects of relatively reduced dimensions and for structures with a length of ten meters or more, such as coral barriers, wrecks and long walls. The paper describes underwater photogrammetric surveys on sites at different extensions, the geodetic GCPs reference network installation and measurements (distance and elevation difference observations) as well as preliminary results of the network adjustment. A brief description of image acquisition at a different scales and the resulting 3D model of first campaign are also shown.more » « less
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Coral recruitment represents a key element for coral reef persistence and resilience in the face of environmental disturbances. Studying coral recruitment patterns is fundamental for assessing reef health and implementing appropriate management strategies in an era of climate change. The FluorIS system has been developed to acquire high resolution, wide field-of-view (FOV) in situ images of coral recruits fluorescence and has proven successful in shallow reef environments. However, up to now, its applicability to mesophotic coral ecosystems remains unknown due to the complexity of the system and the limited time available when working at mesophotic depth. In this study we optimized the FluorIS system by utilizing a single infrared-converted camera instead of the bulkier regular dual-camera system, substantially reducing the system complexity and significantly decreasing the acquisition time to an average of 10 s for a set of 3 images. Moreover, the speed-FluorIS system is much more economical, decreasing the cost of the full set-up by roughly 40% compared to the original dual-camera system. We tested the utility of the speed-FluorIS by surveying coral recruits across shallow and mesophotic reefs of the Red Sea (Gulf of Eilat) and Bermuda, two of the most northerly reefs in the world with markedly different substrate and topography, and demonstrate that the modified system enables fast imaging of fluorescence to study coral recruitment patterns over a broader range of depths and reef topographies than previous fluorescence methods. Our single-camera system represents a valuable, non-invasive and rapid underwater tool which will help standardize surveys and long-term monitoring of coral recruits, contributing to our understanding of these vital and delicate early life stages of corals.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/rs12183036
