scholarly journals COMPARISON OF COMMERCIAL STRUCTURE-FROM-MOTION PHOTOGRAMMETY SOFTWARE USED FOR UNDERWATER THREE-DIMENSIONAL MODELING OF CORAL REEF ENVIRONMENTS

2017 ◽  
Vol XLII-2/W3 ◽  
pp. 127-131 ◽  
Author(s):  
J. H. R. Burns ◽  
D. Delparte
Keyword(s):  
Coral Reef ◽  
Structural Characteristics ◽  
Spatial Scales ◽  
3D Structure ◽  
Light Availability ◽  
Three Dimensional ◽  
Structural Complexity ◽  
Physical Structure ◽  
Natural Environments ◽  
Ecological Processes

Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

scholarly journals 3D HABITAT COMPLEXITY OF CORAL REEFS IN THE NORTHWESTERN HAWAIIAN ISLANDS IS DRIVEN BY CORAL ASSEMBLAGE STRUCTURE

2019 ◽  
Vol XLII-2/W10 ◽  
pp. 61-67 ◽  
Author(s):  
J. H. R. Burns ◽  
A. Fukunaga ◽  
K. H. Pascoe ◽  
A. Runyan ◽  
B. K. Craig ◽  
...  
Keyword(s):  
Coral Reef ◽  
Habitat Complexity ◽  
Coral Cover ◽  
Light Availability ◽  
Structural Complexity ◽  
Assemblage Structure ◽  
Natural Environments ◽  
Live Coral ◽  
Ecological Processes ◽  
Coral Assemblage

<p><strong>Abstract.</strong> Corals act as ecosystem engineers by secreting structurally complex calcium carbonate skeletons on the benthic substrate that provide habitat for a diverse array of associated reef organisms. Communities of living corals create large and dynamic benthic structures that directly affect ecological parameters such as habitat provisioning and light availability, thus influencing overall ecosystem function. Despite the important role 3D structural complexity plays in ecosystem biodiversity and productivity, the field of coral ecology has lacked accessibility to practical technology capable of quantifying 3D characteristics of underwater habitats. Advancements in the field of computer vision has led to Structure-from-Motion (SfM) photogrammetry, which provides a simple and cost-effective method for creating high-resolution and spatially accurate 3D reconstructions of natural environments. Integrating SfM approaches into coral reef research and monitoring has provided useful insight into the relationship between 3D habitat complexity and ecological processes. In this study, we examined the relationships among 2D estimates of live coral cover and several metrics of 3D habitat structural complexity among eleven long-term monitoring sites at French Frigate Shoals. Our findings show that coral assemblage structure acts as a significant driver of 3D structural complexity of coral reef habitats at this atoll. This study highlights the importance of diverse and abundant coral assemblages in supporting structurally complex coral reef habitats and provides a framework for future investigations into the ecological role of various coral morphotypes.</p>

scholarly journals Convolutional Neural Networks Predict Fish Abundance from Underlying Coral Reef Texture

2018 ◽  
Author(s):  
Grace Young ◽  
Vassileios Balntas ◽  
Victor Prisacariu
Keyword(s):  
Spatial Scales ◽  
A Priori ◽  
3D Structure ◽  
Three Dimensional ◽  
Structural Complexity ◽  
3D Models ◽  
Fish Abundance ◽  
Ecological Patterns ◽  
Abundance And Diversity ◽  
First Time

Coral reefs are among the most biodiverse ecosystems on Earth in large part owing to their unique three-dimensional (3D) structure, which provides niches for a variety of species. Metrics of structural complexity have been shown to correlate with the abundance and diversity of fish and other marine organisms, but they are imperfect representations of a surface that can oversimplify key structural elements and bias discoveries. Moreover, they require researchers to make relatively uninformed guesses about the features and spatial scales relevant to species of interest. This paper introduces a machine-learning method for automating inferences about fish abundance from reef 3D models. It demonstrates the capacity of a convolutional neural network (ConvNet) to learn ecological patterns that are extremely subtle, if not invisible, to the human eye. It is the first time in the literature that no a priori assumptions are made about the bathymetry–fish relationship.

scholarly journals UTILIZING UNDERWATER THREE-DIMENSIONAL MODELING TO ENHANCE ECOLOGICAL AND BIOLOGICAL STUDIES OF CORAL REEFS

2015 ◽  
Vol XL-5/W5 ◽  
pp. 61-66 ◽  
Author(s):  
J. H. R. Burns ◽  
D. Delparte ◽  
R. D. Gates ◽  
M. Takabayashi
Keyword(s):  
Coral Reefs ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Structural Complexity ◽  
Ecological Processes ◽  
3 Dimensional ◽  
Three Dimensional Modeling ◽  
Digital Elevation ◽  
Biological Studies ◽  
Coral Reef Ecosystems

The structural complexity of coral reefs profoundly affects the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional survey techniques utilize 2-dimensional metrics that are inadequate for accurately capturing and quantifying the intricate structural complexity of scleractinian corals. A 3-dimensional (3D) approach improves the capacity to accurately measure architectural complexity, topography, rugosity, volume, and other structural characteristics that play a significant role in habitat facilitation and ecosystem processes. This study utilized Structure-from-Motion (SfM) photogrammetry techniques to create 3D mesh models for several Hawaiian corals that represent distinct morphological phenotypes. The orthophotos and digital elevation models generated from the SfM process were imported into geospatial analysis software in order to quantify several metrics pertaining to 3D complexity that are known to affect ecosystem biodiversity and productivity. The 3D structural properties of the reconstructed coral colonies were statistically analyzed to determine if the each species represents a unique morpho-functional group. The SfM reconstruction techniques described in this paper can be utilized for an array of research purposes to improve our understanding of how changes in coral composition affect habitat structure and ecological processes in coral reef ecosystems.

scholarly journals Microbial Biofilms: Structural Plasticity and Emerging Properties

2022 ◽  
Vol 10 (1) ◽  
pp. 138
Author(s):  
Arnaud Bridier ◽  
Romain Briandet
Keyword(s):  
Spatial Organization ◽  
3D Structure ◽  
Three Dimensional ◽  
Original Data ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Chronic Infections ◽  
Ecological Processes ◽  
Microbial Biofilms ◽  
Technological Advances

Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation— from a single-cell to a multicellular scale— to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.

scholarly journals Using virtual reality to estimate aesthetic values of coral reefs

2018 ◽  
Vol 5 (4) ◽  
pp. 172226 ◽  
Author(s):  
Julie Vercelloni ◽  
Sam Clifford ◽  
M. Julian Caley ◽  
Alan R. Pearse ◽  
Ross Brown ◽  
...  
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Structural Complexity ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Aesthetic Value ◽  
Natural Systems ◽  
Holistic Conservation ◽  
Past Experiences ◽  
Aesthetic Values

Aesthetic value, or beauty, is important to the relationship between humans and natural environments and is, therefore, a fundamental socio-economic attribute of conservation alongside other ecosystem services. However, beauty is difficult to quantify and is not estimated well using traditional approaches to monitoring coral-reef aesthetics. To improve the estimation of ecosystem aesthetic values, we developed and implemented a novel framework used to quantify features of coral-reef aesthetics based on people's perceptions of beauty. Three observer groups with different experience to reef environments (Marine Scientist, Experienced Diver and Citizen) were virtually immersed in Australian's Great Barrier Reef (GBR) using 360° images. Perceptions of beauty and observations were used to assess the importance of eight potential attributes of reef-aesthetic value. Among these, heterogeneity, defined by structural complexity and colour diversity, was positively associated with coral-reef-aesthetic values. There were no group-level differences in the way the observer groups perceived reef aesthetics suggesting that past experiences with coral reefs do not necessarily influence the perception of beauty by the observer. The framework developed here provides a generic tool to help identify indicators of aesthetic value applicable to a wide variety of natural systems. The ability to estimate aesthetic values robustly adds an important dimension to the holistic conservation of the GBR, coral reefs worldwide and other natural ecosystems.

scholarly journals Variability in Mixed Conifer Spatial Structure Changes Understory Light Environments

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1015 ◽  
Author(s):  
Jeffery B. Cannon ◽  
Wade T. Tinkham ◽  
Ryan K. DeAngelis ◽  
Edward M. Hill ◽  
Mike A. Battaglia
Keyword(s):  
Spatial Patterns ◽  
Ponderosa Pine ◽  
Spatial Scales ◽  
Light Availability ◽  
Structural Complexity ◽  
Tree Regeneration ◽  
Conifer Forests ◽  
Mixed Conifer ◽  
Regeneration Dynamics ◽  
Wide Range

In fire-adapted conifer forests of the Western U.S., changing land use has led to increased forest densities and fuel conditions partly responsible for increasing the extent of high-severity wildfires in the region. In response, land managers often use mechanical thinning treatments to reduce fuels and increase overstory structural complexity, which can help improve stand resilience and restore complex spatial patterns that once characterized these stands. The outcomes of these treatments can vary greatly, resulting in a large gradient in aggregation of residual overstory trees. However, there is limited information on how a range of spatial outcomes from restoration treatments can influence structural complexity and tree regeneration dynamics in mixed conifer stands. In this study, we model understory light levels across a range of forest density in a stem-mapped dry mixed conifer forest and apply this model to simulated stem maps that are similar in residual basal area yet vary in degree of spatial complexity. We found that light availability was best modeled by residual stand density index and that consideration of forest structure at multiple spatial scales is important for predicting light availability. Second, we found that restoration treatments differing in spatial pattern may differ markedly in their achievement of objectives such as density reduction, maintenance of horizontal and tree size complexity, and creation of microsite conditions favorable to shade-intolerant species, with several notable tradeoffs. These conditions in turn have cascading effects on regeneration dynamics, treatment longevity, fire behavior, and resilience to disturbances. In our study, treatments with high aggregation of residual trees best balanced multiple objectives typically used in ponderosa pine and dry mixed conifer forests. Simulation studies that consider a wide range of possible spatial patterns can complement field studies and provide predictions of the impacts of mechanical treatments on a large range of potential ecological effects.

Benthic community composition influences within-habitat variation in macroalgal browsing on the Great Barrier Reef

2010 ◽  
Vol 61 (9) ◽  
pp. 999 ◽  
Author(s):  
C. Cvitanovic ◽  
A. S. Hoey
Keyword(s):  
Coral Reefs ◽  
Great Barrier Reef ◽  
Benthic Community ◽  
Spatial Scales ◽  
Structural Complexity ◽  
Barrier Reef ◽  
Removal Rates ◽  
Ecological Processes ◽  
Habitat Variation ◽  
Benthic Composition

The removal of macroalgae by herbivores is fundamental to the long-term persistence of coral reefs. Variation in macroalgal browsing has been documented across a range of spatial scales on coral reefs; however, few studies have examined the factors that influence within-habitat rates of herbivory. The aim of the present study was to quantify herbivory on two species of Sargassum across three bays on an inshore island in the central Great Barrier Reef (GBR), and to determine whether these removal rates were related to the benthic composition or herbivorous fish communities. Removal rates of Sargassum differed significantly among bays, with removal rates in the southern bay (66.9–83.0% per 3 h) being approximately double that of the two other bays (29.2–38.5% per 3 h). The removal rates displayed a direct relationship with the benthic community structure, in particular the cover of macroalgae and live plate corals. Although it is difficult to determine whether these relationships are related to the availability of food resources or the structural complexity of the substratum, they highlight the potential influence of benthic composition on ecological processes. Quantifying and understanding the drivers of herbivory across a range of spatial scales is essential to the future management of coral reefs.

scholarly journals Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
M. González-Rivero ◽  
A. R. Harborne ◽  
A. Herrera-Reveles ◽  
Y.-M. Bozec ◽  
A. Rogers ◽  
...  
Keyword(s):  
Coral Reef ◽  
Three Dimensional ◽  
Structural Complexity ◽  
Multiple Metrics

scholarly journals A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents

2019 ◽  
Vol 122 (6) ◽  
pp. 2220-2242 ◽  
Author(s):  
Walter Vanzella ◽  
Natalia Grion ◽  
Daniele Bertolini ◽  
Andrea Perissinotto ◽  
Marco Gigante ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Tracking System ◽  
3D Structure ◽  
Three Dimensional ◽  
Head Position ◽  
White Background ◽  
Head Tracking ◽  
Sensory Stimuli ◽  
Alternative Approach ◽  
Position And Orientation

Tracking head position and orientation in small mammals is crucial for many applications in the field of behavioral neurophysiology, from the study of spatial navigation to the investigation of active sensing and perceptual representations. Many approaches to head tracking exist, but most of them only estimate the 2D coordinates of the head over the plane where the animal navigates. Full reconstruction of the pose of the head in 3D is much more more challenging and has been achieved only in handful of studies, which employed headsets made of multiple LEDs or inertial units. However, these assemblies are rather bulky and need to be powered to operate, which prevents their application in wireless experiments and in the small enclosures often used in perceptual studies. Here we propose an alternative approach, based on passively imaging a lightweight, compact, 3D structure, painted with a pattern of black dots over a white background. By applying a cascade of feature extraction algorithms that progressively refine the detection of the dots and reconstruct their geometry, we developed a tracking method that is highly precise and accurate, as assessed through a battery of validation measurements. We show that this method can be used to study how a rat samples sensory stimuli during a perceptual discrimination task and how a hippocampal place cell represents head position over extremely small spatial scales. Given its minimal encumbrance and wireless nature, our method could be ideal for high-throughput applications, where tens of animals need to be simultaneously and continuously tracked. NEW & NOTEWORTHY Head tracking is crucial in many behavioral neurophysiology studies. Yet reconstruction of the head’s pose in 3D is challenging and typically requires implanting bulky, electrically powered headsets that prevent wireless experiments and are hard to employ in operant boxes. Here we propose an alternative approach, based on passively imaging a compact, 3D dot pattern that, once implanted over the head of a rodent, allows estimating the pose of its head with high precision and accuracy.

scholarly journals Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs

2013 ◽  
Vol 10 (4) ◽  
pp. 2737-2746 ◽  
Author(s):  
L.-A. Henry ◽  
J. Moreno Navas ◽  
J. M. Roberts
Keyword(s):  
Coral Reef ◽  
Cold Water ◽  
Spatial Scales ◽  
Three Dimensional ◽  
Variance Partitioning ◽  
Habitat Modification ◽  
Fine Scale ◽  
Forward Selection ◽  
Broad Scale ◽  
Water Coral

Abstract. We investigated how interactions between hydrography, topography and species ecology influence the assembly of species and functional traits across multiple spatial scales of a cold-water coral reef seascape. In a novel approach for these ecosystems, we used a spatially resolved complex three-dimensional flow model of hydrography to help explain assembly patterns. Forward-selection of distance-based Moran's eigenvector mapping (dbMEM) variables identified two submodels of spatial scales at which communities change: broad-scale (across reef) and fine-scale (within reef). Variance partitioning identified bathymetric and hydrographic gradients important in creating broad-scale assembly of species and traits. In contrast, fine-scale assembly was related more to processes that created spatially autocorrelated patches of fauna, such as philopatric recruitment in sessile fauna, and social interactions and food supply in scavenging detritivores and mobile predators. Our study shows how habitat modification of reef connectivity and hydrography by bottom fishing and renewable energy installations could alter the structure and function of an entire cold-water coral reef seascape.

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