The power of 3D fractal dimensions for comparative shape and structural complexity analyses of irregularly shaped organisms

Feeding responses of reef-building corals provide species- and concentration-dependent risk assessment of microplastic

The negative impacts of microplastic on reef-building corals are often attributed to the feeding responses to these particles. Although reactions to and ingestion of microplastic are frequently reported, a quantitative comparison to natural particles and of the factors influencing these responses is largely missing. Thus, this study aims to compare the feeding rates of corals to microplastic and natural particles, considering factors influencing these responses. Specifically, we I) studied the feeding responses of corals to microplastic, natural food, and non-food particles, II) examined the influence of biotic factors (i.e., biofilm on the particles and presence of natural food), III) evaluated species-specific differences in feeding responses to microplastic particles, and IV) applied a toxicodynamic model for species- and concentration-dependent risk assessments. We assessed the feeding responses of 11 coral species, spanning different life-history strategies and growth forms in experimental feeding trials. The results showed that the feeding responses of corals to microplastic differ from those to naturally occurring particles. Reactions to microplastic and natural food occurred equally often, while sand was more frequently rejected. Yet, the ingestion process was much more selective, and microplastic was ingested less frequently than natural food. The presence of a biofilm and natural food had activating effects on the feeding behavior of the corals on microplastic. Generally, coral species that exhibit a higher degree of heterotrophic feeding also reacted more often to microplastic. The species- and concentration-dependent toxicodynamic risk model built on these data reveals that most tested coral species are unlikely to be at risk under present environmental concentration levels. However, highly heterotrophic feeders, such as Blastomussa merleti, or generally vulnerable species, such as Pocillopora verrucosa, need special consideration. These findings help to better evaluate the responses of corals to microplastic and their risk in an increasingly polluted ocean.

Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral

Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals' complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.

Complex Morphologic Analysis of Cerebral Aneurysms Through the Novel Use of Fractal Dimension as a Predictor of Rupture Status: A Proof of Concept Study

BACKGROUND

Aneurysm morphology has been correlated with rupture. Previous reports identified several morphologic indices that predict rupture status, but they measure only specific qualities of the morphology of an aneurysm in a semiquantitative fashion. Fractal analysis is a geometric technique whereby the overall complexity of a shape is quantified through the calculation of a fractal dimension (FD). By progressively altering the scale of measurement of a shape and determining the number of segments required to incorporate the entire shape, a noninteger value for the dimension of the shape is derived. We present a proof-of-concept study to calculate the FD of an aneurysm for a small cohort of patients with aneurysms in 2 specific locations to determine whether FD is associated with aneurysm rupture status.

METHODS

Twenty-nine aneurysms of the posterior communicating and middle cerebral arteries were segmented from computed tomography angiograms in 29 patients. FD was calculated using a standard box-counting algorithm extended for use with three-dimensional shapes. Nonsphericity index and undulation index (UI) were used to validate the data against previously reported parameters associated with rupture status.

RESULTS

Nineteen ruptured and 10 unruptured aneurysms were analyzed. Through logistic regression analysis, lower FD was found to be significantly associated with rupture status (P = 0.035; odds ratio, 0.64; 95% confidence interval, 0.42-0.97 per FD increment of 0.05).

CONCLUSIONS

In this proof-of-concept study, we present a novel approach to quantify the geometric complexity of intracranial aneurysms through FD. These data suggest an association between FD and patient-specific aneurysm rupture status.

A word on habitat complexity

In their recent synopsis, Loke and Chisholm (Ecology Letters, 25, 2269-2288, 2022) present an overview of habitat complexity metrics for ecologists. They provide a review and some sound advice. However, we found several of their analyses and opinions misleading. This technical note provides a different perspective on the complexity metrics assessed.

Quantifying maerl (rhodolith) habitat complexity along an environmental gradient at regional scale in the Northeast Atlantic

Maerl beds are ecologically important marine biogenic habitats founded on a few species of free-living coralline algae that aggregate and form highly complex rhodoliths. The high biodiversity found in these habitats have been mainly justified by the structural complexity that they provide. However, few attempts to quantify this complexity have been made. Maerl species distribution, density, rhodolith growth forms, and shapes vary with environmental conditions. Hydrodynamics and depth have been shown to drive morphology. Using species-specific metrics such as sphericity and branching density, as well as diameter and fractal dimension at the rhodolith level, and maerl density at the habitat level, we quantified the habitat complexity within ten maerl beds at a regional scale (along ∼400 km of the coastline of Brittany in Western France). Using both long-term monitoring data and environmental models, we investigated how maerl habitat complexity varies among beds and which environmental conditions drive those differences. The effects of currents, exposure to wind-generated waves, temperature and sediment granulometry were evaluated. We confirmed variations in complexity in maerl beds at the habitat and rhodolith levels at local and regional scales, which might have ecological and conservational implications for their associated biodiversity. The analysed environmental conditions drive around a third of the variance in habitat complexity. Sediment granulometry is the main driver of maerl habitat complexity in Brittany, while the isolated effects of depth and hydrodynamics accounted for less than 5% of the variability each. Our results have important implications for paleoecology, and we suggest that maerl facies should be interpreted carefully. Our study provides a first attempt at explicitly quantifying maerl habitat complexity, and further contributes to the understanding of this fundamental ecological question.

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)

Morphometrics are fundamental for the analysis of size and shape in fossils, particularly because soft parts or DNA are rarely preserved and hard parts such as shells are commonly the only source of information. Geometric morphometrics, that is, landmark analysis, is well established for the description of shape but it exhibits a couple of shortcomings resulting from subjective choices during landmarking (number and position of landmarks) and from difficulties in resolving shape at the level of micro‐sculpture.

With the aid of high‐resolution 3D scanning technology and analyses of fractal dimensions, we test whether such shortcomings of linear and landmark morphometrics can be overcome. As a model group, we selected a clade of modern viviparid gastropods from Lake Lugu, with shells that show a high degree of sculptural variation. Linear and landmark analyses were applied to the same shells in order to establish the fractal dimensions. The genetic diversity of the gastropod clade was assessed.

The genetic results suggest that the gastropod clade represents a single species. The results of all morphometric methods applied are in line with the genetic results, which is that no specific morphotype could be delimited. Apart from this overall agreement, landmark and fractal dimension analyses do not correspond to each other but represent data sets with different information. Generally, the fractal dimension values quantify the roughness of the shell surface, the resolution of the 3D scans determining the level. In our approach, we captured the micro‐sculpture but not the first‐order sculptural elements, which explains that fractal dimension and landmark data are not in phase.

We can show that analyzing fractal dimensions of gastropod shells opens a window to more detailed information that can be considered in evolutionary and ecological contexts. We propose that using low‐resolution 3D scans may successfully substitute landmark analyses because it overcomes the subjective landmarking. Analyses of 3D scans with higher resolution than used in this study will provide surface roughness information at the mineralogical level. We suggest that fractal dimension analyses of a combination of differently resolved 3D models will significantly improve the quality of shell morphometrics.

Reef-building corals act as long-term sink for microplastic

The pollution of the marine environment with microplastics is pervasive. However, microplastic concentrations in the seawater are lower than the number of particles entering the oceans, suggesting that plastic particles accumulate in environmental sinks. Yet, the exact long-term sinks related to the "missing plastic" phenomenon are barely explored. Sediments in nearshore biogenic habitats are known to trap large amounts of microplastics, but also the three-dimensional structures of coral reefs might serve as unique, living long-term sinks. The main framework builders, reef-building corals, have been shown to ingest and overgrow microplastics, potentially leading to a deposition of particles in reef structures. However, little is known about the number of deposited particles and the underlying processes determining the permanent deposition in the coral skeletons. To test whether corals may act as living long-term sink for microplastic, we exposed four reef-building coral species to polyethylene microplastics (200 particles L^-1 ) in an 18-month laboratory experiment. We found microplastics in all treatment specimens, with low numbers of particles trapped in the coral tissue (up to 2 particles per cm² ) and much higher numbers in the skeleton (up to 84 particles per cm³ ). The numbers of particles accumulated in the coral skeletons were mainly related to coral growth (i.e., skeletal growth in volume), suggesting that deposition is a regularly occurring stochastic process. We estimate that reef-building corals may remove 0.09%-2.82% of the bioavailable microplastics from tropical shallow-reef waters per year. Our study shows for the first time that microplastic particles accumulate permanently in a biological sink, helping to explain the "missing plastic" phenomenon. This highlights the importance of coral reefs for the ecological balance of the oceans and reinforces the need to protect them, not only to mitigate the effects of climate change but also to preserve their ecosystem services as long-term sink for microplastic.

Interactive effects of microplastic pollution and heat stress on reef-building corals

Plastic pollution is an emerging stressor that increases pressure on ecosystems such as coral reefs that are already challenged by climate change. However, the effects of plastic pollution in combination with global warming are largely unknown. Thus, the goal of this study was to determine the cumulative effects of microplastic pollution with that of global warming on reef-building coral species and to compare the severity of both stressors. For this, we conducted a series of three controlled laboratory experiments and exposed a broad range of coral species (Acropora muricata, Montipora digitata, Porites lutea, Pocillopora verrucosa, and Stylophora pistillata) to microplastic particles in a range of concentrations (2.5-2500 particles L^-1) and mixtures (from different industrial sectors) at ambient temperatures and in combination with heat stress. We show that microplastic can occasionally have both aggravating or mitigating effects on the corals' thermal tolerance. In comparison to heat stress, however, microplastic constitutes a minor stressor. While heat stress led to decreased photosynthetic efficiency of algal symbionts, and increased bleaching, tissue necrosis, and mortality, treatment with microplastic particles had only minor effects on the physiology and health of the tested coral species at ambient temperatures. These findings underline that while efforts to reduce plastic pollution should continue, they should not replace more urgent efforts to halt global warming, which are immediately needed to preserve remaining coral reef ecosystems.

Space-filling and benthic competition on coral reefs

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.

Comparing UAS LiDAR and Structure-from-Motion Photogrammetry for Peatland Mapping and Virtual Reality (VR) Visualization

The mapping of peatland microtopography (e.g., hummocks and hollows) is key for understanding and modeling complex hydrological and biochemical processes. Here we compare unmanned aerial system (UAS) derived structure-from-motion (SfM) photogrammetry and LiDAR point clouds and digital surface models of an ombrotrophic bog, and we assess the utility of these technologies in terms of payload, efficiency, and end product quality (e.g., point density, microform representation, etc.). In addition, given their generally poor accessibility and fragility, peatlands provide an ideal model to test the usability of virtual reality (VR) and augmented reality (AR) visualizations. As an integrated system, the LiDAR implementation was found to be more straightforward, with fewer points of potential failure (e.g., hardware interactions). It was also more efficient for data collection (10 vs. 18 min for 1.17 ha) and produced considerably smaller file sizes (e.g., 51 MB vs. 1 GB). However, SfM provided higher spatial detail of the microforms due to its greater point density (570.4 vs. 19.4 pts/m2). Our VR/AR assessment revealed that the most immersive user experience was achieved from the Oculus Quest 2 compared to Google Cardboard VR viewers or mobile AR, showcasing the potential of VR for natural sciences in different environments. We expect VR implementations in environmental sciences to become more popular, as evaluations such as the one shown in our study are carried out for different ecosystems.

A Review of Remote Sensing of Submerged Aquatic Vegetation for Non-Specialists

Submerged aquatic vegetation (SAV) is a critical component of aquatic ecosystems. It is however understudied and rapidly changing due to global climate change and anthropogenic disturbances. Remote sensing (RS) can provide the efficient, accurate and large-scale monitoring needed for proper SAV management and has been shown to produce accurate results when properly implemented. Our objective is to introduce RS to researchers in the field of aquatic ecology. Applying RS to underwater ecosystems is complicated by the water column as water, and dissolved or suspended particulate matter, interacts with the same energy that is reflected or emitted by the target. This is addressed using theoretical or empiric models to remove the water column effect, though no model is appropriate for all aquatic conditions. The suitability of various sensors and platforms to aquatic research is discussed in relation to both SAV as the subject and to project aims and resources. An overview of the required corrections, processing and analysis methods for passive optical imagery is presented and discussed. Previous applications of remote sensing to identify and detect SAV are briefly presented and notable results and lessons are discussed. The success of previous work generally depended on the variability in, and suitability of, the available training data, the data’s spatial and spectral resolutions, the quality of the water column corrections and the level to which the SAV was being investigated (i.e., community versus species.)

An Automated Pipeline for Image Processing and Data Treatment to Track Activity Rhythms of Paragorgia arborea in Relation to Hydrographic Conditions

Imaging technologies are being deployed on cabled observatory networks worldwide. They allow for the monitoring of the biological activity of deep-sea organisms on temporal scales that were never attained before. In this paper, we customized Convolutional Neural Network image processing to track behavioral activities in an iconic conservation deep-sea species—the bubblegum coral Paragorgia arborea—in response to ambient oceanographic conditions at the Lofoten-Vesterålen observatory. Images and concomitant oceanographic data were taken hourly from February to June 2018. We considered coral activity in terms of bloated, semi-bloated and non-bloated surfaces, as proxy for polyp filtering, retraction and transient activity, respectively. A test accuracy of 90.47% was obtained. Chronobiology-oriented statistics and advanced Artificial Neural Network (ANN) multivariate regression modeling proved that a daily coral filtering rhythm occurs within one major dusk phase, being independent from tides. Polyp activity, in particular extrusion, increased from March to June, and was able to cope with an increase in chlorophyll concentration, indicating the existence of seasonality. Our study shows that it is possible to establish a model for the development of automated pipelines that are able to extract biological information from times series of images. These are helpful to obtain multidisciplinary information from cabled observatory infrastructures.

Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models

Underwater photogrammetry has been increasingly used in coral-reef research in recent years. Habitat metrics extracted from resulting three-dimensional (3D) reconstructions can be used to examine associations between the structural complexity of the reef habitats and the distribution of reef organisms. We created simulated 3D models of bare surface structures and 3D reconstructions of coral morphologies to investigate the behavior of various habitat metrics that were extracted from both Digital Elevation Models (DEMs) and 3D mesh models. Analyzing the resulting values provided us with important insights into how these metrics would compare with one another in the characterization of coral-reef habitats. Surface complexity (i.e., reef rugosity), fractal dimension extracted from DEMs and vector dispersion obtained from 3D mesh models exhibited consistent patterns in the ranking of structural complexity among the simulated bare surfaces and coral morphologies. The vector ruggedness measure obtained from DEMs at three different resolutions of 1, 2, and 4 cm effectively captured differences in the structural complexity among different coral morphologies. Profile curvature and planform curvature, on the other hand, were better suited to capture the structural complexity derived from surface topography such as walls and overhanging ledges. Our results indicate that habitat metrics extracted from DEMs are generally suitable when characterizing a relatively large plot of a coral reef captured from an overhead planar angle, while the 3D metric of vector dispersion is suitable when characterizing a coral colony or a relatively small plot methodically captured from various angles.

Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions

Quantifying the three-dimensional (3D) habitat structure of coral reefs is an important aspect of coral reef monitoring, as habitat architecture affects the abundance and diversity of reef organisms. Here, we used photogrammetric techniques to generate 3D reconstructions of coral reefs and examined relationships between benthic cover and various habitat metrics obtained at six different resolutions of raster cells, ranging from 1 to 32 cm. For metrics of 3D structural complexity, fractal dimension, which utilizes information on 3D surface areas obtained at different resolutions, and vector ruggedness measure (VRM) obtained at 1-, 2- or 4-cm resolution correlated well with benthic cover, with a relatively large amount of variability in these metrics being explained by the proportions of corals and crustose coralline algae. Curvature measures were, on the other hand, correlated with branching and mounding coral cover when obtained at 1-cm resolution, but the amount of variability explained by benthic cover was generally very low when obtained at all other resolutions. These results show that either fractal dimension or VRM obtained at 1-, 2- or 4-cm resolution, along with curvature obtained at 1-cm resolution, can effectively capture the 3D habitat structure provided by specific benthic organisms.

Three-dimensional digital mapping of ecosystems: a new era in spatial ecology

Ecological processes occur over multiple spatial, temporal and thematic scales in three-dimensional (3D) ecosystems. Characterizing and monitoring change in 3D structure at multiple scales is challenging within the practical constraints of conventional ecological tools. Remote sensing from satellites and crewed aircraft has revolutionized broad-scale spatial ecology, but fine-scale patterns and processes operating at sub-metre resolution have remained understudied over continuous extents. We introduce two high-resolution remote sensing tools for rapid and accurate 3D mapping in ecology—terrestrial laser scanning and structure-from-motion photogrammetry. These technologies are likely to become standard sampling tools for mapping and monitoring 3D ecosystem structure across currently under-sampled scales. We present practical guidance in the use of the tools and address barriers to widespread adoption, including testing the accuracy of structure-from-motion models for ecologists. We aim to highlight a new era in spatial ecology that uses high-resolution remote sensing to interrogate 3D digital ecosystems.

Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs

Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats.

UAV-Based 3D Point Clouds of Freshwater Fish Habitats, Xingu River Basin, Brazil

Dense 3D point clouds were generated from Structure-from-Motion Multiview Stereo (SFM-MVS) photogrammetry for five representative freshwater fish habitats in the Xingu river basin, Brazil. The models were constructed from Unmanned Aerial Vehicle (UAV) photographs collected in 2016 and 2017. The Xingu River is one of the primary tributaries of the Amazon River. It is known for its exceptionally high aquatic biodiversity. The dense 3D point clouds were generated in the dry season when large areas of aquatic substrate are exposed due to the low water level. The point clouds were generated at ground sampling distances of 1.20–2.38 cm. These data are useful for studying the habitat characteristics and complexity of several fish species in a spatially explicit manner, such as calculation of metrics including rugosity and the Minkowski–Bouligand fractal dimension (3D complexity). From these dense 3D point clouds, substrate complexity can be determined more comprehensively than from conventional arbitrary cross sections.

Alpha shapes: determining 3D shape complexity across morphologically diverse structures

Background

Following recent advances in bioimaging, high-resolution 3D models of biological structures are now generated rapidly and at low-cost. To use this data to address evolutionary and ecological questions, an array of tools has been developed to conduct shape analysis and quantify topographic complexity. Here we focus particularly on shape techniques applied to irregular-shaped objects lacking clear homologous landmarks, and propose a new ‘alpha-shapes’ method for quantifying 3D shape complexity.

Methods

We apply alpha-shapes to quantify shape complexity in the mammalian baculum as an example of a morphologically disparate structure. Micro- computed-tomography (μCT) scans of bacula were conducted. Bacula were binarised and converted into point clouds. Following application of a scaling factor to account for absolute size differences, a suite of alpha-shapes was fitted per specimen. An alpha shape is formed from a subcomplex of the Delaunay triangulation of a given set of points, and ranges in refinement from a very coarse mesh (approximating convex hulls) to a very fine fit. ‘Optimal’ alpha was defined as the refinement necessary in order for alpha-shape volume to equal CT voxel volume, and was taken as a metric of overall ‘complexity’.

Results

Our results show that alpha-shapes can be used to quantify interspecific variation in shape ‘complexity’ within biological structures of disparate geometry. The ‘stepped’ nature of alpha curves is informative with regards to the contribution of specific morphological features to overall ‘complexity’. Alpha-shapes agrees with other measures of complexity (dissection index, Dirichlet normal energy) in identifying ursid bacula as having low shape complexity. However, alpha-shapes estimates mustelid bacula as being most complex, contrasting with other shape metrics. 3D fractal dimension is identified as an inappropriate metric of complexity when applied to bacula.

Conclusions

Alpha-shapes is used to calculate ‘optimal’ alpha refinement as a proxy for shape ‘complexity’ without identifying landmarks. The implementation of alpha-shapes is straightforward, and is automated to process large datasets quickly. We interpret alpha-shapes as being particularly sensitive to concavities in surface topology, potentially distinguishing it from other shape complexity metrics. Beyond genital shape, the alpha-shapes technique holds considerable promise for new applications across evolutionary, ecological and palaeoecological disciplines.

Freshwater Fish Habitat Complexity Mapping Using Above and Underwater Structure-From-Motion Photogrammetry

Substrate complexity is strongly related to biodiversity in aquatic habitats. We illustrate a novel framework, based on Structure-from-Motion photogrammetry (SfM) and Multi-View Stereo (MVS) photogrammetry, to quantify habitat complexity in freshwater ecosystems from Unmanned Aerial Vehicle (UAV) and underwater photography. We analysed sites in the Xingu river basin, Brazil, to reconstruct the 3D structure of the substrate and identify and map habitat classes important for maintaining fish assemblage biodiversity. From the digital models we calculated habitat complexity metrics including rugosity, slope and 3D fractal dimension. The UAV based SfM-MVS products were generated at a ground sampling distance (GSD) of 1.20–2.38 cm while the underwater photography produced a GSD of 1 mm. Our results show how these products provide spatially explicit complexity metrics, which are more comprehensive than conventional arbitrary cross sections. Shallow neural network classification of SfM-MVS products of substrate exposed in the dry season resulted in high accuracies across classes. UAV and underwater SfM-MVS is robust for quantifying freshwater habitat classes and complexity and should be chosen whenever possible over conventional methods (e.g., chain-and-tape) because of the repeatability, scalability and multi-dimensional nature of the products. The SfM-MVS products can be used to identify high priority freshwater sectors for conservation, species occurrences and diversity studies to provide a broader indication for overall fish species diversity and provide repeatability for monitoring change over time.