Assessment of storm impact on coral reef structural complexity.

Extreme weather events are increasing in frequency and magnitude. Consequently, it is important to understand their effects and remediation. Resilience reflects the ability of an ecosystem to absorb change, which is important for understanding ecological dynamics and trajectories. To describe the impact of a powerful storm on coral reef structural complexity, we used novel computational tools and detailed 3D reconstructions captured at three time points over three years. Our data-set Reefs4D of 21 co-registered image-based models enabled us to calculate the differences at seven sites over time and is released with the paper. We employed six geometrical metrics, two of which are new algorithms for calculating fractal dimension of reefs in full 3D. We conducted a multivariate analysis to reveal which sites were affected the most and their relative recovery. We also explored the changes in fractal dimension per size category using our cube-counting algorithm. Three metrics showed a significant difference between time points, i.e., decline and subsequent recovery in structural complexity. The multivariate analysis and the results per size category showed a similar trend. Coral reef resilience has been the subject of seminal studies in ecology. We add important information to the discussion by focusing on 3D structure through image-based modeling. The full picture shows resilience in structural complexity, suggesting that the reef has not gone through a catastrophic phase shift. Our novel analysis framework is widely transferable and useful for research, monitoring, and management.

Emerging 3D technologies for future reformation of coral reefs: Enhancing biodiversity using biomimetic structures based on designs by nature.

The rapid decline of vulnerable coral reefs has increased the necessity of exploring interdisciplinary methods for reef restoration. Examining how to upgrade these tools may uncover options to better support or increase biodiversity of coral reefs. As many of the issues facing reef restoration today deal with the scalability and effectiveness of restoration efforts, there is an urgency to invest in technology that can help reach ecosystem-scale. Here, we provide an overview on the evolution to current state of artificial reefs as a reef reformation tool and discuss a blueprint with which to guide the next generation of biomimetic artificial habitats for ecosystem support. Currently, existing artificial structures have difficulty replicating the 3D complexity of coral habitats and scaling them to larger areas can be problematic in terms of production and design. We introduce a novel customizable 3D interface for producing scalable, biomimetic artificial structures, utilizing real data collected from coral ecosystems. This interface employs 3D technologies, 3D imaging and 3D printing, to extract core reef characteristics, which can be translated and digitized into a 3D printed artificial reef. The advantages of 3D printing lie in providing customized tools by which to integrate the vital details of natural reefs, such as rugosity and complexity, into a sustainable manufacturing process. This methodology can offer economic solutions for developing both small and large-scale biomimetic structures for a variety of restoration situations, that closely resemble the coral reefs they intend to support.

Underwater Single Image Color Restoration Using Haze-Lines and a New Quantitative Dataset.

Underwater images suffer from color distortion and low contrast, because light is attenuated while it propagates through water. Attenuation under water varies with wavelength, unlike terrestrial images where attenuation is assumed to be spectrally uniform. The attenuation depends both on the water body and the 3D structure of the scene, making color restoration difficult. Unlike existing single underwater image enhancement techniques, our method takes into account multiple spectral profiles of different water types. By estimating just two additional global parameters: the attenuation ratios of the blue-red and blue-green color channels, the problem is reduced to single image dehazing, where all color channels have the same attenuation coefficients. Since the water type is unknown, we evaluate different parameters out of an existing library of water types. Each type leads to a different restored image and the best result is automatically chosen based on color distribution. We also contribute a dataset of 57 images taken in different locations. To obtain ground truth, we placed multiple color charts in the scenes and calculated its 3D structure using stereo imaging. This dataset enables a rigorous quantitative evaluation of restoration algorithms on natural images for the first time.

Single Image Dehazing Using Haze-Lines.

Haze often limits visibility and reduces contrast in outdoor images. The degradation varies spatially since it depends on the objects' distances from the camera. This dependency is expressed in the transmission coefficients, which control the attenuation. Restoring the scene radiance from a single image is a highly ill-posed problem, and thus requires using an image prior. Contrary to methods that use patch-based image priors, we propose an algorithm based on a non-local prior. The algorithm relies on the assumption that colors of a haze-free image are well approximated by a few hundred distinct colors, which form tight clusters in RGB space. Our key observation is that pixels in a given cluster are often non-local, i.e., spread over the entire image plane and located at different distances from the camera. In the presence of haze these varying distances translate to different transmission coefficients. Therefore, each color cluster in the clear image becomes a line in RGB space, that we term a haze-line. Using these haze-lines, our algorithm recovers the atmospheric light, the distance map and the haze-free image. The algorithm has linear complexity, requires no training, and performs well on a wide variety of images compared to other state-of-the-art methods.

Optical wide-field tomography of sediment resuspension.

We present a wide-field imaging approach to optically sense underwater sediment resuspension events. It uses wide-field multi-directional views and diffuse backlight. Our approach algorithmically quantifies the amount of material resuspended and its spatiotemporal distribution. The suspended particles affect the radiation that reaches the cameras, hence the captured images. By measuring the radiance during and prior to resuspension, we extract the optical depth on the line of sight per pixel. Using computed tomography (CT) principles, the optical depths yield estimation of the extinction coefficient of the suspension, per voxel. The suspended density is then derived from the reconstructed extinction coefficient.

Caribbean massive corals not recovering from repeated thermal stress events during 2005-2013.

Massive coral bleaching events associated with high sea surface temperatures are forecast to become more frequent and severe in the future due to climate change. Monitoring colony recovery from bleaching disturbances over multiyear time frames is important for improving predictions of future coral community changes. However, there are currently few multiyear studies describing long-term outcomes for coral colonies following acute bleaching events. We recorded colony pigmentation and size for bleached and unbleached groups of co-located conspecifics of three major reef-building scleractinian corals (Orbicella franksi, Siderastrea siderea, and Stephanocoenia michelini; n = 198 total) in Bocas del Toro, Panama, during the major 2005 bleaching event and then monitored pigmentation status and changes live tissue colony size for 8 years (2005-2013). Corals that were bleached in 2005 demonstrated markedly different response trajectories compared to unbleached colony groups, with extensive live tissue loss for bleached corals of all species following bleaching, with mean live tissue losses per colony 9 months postbleaching of 26.2% (±5.4 SE) for O. franksi, 35.7% (±4.7 SE) for S. michelini, and 11.2% (±3.9 SE) for S. siderea. Two species, O. franksi and S. michelini, later recovered to net positive growth, which continued until a second thermal stress event in 2010. Following this event, all species again lost tissue, with previously unbleached colony species groups experiencing greater declines than conspecific sample groups, which were previously bleached, indicating a possible positive acclimative response. However, despite this beneficial effect for previously bleached corals, all groups experienced substantial net tissue loss between 2005 and 2013, indicating that many important Caribbean reef-building corals will likely suffer continued tissue loss and may be unable to maintain current benthic coverage when faced with future thermal stress forecast for the region, even with potential benefits from bleaching-related acclimation.

Photometric Stereo in a Scattering Medium.

Photometric stereo is widely used for 3D reconstruction. However, its use in scattering media such as water, biological tissue and fog has been limited until now, because of forward scattered light from both the source and object, as well as light scattered back from the medium (backscatter). Here we make three contributions to address the key modes of light propagation, under the common single scattering assumption for dilute media. First, we show through extensive simulations that single-scattered light from a source can be approximated by a point light source with a single direction. This alleviates the need to handle light source blur explicitly. Next, we model the blur due to scattering of light from the object. We measure the object point-spread function and introduce a simple deconvolution method. Finally, we show how imaging fluorescence emission where available, eliminates the backscatter component and increases the signal-to-noise ratio. Experimental results in a water tank, with different concentrations of scattering media added, show that deconvolution produces higher-quality 3D reconstructions than previous techniques, and that when combined with fluorescence, can produce results similar to that in clear water even for highly turbid media.

Underwater microscopy for in situ studies of benthic ecosystems.

Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales.

Improving Automated Annotation of Benthic Survey Images Using Wide-band Fluorescence.

Large-scale imaging techniques are used increasingly for ecological surveys. However, manual analysis can be prohibitively expensive, creating a bottleneck between collected images and desired data-products. This bottleneck is particularly severe for benthic surveys, where millions of images are obtained each year. Recent automated annotation methods may provide a solution, but reflectance images do not always contain sufficient information for adequate classification accuracy. In this work, the FluorIS, a low-cost modified consumer camera, was used to capture wide-band wide-field-of-view fluorescence images during a field deployment in Eilat, Israel. The fluorescence images were registered with standard reflectance images, and an automated annotation method based on convolutional neural networks was developed. Our results demonstrate a 22% reduction of classification error-rate when using both images types compared to only using reflectance images. The improvements were large, in particular, for coral reef genera Platygyra, Acropora and Millepora, where classification recall improved by 38%, 33%, and 41%, respectively. We conclude that convolutional neural networks can be used to combine reflectance and fluorescence imagery in order to significantly improve automated annotation accuracy and reduce the manual annotation bottleneck.

Methods and measurement variance for field estimations of coral colony planar area using underwater photographs and semi-automated image segmentation.

Size and growth rates for individual colonies are some of the most essential descriptive parameters for understanding coral communities, which are currently experiencing worldwide declines in health and extent. Accurately measuring coral colony size and changes over multiple years can reveal demographic, growth, or mortality patterns often not apparent from short-term observations and can expose environmental stress responses that may take years to manifest. Describing community size structure can reveal population dynamics patterns, such as periods of failed recruitment or patterns of colony fission, which have implications for the future sustainability of these ecosystems. However, rapidly and non-invasively measuring coral colony sizes in situ remains a difficult task, as three-dimensional underwater digital reconstruction methods are currently not practical for large numbers of colonies. Two-dimensional (2D) planar area measurements from projection of underwater photographs are a practical size proxy, although this method presents operational difficulties in obtaining well-controlled photographs in the highly rugose environment of the coral reef, and requires extensive time for image processing. Here, we present and test the measurement variance for a method of making rapid planar area estimates of small to medium-sized coral colonies using a lightweight monopod image-framing system and a custom semi-automated image segmentation analysis program. This method demonstrated a coefficient of variation of 2.26% for repeated measurements in realistic ocean conditions, a level of error appropriate for rapid, inexpensive field studies of coral size structure, inferring change in colony size over time, or measuring bleaching or disease extent of large numbers of individual colonies.

Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

Spectral Diversity and Regulation of Coral Fluorescence in a Mesophotic Reef Habitat in the Red Sea.

The phenomenon of coral fluorescence in mesophotic reefs, although well described for shallow waters, remains largely unstudied. We found that representatives of many scleractinian species are brightly fluorescent at depths of 50-60 m at the Interuniversity Institute for Marine Sciences (IUI) reef in Eilat, Israel. Some of these fluorescent species have distribution maxima at mesophotic depths (40-100 m). Several individuals from these depths displayed yellow or orange-red fluorescence, the latter being essentially absent in corals from the shallowest parts of this reef. We demonstrate experimentally that in some cases the production of fluorescent pigments is independent of the exposure to light; while in others, the fluorescence signature is altered or lost when the animals are kept in darkness. Furthermore, we show that green-to-red photoconversion of fluorescent pigments mediated by short-wavelength light can occur also at depths where ultraviolet wavelengths are absent from the underwater light field. Intraspecific colour polymorphisms regarding the colour of the tissue fluorescence, common among shallow water corals, were also observed for mesophotic species. Our results suggest that fluorescent pigments in mesophotic reefs fulfil a distinct biological function and offer promising application potential for coral-reef monitoring and biomedical imaging.

Wide field-of-view fluorescence imaging of coral reefs.

Coral reefs globally are declining rapidly because of both local and global stressors. Improved monitoring tools are urgently needed to understand the changes that are occurring at appropriate temporal and spatial scales. Coral fluorescence imaging tools have the potential to improve both ecological and physiological assessments. Although fluorescence imaging is regularly used for laboratory studies of corals, it has not yet been used for large-scale in situ assessments. Current obstacles to effective underwater fluorescence surveying include limited field-of-view due to low camera sensitivity, the need for nighttime deployment because of ambient light contamination, and the need for custom multispectral narrow band imaging systems to separate the signal into meaningful fluorescence bands. Here we describe the Fluorescence Imaging System (FluorIS), based on a consumer camera modified for greatly increased sensitivity to chlorophyll-a fluorescence, and we show high spectral correlation between acquired images and in situ spectrometer measurements. This system greatly facilitates underwater wide field-of-view fluorophore surveying during both night and day, and potentially enables improvements in semi-automated segmentation of live corals in coral reef photographs and juvenile coral surveys.

Use of commercial off-the-shelf digital cameras for scientific data acquisition and scene-specific color calibration.

Commercial off-the-shelf digital cameras are inexpensive and easy-to-use instruments that can be used for quantitative scientific data acquisition if images are captured in raw format and processed so that they maintain a linear relationship with scene radiance. Here we describe the image-processing steps required for consistent data acquisition with color cameras. In addition, we present a method for scene-specific color calibration that increases the accuracy of color capture when a scene contains colors that are not well represented in the gamut of a standard color-calibration target. We demonstrate applications of the proposed methodology in the fields of biomedical engineering, artwork photography, perception science, marine biology, and underwater imaging.

Resolution loss without imaging blur.

Image recovery under noise is widely studied. However, there is little emphasis on performance as a function of object size. In this work we analyze the probability of recovery as a function of object spatial frequency. The analysis uses a physical model for the acquired signal and noise, and also accounts for potential postacquisition noise filtering. Linear-systems analysis yields an effective cutoff frequency, which is induced by noise, despite having no optical blur in the imaging model. This means that a low signal-to-noise ratio (SNR) in images causes resolution loss, similar to image blur. We further consider the effect on SNR of pointwise image formation models, such as added specular or indirect reflections, additive scattering, radiance attenuation in haze, and flash photography. The result is a tool that assesses the ability to recover (within a desirable success rate) an object or feature having a certain size, distance from the camera, and radiance difference from its nearby background, per attenuation coefficient of the medium. The bounds rely on the camera specifications.

Turbid scene enhancement using multi-directional illumination fusion.

Ambient light is strongly attenuated in turbid media. Moreover, natural light is often more highly attenuated in some spectral bands, relative to others. Hence, imaging in turbid media often relies heavily on artificial sources for illumination. Scenes irradiated by an off-axis single point source have enhanced local object shadow edges, which may increase object visibility. However, the images may suffer from severe nonuniformity, regions of low signal (being distant from the source), and regions of strong backscatter. On the other hand, simultaneously illuminating the scene from multiple directions increases the backscatter and fills-in shadows, both of which degrade local contrast. Some previous methods tackle backscatter by scanning the scene, either temporally or spatially, requiring a large number of frames. We suggest using a few frames, in each of which wide field scene irradiance originates from a different direction. This way, shadow contrast can be maintained and backscatter can be minimized in each frame, while the sequence at large has a wider, more spatially uniform illumination. The frames are then fused by post processing to a single, clearer image. We demonstrate significant visibility enhancement underwater using as little as two frames.

Active polarization descattering.

Vision in scattering media is important but challenging. Images suffer from poor visibility due to backscattering and attenuation. Most prior methods for scene recovery use active illumination scanners (structured and gated), which can be slow and cumbersome, while natural illumination is inapplicable to dark environments. The current paper addresses the need for a non-scanning recovery method, that uses active scene irradiance. We study the formation of images under widefield artificial illumination. Based on the formation model, the paper presents an approach for recovering the object signal. It also yields rough information about the 3D scene structure. The approach can work with compact, simple hardware, having active widefield, polychromatic polarized illumination. The camera is fitted with a polarization analyzer. Two frames of the scene are taken, with different states of the analyzer or polarizer. A recovery algorithm follows the acquisition. It allows both the backscatter and the object reflection to be partially polarized. It thus unifies and generalizes prior polarization-based methods, which had assumed exclusive polarization of either of these components. The approach is limited to an effective range, due to image noise and illumination falloff. Thus, the limits and noise sensitivity are analyzed. We demonstrate the approach in underwater field experiments.