Automated 2D, 2.5D, and 3D Segmentation of Coral Reef Pointclouds and Orthoprojections.

Enabled by advancing technology, coral reef researchers increasingly prefer use of image-based surveys over approaches depending solely upon in situ observations, interpretations, and recordings of divers. The images collected, and derivative products such as orthographic projections and 3D models, allow researchers to study a comprehensive digital twin of their field sites. Spatio-temporally located twins can be compared and annotated, enabling researchers to virtually return to sites long after they have left them. While these new data expand the variety and specificity of biological investigation that can be pursued, they have introduced the much-discussed Big Data Problem: research labs lack the human and computational resources required to process and analyze imagery at the rate it can be collected. The rapid development of unmanned underwater vehicles suggests researchers will soon have access to an even greater volume of imagery and other sensor measurements than can be collected by diver-piloted platforms, further exacerbating data handling limitations. Thoroughly segmenting (tracing the extent of and taxonomically identifying) organisms enables researchers to extract the information image products contain, but is very time-consuming. Analytic techniques driven by neural networks offer the possibility that the segmentation process can be greatly accelerated through automation. In this study, we examine the efficacy of automated segmentation on three different image-derived data products: 3D models, and 2D and 2.5D orthographic projections thereof; we also contrast their relative accessibility and utility to different avenues of biological inquiry. The variety of network architectures and parameters tested performed similarly, ∼80% IoU for the genus Porites, suggesting that the primary limitations to an automated workflow are 1) the current capabilities of neural network technology, and 2) consistency and quality control in image product collection and human training/testing dataset generation.

Evaluation of Particle Size Distribution Metrics to Estimate the Relative Contributions of Different Size Fractions Based on Measurements in Arctic Waters.

The size distribution of suspended particles influences several processes in aquatic ecosystems, including light propagation, trophic interactions, and biogeochemical cycling. The shape of the particle size distribution (PSD) is commonly modeled as a single-slope power law in oceanographic studies, which can be used to further estimate the relative contributions of different particle size classes to particle number, area, and volume concentration. We use a data set of 168 high size-resolution PSD measurements in Arctic oceanic waters to examine variability in the shape of the PSD over the particle diameter range 0.8 to 120 µm. An average value of -3.6 ± 0.33 was obtained for the slope of a power law fitted over this size range, consistent with other studies. Our analysis indicates, however, that this model has significant limitations in adequately parameterizing the complexity of the PSD, and thus performs poorly in predicting the relative contributions of different size intervals such as those based on picoplankton, nanoplankton, and microplankton size classes. Similarly, median particle size was also generally a poor indicator of these size class contributions. Our results suggest that alternative percentile diameters derived from the cumulative distribution functions of particle number, cross-sectional area, and volume concentration may provide better metrics to capture the overall shape of the PSD and to quantify the contributions of different particle size classes.