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Coral reefs are fast-changing and complex ecosystems that are crucial to monitor and study. Biological hotspot detection can help coral reef managers prioritize limited resources for monitoring and intervention tasks. Here, we explore the use of autonomous underwater vehicles (AUVs) with cameras, coupled with visual detectors and photogrammetry, to map and identify these hotspots. This approach can provide high spatial resolution information in fast feedback cycles. To the best of our knowledge, we present one of the first attempts at using an AUV to gather visually-observed, fine-grain biological hotspot maps in concert with topography of a coral reefs. Our hotspot maps correlate with rugosity, an established proxy metric for coral reef biodiversity and abundance, as well as with our visual inspections of the 3D reconstruction. We also investigate issues of scaling this approach when applied to new reefs by using these visual detectors pre-trained on large public datasets.

Successful applications of complex vision-based behaviours underwater have lagged behind progress in terrestrial and aerial domains. This is largely due to the degraded image quality resulting from the physical phenomena involved in underwater image formation. Spectrally-selective light attenuation drains some colors from underwater images while backscattering adds others, making it challenging to perform vision-based tasks underwater. State-of-the-art methods for underwater color correction optimize the parameters of image formation models to restore the full spectrum of color to underwater imagery. However, these methods have high computational complexity that is unfavourable for realtime use by autonomous underwater vehicles (AUVs), as a result of having been primarily designed for offline color correction. Here, we present DeepSeeColor, a novel algorithm that combines a state-of-the-art underwater image formation model with the computational efficiency of deep learning frameworks. In our experiments, we show that DeepSeeColor offers comparable performance to the popular "Sea-Thru" algorithm (Akkaynak & Treibitz, 2019) while being able to rapidly process images at up to 60Hz, thus making it suitable for use onboard AUVs as a preprocessing step to enable more robust vision-based behaviours., 7 pages, 5 figures, 2 tables. Presented at the 2023 International Conference on Robotics and Automation (ICRA)

The current approach to exploring and monitoring complex underwater ecosystems, such as coral reefs, is to conduct surveys using diver-held or static cameras, or deploying sensor buoys. These approaches often fail to capture the full variation and complexity of interactions between different reef organisms and their habitat. The CUREE platform presented in this paper provides a unique set of capabilities in the form of robot behaviors and perception algorithms to enable scientists to explore different aspects of an ecosystem. Examples of these capabilities include low-altitude visual surveys, soundscape surveys, habitat characterization, and animal following. We demonstrate these capabilities by describing two field deployments on coral reefs in the US Virgin Islands. In the first deployment, we show that CUREE can identify the preferred habitat type of snapping shrimp in a reef through a combination of a visual survey, habitat characterization, and a soundscape survey. In the second deployment, we demonstrate CUREE's ability to follow arbitrary animals by separately following a barracuda and stingray for several minutes each in midwater and benthic environments, respectively., 7 pages

In this work we develop and demonstrate a probabilistic generative model for phytoplankton communities. The proposed model takes counts of a set of phytoplankton taxa in a timeseries as its training data, and models communities by learning sparse co-occurrence structure between the taxa. Our model is probabilistic, where communities are represented by probability distributions over the species, and each time-step is represented by a probability distribution over the communities. The proposed approach uses a non-parametric, spatiotemporal topic model to encourage the communities to form an interpretable representation of the data, without making strong assumptions about the communities. We demonstrate the quality and interpretability of our method by its ability to improve performance of a simplistic regression model. We show that simple linear regression is sufficient to predict the community distribution learned by our method, and therefore the taxon distributions, from a set of naively chosen environment variables. In contrast, a similar regression model is insufficient to predict the taxon distributions directly or through PCA with the same level of accuracy.

Topic modeling of streaming sensor data can be used for high level perception of the environment by a mobile robot. In this paper we compare various Gibbs sampling strategies for topic modeling of streaming spatiotemporal data, such as video captured by a mobile robot. Compared to previous work on online topic modeling, such as o-LDA and incremental LDA, we show that the proposed technique results in lower online and final perplexity, given the realtime constraints.