Measuring the ever-changing 3-dimensional (3D) motions of the ocean requires simultaneous sampling at multiple locations. In particular, sampling the complex, nonlinear dynamics associated with submesoscales (<1–10 km) requires new technologies and approaches. Here we introduce the Mini-Autonomous Underwater Explorer (M-AUE), deployed as a swarm of 16 independent vehicles whose 3D trajectories are measured near-continuously, underwater. As the vehicles drift with the ambient flow or execute preprogrammed vertical behaviours, the simultaneous measurements at multiple, known locations resolve the details of the flow within the swarm. We describe the design, construction, control and underwater navigation of the M-AUE. A field programme in the coastal ocean using a swarm of these robots programmed with a depth-holding behaviour provides a unique test of a physical–biological interaction leading to plankton patch formation in internal waves. The performance of the M-AUE vehicles illustrates their novel capability for measuring submesoscale dynamics.

The large data sets provided by in situ optical microscopes are allowing us to answer longstanding questions about the dynamics of planktonic ecosystems. To deal with the influx of information, while facilitating ecological insights, the design of these instruments increasingly must consider the data: storage standards, human annotation, and automated classification. In that context, we detail the design of the Scripps Plankton Camera (SPC) system, an in situ microscopic imaging system. Broadly speaking, the SPC consists of three units: (1) an underwater, free-space, dark-field imaging microscope; (2) a server-based management system for data storage and analysis; and (3) a web-based user interface for real-time data browsing and annotation. Combined, these components facilitate observations and insights into the diverse planktonic ecosystem. Here, we detail the basic design of the SPC and briefly present several preliminary, machine-learning-enabled studies illustrating its utility and efficacy.

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.