In situ measurements were undertaken to characterize particle fields in undisturbed oceanic environments. Simultaneous, co‐located depth profiles of particle fields and flow characteristics were recorded using a submersible holographic imaging system and an acoustic Doppler velocimeter, under different flow conditions and varying particle concentration loads, typical of those found in coastal oceans and lakes. Nearly one million particles with major axis lengths ranging from ∼14 μm to 11.6 mm, representing diverse shapes, sizes, and aspect ratios were characterized as part of this study. The particle field consisted of marine snow, detrital matter, and phytoplankton, including colonial diatoms, which sometimes formed “thin layers” of high particle abundance. Clear evidence of preferential alignment of particles was seen at all sampling stations, where the orientation probability density function (PDF) peaked at near horizontal angles and coincided with regions of low velocity shear and weak turbulent dissipation rates. Furthermore, PDF values increased with increasing particle aspect ratios, in excellent agreement with models of spheroidal particle motion in simple shear flows. To the best of our knowledge, although preferential particle orientation in the ocean has been reported in two prior cases, our findings represent the first comprehensive field study examining this phenomenon. Evidence of nonrandom particle alignment in aquatic systems has significant consequences to aquatic optics theory and remote sensing, where perfectly random particle orientation and thus isotropic symmetry in optical parameters is assumed. Ecologically, chain‐forming phytoplankton may have evolved to form large aspect ratio chains as a strategy to optimize light harvesting.

There is a growing use of remote sensing observations for detecting and quantifying freshwater cyanobacteria populations, yet the inherent optical properties of these communities in natural settings, fundamental to bio-optical algorithms, are not well known. Toward bridging this knowledge gap, we measured a full complement of optical properties in western Lake Erie during cyanobacteria blooms in the summers of 2013 and 2014. Our measurements focus attention on the optical uniqueness of cyanobacteria blooms, which have consequences for remote sensing and bio-optical modeling. We found the cyanobacteria blooms in the western basin during our field work were dominated by Microcystis, while the waters in the adjacent central basin were dominated by Planktothrix. Chlorophyll concentrations ranged from 1 to over 135 µg/L across the study area with the highest concentrations associated with Microcystis in the western basin. We observed large, amorphous colonial Microcystis structures in the bloom area characterized by high phytoplankton absorption and high scattering coefficients with a mean particle backscatter ratio at 443 nm > 0.03, which is higher than other plankton types and more comparable to suspended inorganic sediments. While our samples contained mixtures of both, our analysis suggests high contributions to the measured scatter and backscatter coefficients from cyanobacteria. Our measurements provide new insights into the optical properties of cyanobacteria blooms, and indicate that current semi-analytic models are likely to have problems resolving a closed solution in these types of waters as many of our observations are beyond the range of existing model components. We believe that different algorithm or model approaches are needed for these conditions, specifically for phytoplankton absorption and particle backscatter components. From a remote sensing perspective, this presents a challenge not only in terms of a need for new algorithms, but also for determining when to apply the best Moore et al. Lake Erie IOPs algorithm for a given situation. These results are new in the sense that they represent a complete description of the optical properties of freshwater cyanobacteria blooms, and are likely to be representative of bloom conditions for other systems containing Microcystis cells and colonies.

harmful algal blooms (Donaghay & Osborn 1997, McManus et al. 2008). Early studies of the patchiness in physical and biochemical patterns focused on large scales, typically tens of meters or larger (e.g. Cassie 1963, Haury et al. 1978). It has been recognized that fine-scale patchiness is critical to the interaction between physicochemical parameters and biology (Valiela 1995, Ryan et al. 2010). A particular phenomenon that has received substantial attention is formation of vertically layered, thin patches of © Inter-Research 2013 • www.int-res.com

The Kelvin–Helmholtz stability of the cylindrical interface between the vapor and liquid phases of a fluid is studied when the vapor is hotter than the liquid and the two phases are enclosed between two cylindrical surfaces coaxial with the interface, and when there is a mass and heat transfer across the interface. Both axisymmetric and asymmetric disturbances are considered. A comparison of the results obtained here with those for the corresponding problem with plane geometry reveals that the plane geometry configuration is more stable than the cylindrical one, and, contrary to the case of Rayleigh–Taylor instability problem, the heat and mass transfer has a destabilizing influence on the system.

In situ digital inline holography is a technique which can be used to acquire high‐resolution imagery of plankton and examine their spatial and temporal distributions within the water column in a nonintrusive manner. However, for effective expert identification of an organism from digital holographic imagery, it is necessary to apply a computationally expensive numerical reconstruction algorithm. This lengthy process inhibits real‐time monitoring of plankton distributions. Deep learning methods, such as convolutional neural networks, applied to interference patterns of different organisms from minimally processed holograms can eliminate the need for reconstruction and accomplish real‐time computation. In this article, we integrate deep learning methods with digital inline holography to create a rapid and accurate plankton classification network for 10 classes of organisms that are commonly seen in our data sets. We describe the procedure from preprocessing to classification. Our network achieves 93.8% accuracy when applied to a manually classified testing data set. Upon further application of a probability filter to eliminate false classification, the average precision and recall are 96.8% and 95.0%, respectively. Furthermore, the network was applied to 7500 in situ holograms collected at East Sound in Washington during a vertical profile to characterize depth distribution of the local diatoms. The results are in agreement with simultaneously recorded independent chlorophyll concentration depth profiles. This lightweight network exemplifies its capability for real‐time, high‐accuracy plankton classification and it has the potential to be deployed on imaging instruments for long‐term in situ plankton monitoring.

The characterization of particle and plankton populations, as well as microscale biophysical interactions, is critical to several important research areas in oceanography and limnology. A growing number of aquatic researchers are turning to holography as a tool of choice to quantify particle fields in diverse environments, including but not limited to, studies on particle orientation, thin layers, phytoplankton blooms, and zooplankton distributions and behavior. Holography provides a non-intrusive, free-stream approach to imaging and characterizing aquatic particles, organisms, and behavior in situ at high resolution through a 3-D sampling volume. Compared to other imaging techniques, e.g., flow cytometry, much larger volumes of water can be processed over the same duration, resolving particle sizes ranging from a few microns to a few centimeters. Modern holographic imaging systems are compact enough to be deployed through various modes, including profiling/towed platforms, buoys, gliders, long-term observatories, or benthic landers. Limitations of the technique include the data-intensive hologram acquisition process, computationally expensive image reconstruction, and coherent noise associated with the holograms that can make post-processing challenging. However, continued processing refinements, rapid advancements in computing power, and development of powerful machine learning algorithms for particle/organism classification are paving the way for holography to be used ubiquitously across different disciplines in the aquatic sciences. This review aims to provide a comprehensive overview of holography in the context of aquatic studies, including historical developments, prior research applications, as well as advantages and limitations of the technique. Ongoing technological developments that can facilitate larger employment of this technique toward in situ measurements in the future, as well as potential applications in emerging research areas in the aquatic sciences are also discussed.

[1] In situ particle image velocimetry measurements, at a resolution of 3.5 Kolmogorov scales, have been performed in the inner part of the coastal bottom boundary layer. The spatial details enable us to directly determine the vertical distributions of mean velocity, Reynolds shear stress, shear production and dissipation rates, energy spectra, and abundance of eddies. Focusing on cases with wave velocity of similar magnitude as the mean current, velocity profiles have logarithmic distributions in the upper half of the sample area. Below the log layer, but well above the bottom ripples, an inflection point appears, indicating a region of flow instability. Based on data interpretation, which includes variations in wave phase with height, this inflection occurs near the interface between current and thinner wave boundary layer (WBL) below it. Scaling of mean velocity profiles with shear velocity and characteristic roughness is effective only above the inflection point, while turbulence parameters scale reasonably well at all elevations. Instabilities associated with the inflection are manifested by a peak in turbulent shear production rate and a rapid increase in small-scale turbulence, as is evident from trends of the dissipation rate, energy spectra, and distribution of eddies with elevation. Therefore, the presence of a WBL generates a shear production peak and rapid increase in the dissipation rate at higher elevations than those found in rough-wall steady boundary layers. Transition between current and wave boundary layers is also characterized by broad Reynolds stress peaks and shear production exceeding the dissipation rate.Citation: Hackett, E. E., L. Luznik, A. R. Nayak, J. Katz, and T. R. Osborn (2011), Field measurements of turbulence at an unstable interface between current and wave bottom boundary layers,

Interactions of currents and waves with a rippled seabed in the inner part of the coastal ocean bottom boundary layer are studied using particle image velocimetry, ADV, and bottom roughness measurements. Mean velocity profiles collapse with appropriate scaling in the log layer, but vary substantially in the roughness sublayer. When wave-induced motions are similar or greater than the mean current, the hydrodynamic roughness (z 0 ) determined from velocity profiles is substantially larger than directly measured values. The roughness signature in turbulent energy spectra persists with elevation when its scale falls in the dissipation range, but decays in the log layer for larger roughness elements. Reynolds shear stress profiles peak in the lower parts of the log layer, diminishing below it, and gradually decaying at higher elevations. In contrast, wave shear stresses are negligible within the log layer, but become significant within the roughness sublayer. This phenomenon is caused by an increase in the magnitude and phase lag of the vertical component of wave-induced motion. No single boundary layer length scale collapses the Reynolds stresses, but both the Prandtl mixing length and eddy viscosity profiles agree well with the classical model of linear increase with elevation, especially near the seabed. Within the log region, profiles of shear production and dissipation rates of turbulence converge. Below it, dissipation rapidly increases, peaking near the seabed. Conversely, the shear production decays near the seabed, in agreement with the eddy viscosity model, but in contrast to both laboratory and computational rough wall studies.