A method for semi-automated objective quantification of linear bedforms from multi-scale Digital Elevation Models

The increasing availability of large, detailed digital representations of the Earth’s surface demands the application of objective and quantitative analyses. Given recent advances in the understanding of the mechanisms of formation of linear bedform features from a range of environments, objective measurement of their wavelength, orientation, crest and trough positions, height and asymmetry is highly desirable. These parameters are also of use when determining observation-based parameters for use in many applications such as numerical modelling, surface classification and sediment transport pathway analysis. Here, we (i) adapt and extend extant techniques to provide a suite of semi-automatic tools which calculate crest orientation, wavelength, height, asymmetry direction and asymmetry ratios of bedforms, and then (ii) undertake sensitivity tests on synthetic data, increasingly complex seabeds and a very large-scale (39 000km2) aeolian dune system. The automated results are compared with traditional, manually derived,measurements at each stage. This new approach successfully analyses different types of topographic data (from aeolian and marine environments) from a range of sources, with tens of millions of data points being processed in a semi-automated and objective manner within minutes rather than hours or days. The results from these analyses show there is significant variability in all measurable parameters in what might otherwise be considered uniform bedform fields. For example, the dunes of the Rub’ al Khali on the Arabian peninsula are shown to exhibit deviations in dimensions from global trends. Morphological and dune asymmetry analysis of the Rub’ al Khali suggests parts of the sand sea may be adjusting to a changed wind regime from that during their formation 100 to 10 ka BP.

Effect of Grazing-Mediated Dimethyl Sulfide (DMS) Production on the Swimming Behavior of the Copepod Calanus helgolandicus

Chemical interactions play a fundamental role in the ecology of marine foodwebs. Dimethyl sulfide (DMS) is a ubiquitous marine trace gas that acts as a bioactive compound by eliciting foraging behavior in a range of marine taxa including the copepod Temora longicornis. Production of DMS can rapidly increase following microzooplankton grazing on phytoplankton. Here, we investigated whether grazing-induced DMS elicits an increase in foraging behavior in the copepod Calanus helgolandicus. We developed a semi-automated method to quantify the effect of grazing-mediated DMS on the proportion of the time budget tethered females allocate towards slow swimming, typically associated with feeding. The pooled data showed no differences in the proportion of the 25 min time budget allocated towards slow swimming between high (23.6 +/- 9.74%) and low (29.1 +/- 18.33%) DMS treatments. However, there was a high degree of variability between behavioral responses of individual copepods. We discuss the need for more detailed species-specific studies of individual level responses of copepods to chemical signals at different spatial scales to improve our understanding of chemical interactions between copepods and their prey.

Automated analysis of non-mass-enhancing lesions in breast MRI based on morphological, kinetic, and spatio-temporal moments and joint segmentation-motion compensation technique

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) represents an established method for the detection and diagnosis of breast lesions. While mass-like enhancing lesions can be easily categorized according to the Breast Imaging Reporting and Data System (BI-RADS) MRI lexicon, a majority of diagnostically challenging lesions, the so called non-mass-like enhancing lesions, remain both qualitatively as well as quantitatively difficult to analyze. Thus, the evaluation of kinetic and/or morphological characteristics of non-masses represents a challenging task for an automated analysis and is of crucial importance for advancing current computer-aided diagnosis (CAD) systems. Compared to the well-characterized mass-enhancing lesions, non-masses have no well-defined and blurred tumor borders and a kinetic behavior that is not easily generalizable and thus discriminative for malignant and benign non-masses. To overcome these difficulties and pave the way for novel CAD systems for non-masses, we will evaluate several kinetic and morphological descriptors separately and a novel technique, the Zernike velocity moments, to capture the joint spatio-temporal behavior of these lesions, and additionally consider the impact of non-rigid motion compensation on a correct diagnosis.

The emergence of automated high-frequency flow cytometry: revealing temporal and spatial phytoplankton variability

Phytoplankton observation is the product of a number of trade-offs related to sampling processes, required level of diversity and size spectrum analysis capabilities of the techniques involved. Instruments combining the morphological and high-frequency analysis for phytoplankton cells are now available. This paper presents an application of the automated high-resolution flow cytometer Cytosub as a tool for analysing phytoplanktonic cells in their natural environment. High resolution data from a temporal study in the Bay of Marseille (analysis every 30 min over 1 month) and a spatial study in the Southern Indian Ocean (analysis every 5 min at 10 knots over 5 days) are presented to illustrate the capabilities and limitations of the instrument. Automated high-frequency flow cytometry revealed the spatial and temporal variability of phytoplankton in the size range 1−∼50 μm that could not be resolved otherwise. Due to some limitations (instrumental memory, volume analysed per sample), recorded counts could be statistically too low. By combining high-frequency consecutive samples, it is possible to decrease the counting error, following Poisson’s law, and to retain the main features of phytoplankton variability. With this technique, the analysis of phytoplankton variability combines adequate sampling frequency and effective monitoring of community changes.

Coastal upwelling and downwelling forcing of circulation in a semi-enclosed bay: Ria de Vigo

Semi-enclosed bays in upwelling regions are exposed to forcing related to winds, currents and buoyancy over the shelf. The influence of this external forcing is moderated by factors such as connectivity to the open ocean, shelter by surrounding topography, dimensions of the bay, and freshwater outflows. Such bays, preferred locations for ports, mariculture, marine industry, recreational activities and coastal settlement, present a range of characteristics, understanding of which is necessary to their rational management. Observations in such a semi-enclosed bay, the Ria de Vigo in Spain, are used to characterize the influence of upwelling and downwelling pulses on its circulation. In this location, near the northern limit of the Iberian upwelling system, upwelling events dominate during a short summer season and downwelling events the rest of the year. The ria response to the external forcing is central to nutrient supply and resultant plankton productivity that supports its high level of cultured mussel production. Intensive field studies in September 2006 and June 2007 captured a downwelling event and an upwelling event, respectively. Data from eight current profiler moorings and boat-based MiniBat/ADCP surveys provided an unprecedented quasi-synoptic view of the distribution of water masses and circulation patterns in any ria. In the outer ria, circulation was dominated by the introduction of wind-driven alongshore flow from the external continental shelf through the ria entrances and its interaction with the topography. In the middle ria, circulation was primarily related to the upwelling/downwelling cycle, with a cool, salty and dense lower layer penetrating to the inner ria during upwelling over the shelf. A warmer, lower salinity and less dense surface layer of coastal waters flowed inward during downwelling. Without external forcing, the inner ria responded primarily to tides and buoyancy changes related to land runoff. Under both upwelling and downwelling conditions, the flushing of the ria involved shelf responses to wind pulses. Their persistence for a few days was sufficient to allow waters from the continental shelf to penetrate the innermost ria. Longer term observations supported by numerical modeling are required to confirm the generality of such flushing events in the ria and determine their typical frequency, while comparative studies should explore how these scenarios fit into the range of conditions experienced in other semi-enclosed bays.