An Overview
Major: Environmental Science, Geography, GIS Science
Academic Affiliation: University of Maryland Baltimore County
Biography
Growing up in Baltimore, Maryland, Zachary became fascinated in geoscience during his childhood explorations along the shorelines of Ocean City, Maryland. Zachary’s curiosity in coastal processes and the natural environment has inspired him to pursue a career as a professor and researcher of coastal and fluvial geomorphology. This summer as a RESESS intern, he focused on developing a new method to automate particle analysis processing of diatoms, a type of single-celled algae. His work is the first to use VisualSpreadsheet software, independent of its complementary FlowCam hardware, to conduct automated particle analysis on microscope images of diatoms and will contribute to techniques of diatom enumeration employed by academic institutions and federal agencies.
Abstract
2017- Automated Diatom Analysis Applied to Traditional Light Microscopy: A Proof-of-Concept Study
Diatom identification and enumeration by high resolution light microscopy is required for many areas of research and water quality assessment. Such analyses, however, are both expertise and labor-intensive. These challenges motivate the need for an automated process to efficiently and accurately identify and enumerate diatoms. Improvements in particle analysis software have increased the likelihood that diatom enumeration can be automated. VisualSpreadsheet software provides a possible solution for automated particle analysis of high-resolution light microscope diatom images. We applied the software, independent of its complementary FlowCam hardware, to automated analysis of light microscope images containing diatoms. Through numerous trials, we arrived at threshold settings to correctly segment 67% of the total possible diatom valves and fragments from broad fields of view. (183 light microscope images were examined containing 255 diatom particles. Of the 255 diatom particles present, 216 diatoms valves and fragments of valves were processed, with 170 properly analyzed and focused upon by the software). Manual analysis of the images yielded 255 particles in 400 seconds, whereas the software yielded a total of 216 particles in 68 seconds, thus highlighting that the software has an approximate five-fold efficiency advantage in particle analysis time. As in past efforts, incomplete or incorrect recognition was found for images with multiple valves in contact or valves with little contrast. The software has potential to be an effective tool in assisting taxonomists with diatom enumeration by completing a large portion of analyses. Benefits and limitations of the approach are presented to allow for development of future work in `image analysis and automated enumeration of traditional light microscope images containing diatoms.
2018- Modeling river delta evolution under different wave climates
Deltas, dynamic landforms that are heavily inhabited by humans, result from a combination of river and coastal processes (Neinhuis and Ashton, 2013). As river sediment lengthens a river course and builds a delta lobe, wave driven alongshore transport reshapes the coastline. River lengthening promotes channel aggradation and eventually avulsions. Coastal processes affect river lengthening, and therefore avulsions. On the other hand, avulsions change where the sediment is delivered to the coastline, affecting coastline shape and processes. In previous numerical modeling analyses, Ratliff and others (2018) began to investigate how this coupling affected delta morphology and avulsion dynamics. As a simplification, the initial work involved symmetric wave climates – wave climates that produce no net alongshore sediment transport on average. Here we broaden these initial investigations by implementing asymmetric wave climates (and net alongshore sediment transport). In the numerical model experiments we manipulate four parameters: wave height; degree of asymmetry of wave climate; effectiveness of waves at smoothing coastlines (ratio of “high angle” to “low angle” waves); and critical threshold channel superelevation for avulsions. As expected increasing asymmetry yields asymmetric delta shapes; however, increasing wave heights can inhibit delta asymmetry. Lowering superelevation threshold for avulsions also tends to inhibit delta asymmetry. Unexpectedly, the migration of asymmetric deltas inhibited avulsions in the downdrift direction. In addition, the rotation of the coastline on the updrift side of asymmetric deltas produced avulsions that only minimally change channel lengths (and also minimal change in sediment flux out of the river mouth). As migration of an asymmetric delta becomes sufficiently pronounced, the erosive updrift side of the delta impinges on the river mouth – tending to slow progradation and inhibiting avulsions.
Posters
Automated Diatom Analysis Applied to Traditional Light Microscopy: A Proof-of-Concept Study
Modeling river delta evolution under different wave climates