GRAPHical Insect Tracking Environment (GRAPHITE)

Methods for measuring animal movement are critical for understanding numerous ecological and evolutionary processes. However, few methods are available for small organisms, and even fewer methods offer consistent individual‐level resolution while remaining affordable, scalable and operable in the field. We describe a low‐cost animal movement tracking method with a user‐friendly graphical interface, called GRAPHITE. Our automated software can quantify motions of insects by offline video analysis of inexpensive and lightweight human‐readable tags attached to individual insects.

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Dynamic gigapixel Image Registration

High-throughput serial histology imaging provides a new avenue for the routine study of micro-anatomical structures in a 3D space. However, the emergence of serial whole slide imaging poses a new registration challenge, as the gigapixel image size precludes the direct application of conventional registration techniques. In this paper, we develop a three-stage registration with multi-resolution mapping and propagation method to dynamically produce registered subvolumes from serial whole slide images. We validate our algorithm with gigapixel images of serial brain tumor sections and synthetic image volumes.

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Biogeography of the Oral Microbiome

The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque.

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SpectralMagic

Spectral microscopy has the ability to generate a large volume of data in a short period of time. Unfortunately, commercial software has been limited in its ability to handle batch data. I developed a suite of MATLAB scripts called SpectralMagic to address these problems. SpectralMagic leverages the Bio-Formats library to gain access to microscope metadata. Using their unique metadata attributes, images are automagically processed with parallelized spectral unmixing algorithms. The batch functionality of the software allows users to set up an analysis job and get back to the wet bench.

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rBLAST

I started my undergraduate research at an exciting period in Cell and Developmental Biology. The late 1990’s marked a time when biologists truly got a handle on the genome sequencing business, and, at the turn of the millennium, a new genome was being sequenced each year. Much to the delight of urchinologists, the purple sea urchin, Strongylocentrotus purpuratus, was one of many model organisms to make its way through the sequencing pipeline. That’s where I came in…

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