Douglas P. Shepherd

This study shows that stochastic colonization and host-to-host transmission significantly influence gut bacterial variability in C. elegans using E. coli under different diets.

The paper introduces curved axially scanned light-sheet microscopy to overcome field curvature limitations in light-sheet imaging, increasing the usable field of view while maintaining sub-cellular resolution.

This study shows that evolving larger cell size reduces internal cellular density, as material accumulation does not keep pace with volume increase, both in experimental evolution and across species.

This paper introduces a GPU-accelerated framework for processing 3D multiplexed RNA-FISH data, quantifies information loss from axial sampling, and improves post-mortem sample quality.

This paper develops a framework for simultaneous particle tracking, phase retrieval, and PSF reconstruction to improve 3D tracking of lytic granules in T cells.

REPOP reconstructs bacterial populations from platecounts by accounting for dilution and plating uncertainties, revealing hidden multimodality that standard methods obscure.

This paper presents an open-source, fully-automated two-color structured illumination module for super-resolution microscopy, achieving 1.55-fold improved lateral resolution over conventional wide-field microscopy.

This paper introduces B-SIM, an unsupervised Bayesian framework for structured illumination microscopy that improves resolution and contrast by accurately modeling noise, outperforming existing methods in both simulated and experimental data.

navigate provides an open-source platform for smart light-sheet microscopy, enabling automated and user-friendly LSFM workflows without requiring specialized expertise.

The paper develops a computational approach to model gene regulation by addressing distributional challenges in single-cell mRNA data, leading to predictive insights into transcription mechanisms.