Research

To advance our understanding of how the architecture of biological systems impacts their function, I engineer analysis methods and bioinstrumentation to quantify morphology and organization across all biologically-relevant length scales. In collaboration with biologists and theoreticians, I apply these methods to study the physical and chemical mechanisms that shape our cells, tissues, and organs.

You can find a full list of my papers and patents on my Google Scholar profile.

Multimodal spatial omics

Morphogenesis is a carefully choreographed dance of molecular and morphological patterning. Yet, it remains difficult to quantify interactions between molecular and morphological features in biological organisms. Towards bridging this gap, I develop computational frameworks for integrating spatial molecular profiling and imaging data. This work comprises community-driven data standards, interactive data visualization, and performant software libraries.

• SpatialData: an open and universal framework for multimodal spatial omics. See our preprint and peer-reviewed paper for details.
• starfish: a scaleable pipeline for image-based transcriptomics. See our peer-reviewed paper for details.
• insta: a tool for using crowd-sourced annotations to calibrate and validate in situ transcriptomics image processing pipelines. See our preprint and peer-reviewed paper for details.

Human-in-the-loop data visualization and analysis

Thanks to advances in imaging and computation, there is an opportunity to observe and quantify the architecture of organisms across all biologically-relevant length scales. However, due to the size and complexity, it remains challenging to view and explore these data. To address this need, I have developed software for interactive viewing, annotation, and analysis of complex imaging data.

• napari: python-based, GPU-accelerated n-dimensional image viewer for annotating images and exploring analysis results that integrates with modern deep learning algorithms and big data tools.
• napari-threedee: toolkit for building interactive applications for 3D annotation and analysis of images. See our pre-print here.

Computational biomechanics

To elucidate the mechanisms through which soft tissues (e.g., articular cartilage) transduce mechanical signals into microstructual and biochemical changes, we integrated experimental systems and computional models to study how mechanical properties change in response to mechanical stimulus.

Selected publications

Microfluidic tools for single-cell analysis

Protein localization and post translational modifications are key to understanding cell state, yet remain difficult to measure with single cell resolution. To meet this need, as a graduate student in the Herr Lab, I developed microfluidic tools for single cell protein analysis. Leveraging the favorable mass transport scaling of microfluidic length scales, we extended the sensitivity of traditional protein assays. In particular, we developed tools for measuring the subcellular localization of proteins from single cells and for highly-selective measurement of protein isoforms from single cells.

Selected publications

Microfabrication of functional hydrogels

To extend the capabilities of microfluidic devices for biological assays, I developed fabrication methods that add new functions to hydrogels.

Selected publications