About

I'm a Seattle based computational biologist at the Allen Institute for Cell Science. I design computer vision and machine learning tools to describe how cells organize and interact with their environment.

Previously, I went to grad school at Carnegie Mellon University & University of Pittsburgh, with Robert Murphy. I have collaborated with Devin Sullivan, Gustavo Rohde, Jörn Dengjel, Klaus Palme and many others.

Before that, I developed regulated document management software at Amgen.

Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy

Allen Institute for Cell Science 2016 - Ongoing

With collaborators from the Allen Institute for Brain Science, I've been developing tools to determine relationships across image modalities. We use a very simple deep learning model to predict the organization of many types of subcellular structures from three-dimensional brightfield images. We also show that this method works for electron micrographs, allowing us to solve very difficult image registration problems.

You can read our manuscript from September 2018 at Nature Methods.
The software to build and run our models is here.

Integrated Cell Models

Allen Institute for Cell Science 2016 - Ongoing

I've been working in collaboration with Rory Donovan-Maiye to build integrated models of single cells. We use some cool deep learning tricks and conditional generative adversarial networks (GANs) to fuse data from multiple fluorescence microscopy experiments into a coherent model of sub-cellular structure localization in single cells.

Our preprints for 2D models and 3D models are available.
Our software can be found here.

Dose-response screening in the low-replicate high-content regime

Carnegie Mellon University 2015 - 2017

To efficiently determine the effects of perturbations on cells (drugs), we need to build quantitative automated analysis tools to analyze the results of experiments. With collaborators at the University of Freiburg, we designed a pipeline to detect dose-dependent responses in plant cells in experiments with low numbers of replicates and high experimental variation. By labeling different components, we learn when and where these drugs affect the cell.

Our paper can be found in Cytometry.

Characterization of Starvation-Induced Macroautophagy

Carnegie Mellon University 2014 - 2017

When cells get hungry they eat themselves. With different collaborators at the University of Freiburg, we showed that depending on how they get hungry they eat themselves in different ways. We characterized how, when, and where this happens. Our publication made it on the cover of the journal Autophagy.

The manuscript can be found in the journal Autophagy.

CellOrganizer

Carnegie Mellon University 2012 - 2016

A large part of my Ph.D. was working on a software tool called CellOrganizer that builds generative models of how cells are put together. That resulted in a few projects:

A non-parametric model of how cell and nuclear shape are coordinated across cell states and drug conditions was published in Molecular Biology of the Cell.

Two models of how compartments of the cell are organized with the cell superstructure were published in PLOS Computational Biology and Cytometry.