Methods
We develop high-plex quantitative methods that provide subcellular spatial data about the complex biological interactions occurring within tissues. Our methods enable next-generation breakthroughs in precision medicine, such as AI-assisted predictive models, early detection of cancer, and targeted approaches to treating disease.
Much of our work relies on the cyclic immunofluorescence (CyCIF) method, which generates high-plex tissue images using multiple cycles of staining, imaging, and bleaching. More recently, we developed the Orion method, which collects rapid, one-shot 18-channel immunofluorescence images and clinical-grade H&E images of the same slide.
CyCIF
CyCIF (cyclic immunofluorescence) is a robust, inexpensive method for highly multiplexed immunofluorescence imaging of human tissue samples. CyCIF generates multiplexed images using an iterative process in which low-plex fluorescence images are repeatedly collected from the same sample and assembled into a high-dimensional mosaic image. High-plex images of tumors can be used to quantify signal transduction cascades, measure the levels of tumor antigens, determine precise immune phenotypes, and more.
Orion
Orion is a method for collecting one-shot 18-plex immunofluorescence images and diagnostic-grade H&E images from the same samples. The Orion method was developed in collaboration with RareCyte Inc. and uses a specialized microscope and fluorescent antibodies (known as ArgoFluors™), which can be imaged simultaneously and spectrally unmixed. We show that same-slide H&E and IF images provide complementary information that can be used to train ML models that effectively predict cancer progression.
Deep Dye Drop
The Dye Drop assay is a versatile, low-cost, multiplexed microscopy method for obtaining detailed single-cell viability and cell cycle data. The Dye Drop method uses a set of incrementally more dense solutions to prevent cell loss and improve the consistency of cell perturbation experiments. Dye Drop can also be combined with CyCIF to yield further molecular and spatial information. The method is paired with computational analysis tools that calculate cell state and growth rate metrics from the high throughput data.