Athey Lab Projects

High-throughput, four dimensional (4D) imaging of the transcriptional architecture of cells and tissue

This strategy involves the intersection of innovative methods in light microscopy including fluorescence in situ hybridization (FISH), image segmentation and extraction, texture analysis and imaging in three dimensions (3D), and rapid processing of large datasets using machine learning.


In collaboration with Assurex Health, Inc. of Mason, OH ( and its R&D network, the laboratory is leading the development of next generation pharmacogenomic testing for optimization of medication selection in psychiatry and neurology. Emphasis is placed on noncoding regulatory elements in the human genome and epigenome as determinants of drug response, adverse drug events and addiction. The following projects are underway and have led to transformative discoveries.

Brady Urological Institute at Johns Hopkins Medicine Collaboration

A collaboration with the Brady Urological Institute at Johns Hopkins Medicine, lead by Dr. Ken Pienta, to build on their extensive 2D characterization of prostate tumors, by the introduction of simple chromatin dyes, advanced biomarkers, and 3D imaging systems.

Dr. John Wiley Collaboration- Brain-Gut Axis

In collaboration with Dr. John Wiley of University of Michigan Health System, the effect of glucocorticoids on the neuroblastoma based cell line Sy5y before and after treatment with retinoic acid and BDNF, particularly in their terminally differentiated condition.

Super-resolution Microscopy Techniques

super resolution 3d microscopy

The laboratory is investigating super-resolution microscopy techniques including collaborating with Dr. Christoph Cremer from the Institute of Molecular Biology in Mainz, Germany and LuciaOptics.

Past Projects:

The Visible Human Project

visible human

The University of Michigan Visible Human project, lead by Dr. Brian Athey, serves The National Library of Medicine's Visible Human data to health science students, clinicians, educators, and researchers. Novel 2D and 3D navigational browsers display Visible Human content in an educationally relevant manner. Arbitrary slices, text, models, and flythroughs are being packaged into learning modules organized systemically or regionally to be delivered to many simultaneous users. Future goals of the project include an integrated physiological representation of the human body, from molecular, biochemical, genetic, cellular, to system levels. For more information go to

The Virtual Soldier Project

virtual soldier

The DARPA Virtual Soldier Project has developed complex mathematical models to create physiological representations of individual soldiers. These holographic medical representations (known as Holomers) can be used to improve medical diagnosis on and off the battlefield. For more information got to

The National Center for Integrative Biomedical Information

virtual soldier

The National Center for Integrative Biomedical Informatics (NCIBI) is one of eight National Centers for Biomedical Computing (NCBC) within the NIH Roadmap. The NCBC program is focused on building a universal computing infrastructure designed to speed progress in biomedical research. NCIBI was founded in September 2005 and is based at the University of Michigan as part of the Department of Computational Medicine and Bioinformatics (DCM&B). For more information go to

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