Big Data, Big Dreams: Greg Scott, MS4

07/25/14  Portland, Ore.

ajrcmb-2014-51-issue-1-cover_1Gregory Scott, MS4 – a student in the joint M.D./Ph.D. education program – is a self-described computer guy. But don’t let that humble moniker fool you: Scott is much, much more.

This month, Scott’s paper, "Tissue Optical Clearing, Three-Dimensional Imaging, and Computer Morphometry in Whole Mouse Lungs and Human Airways," is featured on the July cover of the American Journal of Respiratory Cell and Molecular Biology. Not only is this paper highlighted with a “red alert” as an outstanding paper by a junior investigator, Scott was nominated for the annual junior investigator paper of the year award for his work developing a new method to quantify nerves in the murine lung.

According to Scott’s thesis advisor, David Jacoby, M.D.*, “This is a huge honor for Greg and reflects well on the types of students and programs within the School of Medicine.”


In the course of his graduate and post-graduate experiences, Scott became acutely aware of the limitations of current diagnostic technology and the unavailability of tools for researchers to adequately handle the large amounts of data amassed in their studies. Seeking a solution for the “lack of computer science in medicine,” he called upon his own undergraduate background in computer science to develop a software solution to the data processing issues common in the age of big data.

Scott’s paper – produced while a post-graduate research fellow (see particulars below) in the labs of Dr. Jacoby and Allison Fryer, Ph.D.* – unites and analyzes colabeled epitope images with 3D tissue compartments using an advanced morphometry software which was designed by Scott and will be made available through an open-source license. As Dr. Jacoby explains it, “Imagine trying to measure all the branches and length of each branch on a tree. Greg’s method allows us to do this. His method identifies exactly where the nerves are within the lungs, and we are now using his method to measure how and where nerves change in lung disease."


In the same way that understanding of the human genome has lead to the development of gene-based individualized care for disease such as cancer, Scott is excited by the potential for advanced imaging analysis to help clinicians see and treat a range of other diseases like never before. As the promise of big data is realized and begins to help researchers view the body in greater detail, Scott envisions practicing medicine in a future in which data analysis, diagnostic imaging and 3D printing will help clinicians better grasp the way diseases interact in a specific patient’s body, as in the case of a surgeon who might someday be able to use Scott’s methodology during the pre-operative planning phase.


Greg3DWeb_1As noted in the “red alert” section of the American Journal of Respiratory Cell and Molecular Biology, there is a “wide range of immediately foreseeable applications” for Scott’s methodology, and his work can already be seen proliferating across the OHSU campus. In June 2014, Scott spoke at OHSU Center for Spatial Systems Biomedicine (OCSSB) Symposium, where he connected with Danielle Jorgen, Ph.D. of the Knight Cancer Institute and today is using his method to analyze Dr. Jorgen’s electron microscopy images of breast and pancreatic cancer cells. Scott has also collaborated with Terry Morgan, M.D., Ph.D., associate professor of pathology, to create 3D prints from micro CT scan of murine placenta and has supported the work of Michael Grant M.D., instructor of diagnostic radiology, in developing precise 3D uterine models from MRI scans, models that may someday help to improve the training of surgeons.

As he prepares to enter his fourth year of medical school, Scott remains enthusiastic about the connections between his research and clinical experiences. Next up for Scott: a much-hoped for residency in pathology, the continued joys of new fatherhood and the next phase of his work in pulmonary bioimaging, where his goal is to begin mapping the lung biopsies of asthma patients.

*Particulars: David B. Jacoby, M.D.; professor of medicine (pulmonary and critical care); head of pulmonary and critical care OHSU School of Medicine; vice chair for research in the department of medicine; and director of the M.D./Ph.D. training program

Funded through National Institutes of Health grants; a National Heart, Lung and Blood Institute Predoctoral Fellowship; and by a National Institutes of Health Training Grant

Allison D. Fryer Ph.D.; FBPharmacolS; associate dean for Graduate Studies; professor of medicine (pulmonary and critical care); and professor of physiology and pharmacology OHSU School of Medicine