The Texas Biomedical Research Institute is a private research facility specializing in biomedical studies using non-human primates as a proxy for humans. It is one of the top research laboratories in the nation, housing over 3,000 non-human primates, the largest computing sector dedicated to human genetic analysis, and the Biosafety Level 4 lab, used to research incredibly dangerous incurable infectious diseases. Texas Biomed has three main departments: Genetics, Virology and Immunology, and the Southwest National Primate Research Center. An internship in the genetics department offers students a unique opportunity to participate in professional genetic research while gaining experience in a specialized laboratory.
My project as an intern focused on segmenting knee magnetic resonance images (MRI) for signs of osteoarthritis (OA). MRIs use magnetic fields and radio frequencies to create images of structures inside the body. These digital images can then be edited and analyzed for multiple reasons, including diagnosis of a disease. OA, involving the breakdown of cartilage in joints, leading to severe joint pain, is the leading cause of disability in the United States. While knee MRIs are commonly used to diagnose torn ligaments in the knee, this study used the MRIs to analyze cartilage thickness as a preliminary indicator for the development of OA. If the research hypothesis is supported by evidence, MRIs will be able to be used in patients with a genetic predisposition to the disease to possibly diagnose the disease before its onset. It would also show that cartilage thickness is a hereditary component to the development of OA, allowing future researchers to identify genes responsible for cartilage thickness, which in turn will allow researchers to better understand the disease as a whole.
I was required to segment three different parts of the knee: the femoral cartilage, the tibial cartilage, and the menisci. The process of segmentation is as follows. Once an MRI is uploaded, several filters are applied to clarify the MRI so that the important features can be seen clearly. A Median Filter was first applied to smooth out the image by adjusting pixel colors so that they are the median of the neighboring pixels. The second filter applied was a Curvature Anisotropic Filter, which reduced unwanted detail while still retaining key features such as sharp edges. Combined, these filters provided a smoother image of the MRI while clearly distinguishing the cartilage and menisci from the rest of the knee. After the filters are applied, a paint brush tool is used to highlight each section manually for each of the 160 images. This means that when looking at the MRI after segmentation, one will be able to see the femoral cartilage outlined and shaded in red, the tibial cartilage in yellow, and the meniscus in blue. Once everything is entirely segmented, the computer can use the data to build a three dimensional model of the knee for analysis. From this three dimensional model, further statistical analysis can calculate cartilage thickness and any other dimensional data as needed.
I was also involved with helping other people with their projects. A researcher who looked at cartilage wear in baboon knees occasionally asked me to help organize lab samples. It was through these kinds of interactions that the interns in the department became thoroughly educated on all of the research that was taking place. This balance of individual work and collaboration is a reflection of the institution’s culture of demanding high quality research.
Being surrounded by top researchers and high caliber research is the best part about the internship. At the lab, one is encouraged to attend guest lectures from top researchers. I was fortunate to be able to watch lectures from Dr. Henry McGill on atherosclerosis and by Dr. Sarah Williams-Blangero on genetic field studies around the world. Dr. McGill’s lecture discussed atherosclerosis studies in humans and how research on atherosclerosis in baboons is being used to help diagnose and fight atherosclerosis in humans. Dr. Blangero’s lecture discussed several studies on population genetics around the world conducted to learn more on genetic diseases.
Collaborating with researchers and other interns was an unforgettable experience that could only be obtained through this internship. I was fortunate to learn about empirical research through direct observation and to be able to watch the development of several projects. I highly recommend this internship to any student who is willing to trade hard work for a unique opportunity to conduct research in a prestigious biomedical research laboratory.