Brennan McCarty

 Brennan McCarty
Mentor: Dr. Yiider Tseng
College of Engineering
 
"I got involved with research due to the fact I've always been fascinated by science. I've always had dreams of discovering the next big scientific breakthrough and having my name written in textbooks as someone who helped humanity in a profound and unforgettable way. Research is an ideal outlet for this and allows me to explore the universe around us. Also, research is a great outlet for other opportunities beyond our undergraduate experience that one simply cannot just turn their head from."

Major

Chemical Engineering

Minor

Mathematics; Biomolecular

Research Interests

  • Biomolecular
  • Computational Efficiency
  • Biophysics

Academic Awards

  • UF University Scholars Program

Organizations

  • AIChE

Volunteer

  • St. Francis Homeless Shelter
  • Clearwater Marine Aquarium

Hobbies and Interests

  • Sports
  • Video Games
  • Sciences

Research Description

High Throughput Image Analysis: Design and Implementation
Once the progression of cancer reaches the stage of metastasis, life expectancy is dramatically decreased. Preventative care and regular checkups have the potential to prevent the normal progression of primary tumors to an invasive phenotype, but biopsy analysis performed by visual inspection of patient cell samples lacks the resolution to detect subtle differences in cells that may be important indicators for the presence of aggressive tumor cells. In response to this issue, digital image analysis and cell feature recognition has become a major focus in Dr. Tseng’s group. Widely-accessible software packages designed to analyze images of cell cultures such as ImageJ and CellProfiler currently lack state-of-the-art image processing capability, and so the algorithms developed and used in the lab have been custom designed in Matlab. My role in the ongoing project involves the conversion of the Matlab functions into high efficiency C++ source code. This is expected to boost the throughput of data analysis and support the main project, but also fosters the ability to integrate state-of-the-art methods into more available software packages as optional plug-ins. ImageJ is a Java-based program and CellProfiler has recently transitioned from Matlab to Python to boost computation power. C++ has libraries that support portability from source code into several other languages, including Java and Python, and so my work could further support the ability of researchers worldwide to gain access to powerful image processing tools for applications beyond biopsy analysis. Meanwhile, several algorithms exist that are too complex for implementation in Matlab that can be explored using C++. As a secondary goal, I will assist in the implementation and comparison of these techniques with methods already being developed by Dr. Tseng’s group. It is my high hope that the programs I develop in my time in this lab could be compiled, stored, and re-used with ease so that future student’s and professor’s alike would have an easier way to process and utilize the data they see every day. Since high throughput image processing is desperately sought after in the field of bioinformatics and biology, my project fulfills a need and would aid to further delve into and understand the underlying connection between cells, their microenvironments and their ability to migrate or spread.