UMass Professor Uses App Designer to Study Bacteria DNA
Apps Track Workflow and Help Perform Image Segmentation of Bacterial Cells
“MATLAB had advantages for me as a beginner programmer, including access to MathWorks Technical Support staff. I was able to contact them easily and they would explain various functions and computer conventions to me, as well as always follow up to make sure that I had the most up-to-date information.”
Key Outcomes
- App-based workflows enabled reproducibility and helped non-coding students perform complex microscopy analysis
- Interactive segmentation of bacterial images helped extract information on individual bacterial cells that was previously unobtainable
- MathWorks support staff communicated up-to-date information for bacterial analysis projects and directly answered workflow and coding questions
Capturing bacterial images with fluorescent markers is crucial to how Sandler’s lab studies DNA repair.
Professor Steven Sandler is professor emeritus of microbiology at the University of Massachusetts Amherst. His lab studies the genetics and DNA repair pathways of bacteria, particularly Escherichia coli (E. coli). These bacteria can be found in the intestines of animals and humans, and understanding their repair processes can help researchers better understand DNA repair in cancers as well as the role of bacteria in gut health.
Studying E. coli requires many moving pieces, such as tracking how a bacterial strain was made, whether it’s mutated, and where it is in storage. Extracting information from these bacterial cells also requires processing images from billions of individual cells. Additionally, segmenting images of bacteria can be challenging for standard programs. Professor Sandler observed that there were few dedicated tools to automate these tasks and turned toward MATLAB® to design his own using App Designer.
As a non-coder, Sandler found many resources online and the assistance from MathWorks support staff made it easy to design applications that could help advance his lab work. In particular, Sandler designed an app to track workflow in the lab and another to perform image segmentation of bacterial cells for analysis. Complimentary tools from the MATLAB library were also incorporated to improve the apps’ functionality.
Beyond increasing and managing the large amount of information Sandler’s lab can extract from each bacterial cell, these apps also made it possible for over 50 non-coder students to perform complex microscopy analyses.
