Expediting image analysis for novel biological applications with an automated MATLAB algorithm

William Armstrong (JMU, Engineering '20) worked with me for 2 years to use image analysis tools in MATLAB to count number of cell nuclei present in a fluorescent microscope image. We worked together to find different applications for this, including working with Dr. Marta Bechtel (JMU, Biology) for a year to not only count how many cells were present, but also quantify the amount of actin present in her microscope images. Her work with cornea tissue showed that higher levels of actin (stained red in the images) meant the regenerating tissue was no longer transparent. Will's MATLAB code counted cells present and then recorded the intensity of actin present by looking at the red channel. He continued to work on his program by looking into multiple image analysis methods for counting cells and performed statistical ANOVA analysis to identify the "best" approaches based on parameters for the initial images. He looked at variables such as compactness and size through generating artificial high contrast images with known counts, and then compared the current image analysis quantification methods to the known counts.