EAPSI: Implementation of Advanced Computer Vision Techniques to Improve Real Time Imaging of Single Molecule Conformation Changes

Stuckner Joshua A, Blacksburg VA

Investigators

Abstract

The goal of this project is to implement advanced computer vision algorithms for the automatic analysis of ultra-slow motion movies of single molecules. This research will be conducted in collaboration with Dr. Koji Harano and his team at the University of Tokyo, who have for the first time directly observed a single molecule undergoing a particular and important change in shape. The event was captured on video using a powerful microscope equipped with a high speed camera. Understanding the shape, or conformation, changes of molecules is critical to the analysis of complex chemical systems and reactions. This technique produces over 100 gigabytes of data per second of video. Currently, the brute-force method that is used to compile this data into meaningful information requires tremendous computing time and power. Computer vision techniques will vastly increase the speed and accuracy of this analysis and lead more scientific output in this critical area. This project also represents an important exchange of scientific knowledge and techniques between the United States and Japan and will lead to future collaboration on similar projects. Dr. Harano's team used an advanced imaging technique to observe and measure a molecular ó-bond rotation for the first time using an aberration corrected high resolution transmission electron microscope equipped with a 1600 fps electron counting direct detection camera. The massive datasets generated by this technique must be processed before meaningful analysis can take place. Presently the technique relies on mathematical cross-correlation algorithms for automatic sorting, classification, and alignment of frames; a task far too cumbersome for manual frame by frame sorting at 1600 fps. However, cross-correlation is somewhat of a brute-force approach and the speed and accuracy of this process can be greatly increased by implementing feature matching computer vision algorithms. This project will implement and evaluate advanced computer vision algorithms for the automatic processing of data generated by Dr. Harano's imaging technique. This award, under the East Asia and Pacific Summer Institutes program, supports summer research by a U.S. graduate student and is jointly funded by NSF and the Japan Society for the Promotion of Science.