Author ORCID Identifier


Defense Date


Document Type


Degree Name

Doctor of Philosophy


Physics and Applied Physics

First Advisor

Jason Reed

Second Advisor

Inho Joh

Third Advisor

Joseph Reiner

Fourth Advisor

Milos Manic


The high-speed atomic force microscope (HS-AFM) is a device capable of collecting many full frame nanometer resolution images in real time, enabling investigation of dynamic processes and large areas not previously achievable by other means. Recent research in genomics and applied physics has shown that it is possible to diagnose certain diseases using topographic images of DNA strands immobilized on an atomically flat mica substrate, collected using an HS-AFM. This process produces diagnoses with a high degree of certainty and accuracy, but can be labor-intensive, requiring the cooperation of trained scientists of various disciplines to collect and analyze images of carefully prepared samples.

This thesis proposes a framework for streamlining this process, based on machine learning and other computer vision techniques. Exploration of this area will not only enhance the data collection and analysis process for genomics-based disease diagnosis, but more generally expand upon the growing overlap between machine learning techniques and scanning probe microscopy.


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Available for download on Wednesday, December 13, 2028