Solid-State Nanopore Recognition and Measurement Using Shannon Entropy

Abstract

Solid-state nanopores are structures that can be fabricated using the electron beam of a transmission electron microscope (TEM). Nanopores can be used to electrically detect individual DNA molecules, and they have the potential to be applied to genomic sequencing. Current nanofabrication methods are manual and time-consuming, and thus, they do not allow for the fabrication of large-scale nanopore arrays. One of the requirements in the development of an efficient fabrication process is the automated recognition and measurement of nanopore dimension in real time. Here, we present a method for nanopore edge detection that uses Shannon entropy to identify nanopores in electron microscopy images. The nanostructure edges are determined by applying a Shannon entropy filter. This entropy image is segmented, and the texture-defined edges are determined. The diameters of nanopores as small as 3 nm are directly measured.