Feature Tracking for High Speed AFM Imaging of Biopolymers

Abstract

The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates are needed with scan ranges larger than are currently achievable. Moreover, there is a significant installed base of slower instruments that would benefit from algorithmic approaches to increasing their frame rate without requiring significant hardware modifications. In this paper, we present an experimental demonstration of high speed scanning on an existing, non-high speed instrument, through the use of a feedback-based, feature-tracking algorithm that reduces imaging time by focusing on features of interest to reduce the total imaging area. Experiments on both circular and square gratings, as well as silicon steps and DNA strands show a reduction in imaging time by a factor of 3–12 over raster scanning, depending on the parameters chosen.

Recent development of high‐speed atomic force microscopy in molecular biology

“…Hartman et al [40] designed a feedback-based feature tracking algorithm that reduces imaging time by focusing on the characteristics of the sample, thus reducing the total imaging area. The Hartman team used the same parameters to perform comparative tests on circular gratings, square gratings, silicon steps as well as DNA strands and found that the imaging time of raster scanning was reduced by 3-12 times.…”

Non-raster Methods in Scanning Probe Microscopy

“…The probe is then moved along that predicted path and feedback used to correct any prediction error. The method has been used to image DNA (Hartman and Andersson 2018) and to quickly build contour maps of cells (Zhang et al 2015a). Because it naturally eliminates drift in the microscope over time, the method will likely be particularly beneficial to examine samples over long periods of time.…”

“…(c) Experimental image of a strand of DNA acquired using a feature-tracking method known as local circular scan. Image reproduced with permission from (Hartman and Andersson 2018) to increase probe speed or improve the system hardware.…”

Improving the Image Acquisition Rate of an Atomic Force Microscope Through Spatial Subsampling and Reconstruction

“…Non-raster scan patterns can also improve imaging rate by reducing sampling rather than increasing speed. This class includes local scanning methods that use the measurements in real-time to steer the tip to focus the scan on features of interest [26]- [29]. While these have been shown to yield an order of magnitude or better improvement in imaging rate, they are limited in the class of samples that can be imaged and do not produce a full image with all the context.…”