Design and implementation of high-bandwidth, high-resolution imaging in atomic force microscopy

Video-rate imaging with subnanometer resolution without compromising on the scan range has been a long-awaited goal in Atomic Force Microscopy (AFM). The past decade saw significant advances in hardware used in atomic force microscopes, which further enable the feasibility of high-speed Atomic Force Microscopy. Control design in AFMs plays a vital role in realizing the achievable limits of the device hardware. Almost all AFMs in use today use Proportional-Integral-Derivative(PID) control designs, which can be majorly improved upon for performance and robustness. We address the problem of AFM control design through a systems approach to design model-based control laws that can give major improvements in the performance and robustness of AFM imaging. First, we propose a cascaded control design approach to tapping mode imaging, which is the most common mode of AFM imaging. The proposed approach utilizes the vertical positioning sensor in addition to the cantilever deflection sensor in the feedback loop. The control design problem is broken down into that of an inner control loop and an outer control loop. We show that by appropriate control design, unwanted effects arising out of model uncertainties and nonlinearities of the vertical positioning system are eliminated. Experimental implementation of the proposed control design shows improved imaging quality at up to 30% higher speeds. Secondly, we address a fundamental limitation in tapping mode imaging by proposing a novel transform-based imaging mode to achieve an order of magnitude improvement in AFM imaging bandwidth. We introduce a real-time transform that effects a frequency shift of a given signal. We combine model-based reference generation along with the real-time transform. The proposed method is shown to have linear dynamical characteristics, making it conducive for model-based control designs, thus paving the way for achieving superior performance and robustness in imaging

High-speed large area atomic force microscopy using a quartz resonator

A high-speed atomic force microscope for scanning large areas, utilizing a quartz bar driven close to resonance to provide the motion in the fast scan axis is presented. Images up to 170 × 170 μm2 have been obtained on a polydimethylsiloxane (PDMS) grating in 1 s. This is provided through an average tip-sample velocity of 28 cm s−1 at a line rate of 830 Hz. Scan areas up to 80 × 80 μm2 have been obtained in 0.42 s with a line rate of 1410 Hz. To demonstrate the capability of the scanner the spherulitic crystallization of a semicrystalline polymer was imaged in situ at high speed

Image processing techniques for high-speed atomic force microscopy

Atomic force microscopy (AFM) is a powerful tool for imaging topography or other characteristics of sample surfaces at nanometer-scale spatial resolution by recording the interaction of a sharp probe with the surface. Dispute its excellent spatial resolution, one of the enduring challenges in AFM imaging is its poor temporal resolution relative to the rate of dynamics in many systems of interest. This has led to a large research effort on the development of high-speed AFM (HS-AFM). Most of these efforts focus on mechanical improvement and control algorithm design. This dissertation investigates a complementary HS-AFM approach based on the idea of undersampling which aims at increasing the imaging rate of the instrument by reducing the number of pixels in the sample surface that need to be acquired to create a high-quality image. The first part of this work focuses on the reconstruction of images sub-sampled according to a scheme known as μ path patterns. These patterns consist of randomly placed short and disjoint scans and are designed specifically for fast, efficient, and consistent data acquisition in AFM. We compare compressive sensing (CS) reconstruction methods with inpainting methods on recovering μ-path undersampled images. The results illustrate that the reconstruction quality depends on the choice of reconstruction methods and the sample under study, with CS generally producing a superior result for samples with sparse frequency content and inpainting performing better for samples with information limited to low frequencies. Motivated by the comparison, a basis pursuit vertical variation (BPVV) method, combing CS and inpainting, is proposed. Based on single image reconstruction results, we also extend our analysis to the problem of multiple AFM frames, in which higher overall video reconstruction quality is achieved by pixel sharing among different frames. The second part of the thesis considers patterns for sub-sampling in AFM. The allocation of measurements plays an important role in producing accurate reconstructions of the sample surface. We analyze the expected image reconstruction error using a greedy CS algorithm of our design, termed simplified matching pursuit (SMP), and propose a Monte Carlo-based strategy to create μ-path patterns that minimize the expected error. Because these μ path patterns involve a collection of disjoint scan paths, they require the tip of the instrument to be repeatedly lifted from and re-engaged to the surface. In many cases, the re-engagements make up a significant portion of the total data acquisition time. We therefore extend our Monte Carlo design strategy to find continuous scan patterns that minimize the reconstruction error without requiring the tip to be lifted from the surface. For the final part of the work, we provide a hardware demonstration on a commercial AFM. We describe hardware implementation details and image a calibration grating using the proposed μ-path and continuous scan patterns. The sample surface is reconstructed from acquired data using CS and inpainting methods. The recovered image quality and achievable imaging rate are compared to full raster-scans of the sample. The experimental results show that the proposed scanning combining with reconstruction methods can produce higher image quality with less imaging time

Design of a high-bandwidth tripod scanner for high speed atomic force microscopy

Tip-scanning high-speed atomic force microscopes (HS-AFMs) have several advantages over their sample-scanning counterparts. Firstly, they can be used on samples of almost arbitrary size since the high imaging bandwidth of the system is immune to the added mass of the sample and its holder. Depending on their layouts, they also enable the use of several tip-scanning HS-AFMs in combination. However, the need for tracking the cantilever with the readout laser makes designing tip-scanning HS-AFMs difficult. This often results in a reduced resonance frequency of the HS-AFM scanner, or a complex and large set of precision flexures. Here, we present a compact, simple HS-AFM designed for integrating the self-sensing cantilever into the tip-scanning configuration, so that the difficulty of tracking small cantilever by laser beam is avoided. The position of cantilever is placed to the end of whole structure, hence making the optical viewing of the cantilever possible. As the core component of proposed system, a high bandwidth tripod scanner is designed, with a scan size of 5.8 µm × 5.8 µm and a vertical travel range of 5.9 µm. The hysteresis of the piezoactuators in X- and Y-axes are linearized using input shaping technique. To reduce in-plane crosstalk and vibration-related dynamics, we implement both filters and compensators on a field programmable analog array. Based on these, images with 512 × 256 pixels are successfully obtained at scan rates up to 1024 lines/s, corresponding to a 4 mm/stip velocity

Algorithmic approaches to high speed atomic force microscopy

Thesis (Ph.D.)--Boston UniversityThe atomic force microscope (AFM) has a unique set of capabilities for investigating biological systems, including sub-nanometer spatial resolution and the ability to image in liquid and to measure mechanical properties. Acquiring a high quality image, however, can take from minutes to hours. Despite this limited frame rate, researchers use the instrument to investigate dynamics via time-lapse imaging, driven by the need to understand biomolecular activities at the molecular level. Studies of processes such as DNA digestion with DNase, DNA-RNA polymerase binding and RNA transcription from DNA by RNA polymerase redefined the potential of AFM in biology. As a result of the need for better temporal resolution, advanced AFMs have been developed. The current state of the art in high-speed AFM (HS-AFM) for biological studies is an instrument developed by Toshio Ando at Kanazawa University in Japan. This instrument can achieve 12 frames/sec and has successfully visualized the motion of protein motors at the molecular level. This impressive instrument as well as other advanced AFMs, however, comes with tradeoffs that include a small scan size, limited imaging modes and very high cost. As a result, most AFM users still rely on standard commercial AFMs. The work in this thesis develops algorithmic approaches that can be implemented on existing instruments, from standard commercial systems to cutting edge HS-AFM units, to enhance their capabilities. There are four primary contributions in this thesis. The first is an analysis of the signals available in an AFM with respect to the information they carry and their suitability for imaging at different scan speeds. The next two are algorithmic approaches to HS-AFM that take advantage of these signals in different ways. The first algorithm involves a new sample profile estimator that yields accurate topology at speeds beyond the bandwidth of the limiting actuator. The second involves more efficient sampling, using the data in real time to steer the tip. Both algorithms yield at least an order of magnitude improvement in imaging rate but with different tradeoffs. The first operates beyond the bandwidth of the controller managing the tip-sample interaction and therefore the applied force is not well-regulated. The second keeps this control intact but is effective only on a limited set of samples, namely biopolymers or other string-like samples. Experiments on calibration samples and λ-DNA show that both of the algorithms improve the imaging rate by an order of magnitude. In the fourth contribution, extended applications of AFMs equipped with the algorithmic approaches are the tracking of a macromolecule moving along a string-like sample and a time optimal path for repetitive non-raster scans along string-like samples

Fast Specimen Boundary Tracking and Local Imaging with Scanning Probe Microscopy

An efficient and adaptive boundary tracking method is developed to confine area of interest for high-efficiency local scanning. By using a boundary point determination criterion, the scanning tip is steered with a sinusoidal waveform while estimating azimuth angle and radius ratio of each boundary point to accurately track the boundary of targets. A local scan region and path are subsequently planned based on the prior knowledge of boundary tracking to reduce the scan time. Boundary tracking and local scanning methods have great potential not only for fast dimension measurement but also for sample surface topography and physical characterization, with only scanning region of interest. The performance of the proposed methods was verified by using the alternate current mode scanning ion-conductance microscopy, tapping, and PeakForce modulation atomic force microscopy. Experimental results of single/multitarget boundary tracking and local scanning of target structures with complex boundaries demonstrate the flexibility and validity of the proposed method

High-speed electrochemical imaging

The design, development, and application of high-speed scanning electrochemical probe microscopy is reported. The approach allows the acquisition of a series of high-resolution images (typically 1000 pixels μm–2) at rates approaching 4 seconds per frame, while collecting up to 8000 image pixels per second, about 1000 times faster than typical imaging speeds used up to now. The focus is on scanning electrochemical cell microscopy (SECCM), but the principles and practicalities are applicable to many electrochemical imaging methods. The versatility of the high-speed scan concept is demonstrated at a variety of substrates, including imaging the electroactivity of a patterned self-assembled monolayer on gold, visualization of chemical reactions occurring at single wall carbon nanotubes, and probing nanoscale electrocatalysts for water splitting. These studies provide movies of spatial variations of electrochemical fluxes as a function of potential and a platform for the further development of high speed scanning with other electrochemical imaging techniques