A Fourier-Based Global Denoising Model for Smart Artifacts Removing of Microscopy Images

Microscopy such as Scanning Tunneling Microscopy (STM), Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) are essential tools in material imaging at micro- and nanoscale resolutions to extract physical knowledge and materials structure-property relationships. However, tuning microscopy controls (e.g. scanning speed, current setpoint, tip bias etc.) to obtain a high-quality of images is a non-trivial and time-consuming effort. On the other hand, with sub-standard images, the key features are not accurately discovered due to noise and artifacts, leading to erroneous analysis. Existing denoising models mostly build on generalizing the weak signals as noises while the strong signals are enhanced as key features, which is not always the case in microscopy images, thus can completely erase a significant amount of hidden physical information. To address these limitations, we propose a global denoising model (GDM) to smartly remove artifacts of microscopy images while preserving weaker but physically important features. The proposed model is developed based on 1) first designing a two-imaging input channel of non-pair and goal specific pre-processed images with user-defined trade-off information between two channels and 2) then integrating a loss function of pixel- and fast Fourier-transformed (FFT) based on training the U-net model. We compared the proposed GDM with the non-FFT denoising model over STM-generated images of Copper(Cu) and Silicon(Si) materials, AFM-generated Pantoea sp.YR343 bio-film images and SEM-generated plastic degradation images. We believe this proposed workflow can be extended to improve other microscopy image quality and will benefit the experimentalists with the proposed design flexibility to smartly tune via domain-experts preferences.

A Bi-channel Aided Stitching of Atomic Force Microscopy Images

Microscopy is an essential tool in scientific research, enabling the visualization of structures at micro- and nanoscale resolutions. However, the field of microscopy often encounters limitations in field-of-view (FOV), restricting the amount of sample that can be imaged in a single capture. To overcome this limitation, image stitching techniques have been developed to seamlessly merge multiple overlapping images into a single, high-resolution composite. The images collected from microscope need to be optimally stitched before accurate physical information can be extracted from post analysis. However, the existing stitching tools either struggle to stitch images together when the microscopy images are feature sparse or cannot address all the transformations of images. To address these issues, we propose a bi-channel aided feature-based image stitching method and demonstrate its use on AFM generated biofilm images. The topographical channel image of AFM data captures the morphological details of the sample, and a stitched topographical image is desired for researchers. We utilize the amplitude channel of AFM data to maximize the matching features and to estimate the position of the original topographical images and show that the proposed bi-channel aided stitching method outperforms the traditional stitching approach. Furthermore, we found that the differentiation of the topographical images along the x-axis provides similar feature information to the amplitude channel image, which generalizes our approach when the amplitude images are not available. Here we demonstrated the application on AFM, but similar approaches could be employed of optical microscopy with brightfield and fluorescence channels. We believe this proposed workflow will benefit the experimentalist to avoid erroneous analysis and discovery due to incorrect stitching.