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

TL;DR

This paper introduces a Fourier-based global denoising model for microscopy images that effectively removes artifacts while preserving important physical features, improving image quality for better analysis.

Contribution

The paper presents a novel global denoising model using FFT and a dual-input U-net architecture tailored for microscopy images, addressing limitations of existing methods.

Findings

Outperforms non-FFT denoising models on microscopy images

Preserves physically important features better than traditional methods

Applicable to various microscopy modalities like STM, AFM, SEM

Abstract

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.