An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

The recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets

초점 스택에서 3D 깊이 재구성 및 깊이 개선

학위논문 (박사) -- 서울대학교 대학원 : 공과대학 전기·컴퓨터공학부, 2021. 2. 신영길.Three-dimensional (3D) depth recovery from two-dimensional images is a fundamental and challenging objective in computer vision, and is one of the most important prerequisites for many applications such as 3D measurement, robot location and navigation, self-driving, and so on. Depth-from-focus (DFF) is one of the important methods to reconstruct a 3D depth in the use of focus information. Reconstructing a 3D depth from texture-less regions is a typical issue associated with the conventional DFF. Further more, it is difficult for the conventional DFF reconstruction techniques to preserve depth edges and fine details while maintaining spatial consistency. In this dissertation, we address these problems and propose an DFF depth recovery framework which is robust over texture-less regions, and can reconstruct a depth image with clear edges and fine details. The depth recovery framework proposed in this dissertation is composed of two processes: depth reconstruction and depth refinement. To recovery an accurate 3D depth, We first formulate the depth reconstruction as a maximum a posterior (MAP) estimation problem with the inclusion of matting Laplacian prior. The nonlocal principle is adopted during the construction stage of the matting Laplacian matrix to preserve depth edges and fine details. Additionally, a depth variance based confidence measure with the combination of the reliability measure of focus measure is proposed to maintain the spatial smoothness, such that the smooth depth regions in initial depth could have high confidence value and the reconstructed depth could be more derived from the initial depth. As the nonlocal principle breaks the spatial consistency, the reconstructed depth image is spatially inconsistent. Meanwhile, it suffers from texture-copy artifacts. To smooth the noise and suppress the texture-copy artifacts introduced in the reconstructed depth image, we propose a closed-form edge-preserving depth refinement algorithm that formulates the depth refinement as a MAP estimation problem using Markov random fields (MRFs). With the incorporation of pre-estimated depth edges and mutual structure information into our energy function and the specially designed smoothness weight, the proposed refinement method can effectively suppress noise and texture-copy artifacts while preserving depth edges. Additionally, with the construction of undirected weighted graph representing the energy function, a closed-form solution is obtained by using the Laplacian matrix corresponding to the graph. The proposed framework presents a novel method of 3D depth recovery from a focal stack. The proposed algorithm shows the superiority in depth recovery over texture-less regions owing to the effective variance based confidence level computation and the matting Laplacian prior. Additionally, this proposed reconstruction method can obtain a depth image with clear edges and fine details due to the adoption of nonlocal principle in the construct]ion of matting Laplacian matrix. The proposed closed-form depth refinement approach shows that the ability in noise removal while preserving object structure with the usage of common edges. Additionally, it is able to effectively suppress texture-copy artifacts by utilizing mutual structure information. The proposed depth refinement provides a general idea for edge-preserving image smoothing, especially for depth related refinement such as stereo vision. Both quantitative and qualitative experimental results show the supremacy of the proposed method in terms of robustness in texture-less regions, accuracy, and ability to preserve object structure while maintaining spatial smoothness.Chapter 1 Introduction 1 1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.3 Contribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.4 Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Chapter 2 Related Works 9 2.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2 Principle of depth-from-focus . . . . . . . . . . . . . . . . . . . . 9 2.2.1 Focus measure operators . . . . . . . . . . . . . . . . . . . 12 2.3 Depth-from-focus reconstruction . . . . . . . . . . . . . . . . . . 14 2.4 Edge-preserving image denoising . . . . . . . . . . . . . . . . . . 23 Chapter 3 Depth-from-Focus Reconstruction using Nonlocal Matting Laplacian Prior 38 3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.2 Image matting and matting Laplacian . . . . . . . . . . . . . . . 40 3.3 Depth-from-focus . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 3.4 Depth reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . 47 3.4.1 Problem statement . . . . . . . . . . . . . . . . . . . . . . 47 3.4.2 Likelihood model . . . . . . . . . . . . . . . . . . . . . . . 48 3.4.3 Nonlocal matting Laplacian prior model . . . . . . . . . . 50 3.5 Experimental results . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.5.2 Data configuration . . . . . . . . . . . . . . . . . . . . . . 55 3.5.3 Reconstruction results . . . . . . . . . . . . . . . . . . . . 56 3.5.4 Comparison between reconstruction using local and nonlocal matting Laplacian . . . . . . . . . . . . . . . . . . . 56 3.5.5 Spatial consistency analysis . . . . . . . . . . . . . . . . . 59 3.5.6 Parameter setting and analysis . . . . . . . . . . . . . . . 59 3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 Chapter 4 Closed-form MRF-based Depth Refinement 63 4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 4.2 Problem statement . . . . . . . . . . . . . . . . . . . . . . . . . . 65 4.3 Closed-form solution . . . . . . . . . . . . . . . . . . . . . . . . . 69 4.4 Edge preservation . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 4.5 Texture-copy artifacts suppression . . . . . . . . . . . . . . . . . 73 4.6 Experimental results . . . . . . . . . . . . . . . . . . . . . . . . . 76 4.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 Chapter 5 Evaluation 82 5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 5.2 Evaluation metrics . . . . . . . . . . . . . . . . . . . . . . . . . . 83 5.3 Evaluation on synthetic datasets . . . . . . . . . . . . . . . . . . 84 5.4 Evaluation on real scene datasets . . . . . . . . . . . . . . . . . . 89 5.5 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 5.6 Computational performances . . . . . . . . . . . . . . . . . . . . 93 Chapter 6 Conclusion 96 Bibliography 99Docto

An overview of the fundamental approaches that yield several image denoising techniques

Digital image is considered as a powerful tool to carry and transmit information between people. Thus, it attracts the attention of large number of researchers, among them those interested in preserving the image features from any factors that may reduce the image quality. One of these factors is the noise which affects the visual aspect of the image and makes others image processing more difficult. Thus far, solving this noise problem remains a challenge for the researchers in this field. A lot of image denoising techniques have been introduced in order to remove the noise by taking care of the image features; in other words, getting the best similarity to the original image from the noisy one. However, the findings are still inconclusive. Beside the enormous amount of researches and studies which adopt several mathematical concepts (statistics, probabilities, modeling, PDEs, wavelet, fuzzy logic, etc.), there is also the scarcity of review papers which carry an important role in the development and progress of research. Thus, this review paper intorduce an overview of the different fundamental approaches that yield the several image-denoising techniques, presented with a new classification. Furthermore, the paper presents the different evaluation tools needed on the comparison between these techniques in order to facilitate the processing of this noise problem, among a great diversity of techniques and concepts

BM3D Image Denoising using Learning-Based Adaptive Hard Thresholding

Image denoising is an important pre-processing step in most imaging applications. Block Matching and 3D Filtering (BM3D) is considered to be the current state-of-art algorithm for additive image denoising. But this algorithm uses a fixed hard thresholding scheme to attenuate noise from a 3D block. Experiments show that this fixed hard thresholding deteriorates the performance of BM3D because it does not consider the context of corresponding blocks. In this thesis, we propose a learning based adaptive hard thresholding method to solve this issue. Also, BM3D algorithm requires as an input the value of the noise level in the input image. But in real life it is not practical to pass as an input such noise level. In this thesis, we also attempt to automatically estimate the level of the noise in the input image. Experimental results demonstrate that our proposed algorithm outperforms BM3D in both objective and subjective fidelity criteria

Image Restoration Using Joint Statistical Modeling in Space-Transform Domain

This paper presents a novel strategy for high-fidelity image restoration by characterizing both local smoothness and nonlocal self-similarity of natural images in a unified statistical manner. The main contributions are three-folds. First, from the perspective of image statistics, a joint statistical modeling (JSM) in an adaptive hybrid space-transform domain is established, which offers a powerful mechanism of combining local smoothness and nonlocal self-similarity simultaneously to ensure a more reliable and robust estimation. Second, a new form of minimization functional for solving image inverse problem is formulated using JSM under regularization-based framework. Finally, in order to make JSM tractable and robust, a new Split-Bregman based algorithm is developed to efficiently solve the above severely underdetermined inverse problem associated with theoretical proof of convergence. Extensive experiments on image inpainting, image deblurring and mixed Gaussian plus salt-and-pepper noise removal applications verify the effectiveness of the proposed algorithm.Comment: 14 pages, 18 figures, 7 Tables, to be published in IEEE Transactions on Circuits System and Video Technology (TCSVT). High resolution pdf version and Code can be found at: http://idm.pku.edu.cn/staff/zhangjian/IRJSM

A CANDLE for a deeper in-vivo insight

A new Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) is introduced for the processing of 3D laser scanning multiphoton microscopy images. CANDLE is designed to be robust for low signal-to-noise ratio (SNR) conditions typically encountered when imaging deep in scattering biological specimens. Based on an optimized non-local means filter involving the comparison of filtered patches, CANDLE locally adapts the amount of smoothing in order to deal with the noise inhomogeneity inherent to laser scanning fluorescence microscopy images. An extensive validation on synthetic data, images acquired on microspheres and in vivo images is presented. These experiments show that the CANDLE filter obtained competitive results compared to a state-of-the-art method and a locally adaptive optimized non-local means filter, especially under low SNR conditions (PSNR < 8 dB). Finally, the deeper imaging capabilities enabled by the proposed filter are demonstrated on deep tissue in vivo images of neurons and fine axonal processes in the Xenopus tadpole brain.We want to thank Florian Luisier for providing free plugin of his PureDenoise filter. We also want to thank Markku Makitalo for providing the code of their OVST. This study was supported by the Canadian Institutes of Health Research (CIHR, MOP-84360 to DLC and MOP-77567 to ESR) and Cda (CECR)-Gevas-OE016. MM holds a fellowship from the Deutscher Akademischer Austasch Dienst (DAAD) and a McGill Principal's Award. ESR is a tier 2 Canada Research Chair. This work has been partially supported by the Spanish Health Institute Carlos III through the RETICS Combiomed, RD07/0067/2001. This work benefited from the use of ImageJ.Coupé, P.; Munz, M.; Manjón Herrera, JV.; Ruthazer, ES.; Collins, DL. (2012). A CANDLE for a deeper in-vivo insight. Medical Image Analysis. 16(4):849-864. https://doi.org/10.1016/j.media.2012.01.002S84986416