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Image restoration in sets of noisy electron micrographs

S.J. Ludike, Wah Chiu
Proceedings IEEE International Symposium on Biomedical Imaging  
The imaging process in a transmission electron microscope (TEM) produces a number of artifacts including the contrast transfer function (CTF) and envelope functions.  ...  In addition, when electron cryomicroscopy is performed for purposes of single particle reconstruction, signal to noise ratios are very low, generally peaking between 0.1 and 1.0, and averaging 0.01 to  ...  In this derivation, we consider the process of combining n particles, all in the same orientation, selected from the set of micrographs.  ... 
doi:10.1109/isbi.2002.1029365 dblp:conf/isbi/LudikeC02 fatcat:il6oec6wlzhbxa3nh6tvuak43e

Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer [article]

Hongjia Li, Hui Zhang, Xiaohua Wan, Zhidong Yang, Chengmin Li, Jintao Li, Renmin Han, Ping Zhu, Fa Zhang
2021 bioRxiv   pre-print
from a set of two-dimensional (2D) micrographs.  ...  However, limited by the electron beam dose, the micrographs in cryo-EM generally suffer from extremely low signal-to-noise ratio (SNR), which hampers the efficiency and effectiveness of downstream analysis  ...  by the integrated electron flux and shot noise contributions are added, (3) the Fourier spectrum of that noisy signal is damped by the NT F, (4) the number of electrons are scaled to the image gray values  ... 
doi:10.1101/2021.05.10.443396 fatcat:hug6gzx6ardqtbvw5ev223lugy

Multichannel restoration with limited a priori information [electron microscopy of biological macromolecules]

M.J. Vrhel, M. Unser
1999 IEEE Transactions on Image Processing  
We introduce a method for multichannel restoration of images in which there is severely limited knowledge about the undegraded signal, and possibly the noise.  ...  This post-restoration noise reduction is often performed when working with micrographs of biological macromolecules.  ...  Booy for providing practical information on electron microscopy, B. Trus for discussions on 3-D reconstruction of biological macromolecules, and P. Thevénaz for information on image registration.  ... 
doi:10.1109/83.753740 pmid:18262896 fatcat:gemviiycgfhwzeyu7p42htvevm

Improving Electron Micrograph Signal-to-Noise with an Atrous Convolutional Encoder-Decoder [article]

Jeffrey M. Ede
2018 arXiv   pre-print
We present an atrous convolutional encoder-decoder trained to denoise 512×512 crops from electron micrographs.  ...  Our neural network was trained end-to-end to remove Poisson noise applied to low-dose (≪ 300 counts ppx) micrographs created from a new dataset of 17267 2048×2048 high-dose (> 2500 counts ppx) micrographs  ...  We also present example applications of our network to noisy electron microscopy and scanning transmission electron microscopy (STEM) images.  ... 
arXiv:1807.11234v2 fatcat:ijslzpsvsjbilazrzvkroj7fry

FIRT: Filtered iterative reconstruction technique with information restoration

Yu Chen, Yan Zhang, Kai Zhang, Yuchen Deng, Shengliu Wang, Fa Zhang, Fei Sun
2016 Journal of Structural Biology  
Here, based on the understanding of smooth nature of biological specimen, we present a new iterative image reconstruction algorithm, FIRT (filtered iterative reconstruction technique) for electron tomography  ...  Electron tomography (ET) combining subsequent sub-volume averaging has been becoming a unique way to study the in situ 3D structures of macromolecular complexes.  ...  Zhenxi Guo (CBI) for their helps in sample preparation and data collection, and Yili Chen (an intern student in F.S. lab) and Prof.  ... 
doi:10.1016/j.jsb.2016.04.015 pmid:27134004 fatcat:gakx7a6l2zgclj57ll6i32gude

Improved restoration of noisy images by adaptive least-squares post-filtering

Michael Unser
1990 Signal Processing  
This paper describes a class of post-filtering algorithms that adaptively compute a linear combination between a noisy image and a restored version of it obtained by linear filtering.  ...  A set of optimal weighting coefficients is derived by minimizing the quadratic error between the output of this system and a noise-free signal.  ...  Fig. 5 . 5 Processing of a noisy electron micrograph.  ... 
doi:10.1016/0165-1684(90)90073-8 fatcat:655dp573grae5greenpnuj2bay

On the parameters affecting dual-target-function evaluation of single-particle selection from cryo-electron micrographs [article]

Zhou Yu, Wei Li Wang, Luis R. Castillo-Menendez, Joseph Sodroski, Youdong Mao
2015 arXiv   pre-print
of particle images to be automatically picked from micrographs.  ...  Given a sufficient signal-to-noise ratio in the images and the appropriate choice of references, the DTF approach can expedite the automated assembly of single-particle data sets.  ...  Song for assistance in maintaining the high-performance  ... 
arXiv:1509.06863v1 fatcat:aa32rnvhzre67nirdmtz53an7e

Dual-target function validation of single-particle selection from low-contrast cryo-electron micrographs [article]

Youdong Mao, Luis R. Castillo-Menendez, Joseph Sodroski
2013 arXiv   pre-print
Weak-signal detection and single-particle selection from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) presents a practical challenge.  ...  The DTF approach allows efficient assembly of a large number of single-particle cryo-EM images of smaller biomolecules or specimens containing contrast-degrading agents like detergents in a semi-automatic  ...  Richter for assistance in maintaining the high-  ... 
arXiv:1309.2618v1 fatcat:6lm66ax2pvg4vcnbfokvq3qk7a

High-Quality Image Formation by Nonlocal Means Applied to High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF–STEM) [chapter]

Peter Binev, Francisco Blanco-Silva, Douglas Blom, Wolfgang Dahmen, Philipp Lamby, Robert Sharpley, Thomas Vogt
2012 Modeling Nanoscale Imaging in Electron Microscopy  
We shall present the main conceptual imaging concepts and restoration methods that we believe are suitable for carrying out such a program and, in particular, allow one to correct special acquisition artifacts  ...  Our goal is to keep the overall cumulative electron dose as low as possible while still staying close to an acceptable level of physical resolution.  ...  We are also indebted to Benjamin Berkels for making his image registration code available to us.  ... 
doi:10.1007/978-1-4614-2191-7_5 fatcat:wsyak6f5nfeczcav3oqvdogmiu

Wavelets filtering for classification of very noisy electron microscopic single particles images--application on structure determination of VP5-VP19C recombinant

Ali Samir Saad
2003 BMC Structural Biology  
The wavelet filtering and multi-resolution processing method proposed in this paper offers a new way for processing very noisy images obtained from electron cryo-microscopes.  ...  Images of frozen hydrated [vitrified] virus particles were taken close-to-focus in an electron microscope containing structural signals at high spatial frequencies.  ...  This work was supported by the National Institutes of Health (P41RR002250, R01AI38469) and Human Frontier Science Program.  ... 
doi:10.1186/1472-6807-3-9 pmid:14667245 pmcid:PMC317332 fatcat:wkjhwr3gzjdgnibopgcar6bony

Topaz-Denoise: general deep denoising models for cryoEM [article]

Tristan Bepler, Alex J Noble, Bonnie Berger
2019 bioRxiv   pre-print
By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process  ...  Low signal-to-noise (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations  ...  Acknowledgements The authors wish to thank Simons Electron Microscopy Center (SEMC) OPs for many of the test datasets used in training and the authors of EMPIAR entries XXXXX, YYYYY, … for additional training  ... 
doi:10.1101/838920 fatcat:tpbky7sq6zf6fetk7vd6qyruqe

3I1048 Phase retrieval from noisy x-ray diffraction patterns of single molecules(3I Protein: Measurement & Analysis 1,The 49th Annual Meeting of the Biophysical Society of Japan)
3I1048 単粒子分子のノイズの大きいX線回折データからの位相回復(3I 蛋白質_計測・解析の方法論1,日本生物物理学会第49回年会)

Hidetoshi Kono, Shiro Ikeda, Atsushi Tokuhisa
2011 Seibutsu Butsuri  
electron micrographs, At present, we inspected the optimum referenee area of tilt image and searched for efficient numbers or rcference points.  ...  Ryuzo Azuma Biosc. di Bioin,fo., Focusing on developing a technique suited for restoration of 3D structures imaged with cryo-electron microscopy, we have been addressing the issue of improvements  ... 
doi:10.2142/biophys.51.s137_3 fatcat:ssu6iasvczdsjhh5ueyzacubyi

Filtering of electron images of crystal defects

J. Desseaux, C. d'Anterroches, J.M. Penisson, A. Renault
1980 Journal de Physique  
The optimal mask shape is applied to a real electron micrograph of a high resolution electron image of dislocation.  ...  Abstract. 2014 The interpretation of electron micrographs becomes easier after filtering of the photographic and electronic noise. The filtering process can be optical or numerical.  ...  Finally the real case of numerical filtering of a noisy , electron micrograph of a dislocation is presented. 2. Optical analysis and image reconstruction.  ... 
doi:10.1051/jphys:01980004106056500 fatcat:luzge2kxofdg3f6xqzppcfwgoi

Iterative restoration of noisy elastically distorted periodic images

Michael Unser, Benes L. Trus, Murray Eden
1989 Signal Processing  
Experiments with electron micrographs of thin sections of muscle fibers indicate a significant improvement in signal quality when compared with a previous approach.  ...  The warping function is represented by quasi-hermite twodimensional polynomials, a representation that allows great flexibility in the choice of fiduciary points.  ...  This technique is commonly used in the analysis of electron micrographs, particularly in structural investigations of biological macromolecules in ordered arrays [6] .  ... 
doi:10.1016/0165-1684(89)90001-7 fatcat:ekijlmwtibeyvppjjqsdqv6w64

Computer Vision for Nanoscale Imaging

Eraldo Ribeiro, Mubarak Shah
2006 Machine Vision and Applications  
This paper reviews current advances in computer vision and related areas applied to imaging nanoscale objects.  ...  The main goal of Nanotechnology is to analyze and understand the properties of matter at the atomic and molecular level.  ...  Particles in micrographs tend to have an overall dark appearance when compared to the noisy image brackground.  ... 
doi:10.1007/s00138-006-0021-7 fatcat:ya6gpgvtz5gwbnb3zoih73ttje
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