enhancing-density-maps-removing-majority-particles-single-particle

Enhancing Density Maps by Removing the Majority of Particles in Single Particle Cryogenic Electron Microscopy Final Stacks

Over the past decade, advancements in technology and methodology within the field of cryogenic electron microscopy (cryo-EM) single-particle analysis ...

Yau Mathematical Sciences Center

Yanqi Lake Beijing Institute of Mathematical Sciences and Applications

In this paper, we propose a time-frequency analysis method to obtain instantaneous frequencies and the corresponding decomposition by solving an optimization problem. In this optimization problem, the basis that is used to decompose the signal is not known a priori. Instead, it is adapted to the signal and is determined as part of the optimization problem. In this sense, this optimization problem can be seen as a dictionary adaptation problem, in which the dictionary is adaptive to one signal rather than a training set in dictionary learning. This dictionary adaptation problem is solved by using the augmented Lagrangian multiplier (ALM) method iteratively. We further accelerate the ALM method in each iteration by using the fast wavelet transform. We apply our method to decompose several signals, including signals with poor scale separation, signals with outliers and polluted by noise and a real signal. The results show that this method can give accurate recovery of both the instantaneous frequencies and the intrinsic mode functions.

Sparse time-frequency decomposition based on dictionary adaptation.

Non-line-of-sight imaging aims at recovering obscured objects from multiple scattered lights. It has recently received widespread attention due to its potential applications, such as autonomous driving, rescue operations, and remote sensing. However, in cases with high measurement noise, obtaining high-quality reconstructions remains a challenging task. In this work, we establish a unified regularization framework, which can be tailored for different scenarios, including indoor and outdoor scenes with substantial background noise under both confocal and non-confocal settings. The proposed regularization framework incorporates sparseness and non-local self-similarity of the hidden objects as well as the smoothness of the signals. We show that the estimated signals, albedo, and surface normal of the hidden objects can be reconstructed robustly even with high measurement noise under the proposed framework. Reconstruction results on synthetic and experimental data show that our approach recovers the hidden objects faithfully and outperforms state-of-the-art reconstruction algorithms in terms of both quantitative criteria and visual quality.

Non-line-of-sight reconstruction with signal-object collaborative regularization.

Non-line-of-sight (NLOS) imaging aims at reconstructing targets obscured from the direct line of sight. Existing NLOS imaging algorithms require dense measurements at regular grid points in a large area of the relay surface, which severely hinders their availability to variable relay scenarios in practical applications such as robotic vision, autonomous driving, rescue operations and remote sensing. In this work, we propose a Bayesian framework for NLOS imaging without specific requirements on the spatial pattern of illumination and detection points. By introducing virtual confocal signals, we design a confocal complemented signal-object collaborative regularization (CC-SOCR) algorithm for high-quality reconstructions. Our approach is capable of reconstructing both the albedo and surface normal of the hidden objects with fine details under general relay settings. Moreover, with a regular relay surface, coarse rather than dense measurements are enough for our approach such that the acquisition time can be reduced significantly. As demonstrated in multiple experiments, the proposed framework substantially extends the application range of NLOS imaging.

Non-line-of-sight imaging with arbitrary illumination and detection pattern.

Cryogenic electron microscopy (cryo-EM) is widely used to determine near-atomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a crucial question in the field of cryo-EM remains unanswered: how close can we get to the minimum number of particles required to reach a specific resolution in practice? The absence of an answer to this question has impeded progress in understanding sample behavior and the performance of sample preparation methods. To address this issue, we develop an iterative particle sorting and/or sieving method called CryoSieve. Extensive experiments demonstrate that CryoSieve outperforms other cryo-EM particle sorting algorithms, revealing that most particles are unnecessary in final stacks. The minority of particles remaining in the final stacks yield superior high-resolution amplitude in reconstructed density maps. For some datasets, the size of the finest subset approaches the theoretical limit.

Article	Year
Sparse time-frequency decomposition based on dictionary adaptation. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences\| PubMed ID: 26953172	2016
Non-line-of-sight reconstruction with signal-object collaborative regularization. Light, science & applications\| PubMed ID: 34561418	2021
Non-line-of-sight imaging with arbitrary illumination and detection pattern. Nature communications\| PubMed ID: 37270564	2023
A minority of final stacks yields superior amplitude in single-particle cryo-EM. Nature communications\| PubMed ID: 38072910	2023

Zuoqiang Shi

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