Deep Generative Modeling for Volume Reconstruction in Cryo-Electron Microscopy
Stanford University（斯坦福大学）；SLAC National Accelerator Laboratory（SLAC国家加速器实验室）；Massachusetts Institute of Technology（麻省理工学院）；University of Chicago（芝加哥大学）；University of California Santa Barbara（加州大学圣巴巴拉分校）
Claire Donnat, Axel Levy, Frederic Poitevin, Ellen Zhong, Nina Miolane
Recent breakthroughs in high-resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology, chemistry, and pharmacological research. Recent next-generation volume reconstruction algorithms that combine generative modeling with end-to-end unsupervised deep learning techniques have shown promising preliminary results, but still face considerable technical and theoretical hurdles when applied to experimental cryo-EM images. In light of the proliferation of such methods, we propose here a critical review of recent advances in the field of deep generative modeling for cryo-EM volume reconstruction. The present review aims to (i) unify and compare these new methods using a consistent statistical framework, (ii) present them using a terminology familiar to machine learning researchers and computational biologists with no specific background in cryo-EM, and (iii) provide the necessary perspective on current advances to highlight their relative strengths and weaknesses, along with outstanding bottlenecks and avenues for improvements in the field. This review might also raise the interest of computer vision practitioners, as it highlights significant limits of deep generative models in low signal-to-noise regimes -- therefore emphasizing a need for new theoretical and methodological developments.
SLAC National Accelerator Laboratory（SLAC国家加速器实验室）；University of British Columbia（不列颠哥伦比亚大学）
Cryogenic electron microscopy (cryo-EM) provides images from different copies of the same biomolecule in arbitrary orientations. Here, we present an end-to-end unsupervised approach that learns individual particle orientations from cryo-EM data while reconstructing the average 3D map of the biomolecule, starting from a random initialization. The approach relies on an auto-encoder architecture where the latent space is explicitly interpreted as orientations used by the decoder to form an image according to the linear projection model. We evaluate our method on simulated data and show that it is…
Cryo-Electron Microscopy (Cryo-EM) is a Nobel prize-winning technology for determining the 3D structure of particles at near-atomic resolution. A fundamental step in the recovering of the 3D single-particle structure is to align its 2D projections; thus, the construction of a canonical representation with a fixed rotation angle is required. Most approaches use discrete clustering which fails to capture the continuous nature of image rotation, others suffer from low-quality image reconstruction. We propose a novel method that leverages the recent development in the generative adversarial networ…
Simons Machine Learning Center, Simons Electron Microscopy Center, New York Structural Biology Center（西蒙斯机器学习中心、西蒙斯电子显微镜中心、纽约结构生物学中心）
Over the past decade, cryogenic electron microscopy (cryo-EM) has emerged as a primary method for determining near-native, near-atomic resolution 3D structures of biological macromolecules. In order to meet increasing demand for cryo-EM, automated methods to improve throughput and efficiency while lowering costs are needed. Currently, all high-magnification cryo-EM data collection softwares require human input and manual tuning of parameters. Expert operators must navigate low- and medium-magnification images to find good high-magnification collection locations. Automating this is non-trivial:…
Stanford University（斯坦福大学）；SLAC National Accelerator（SLAC国家加速器实验室）
Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D projections of the target 3D biomolecules. Reconstructing the 3D molecular shape starts with the removal of image outliers, the estimation of the orientation of the biomolecule that has produced the given 2D image, and the estimation of camera parameters to correct for intensity defects. Curr…
A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common lines between projection images of the maps. The algorithm is fully automatic and handles rotations, reflections (handedness), and translations between the maps. In addition, the algorithm is applicable to any type of molecular symmetry without requiring any information regarding the symmetry of the maps. We evaluate our alignment algorithm on publicly available…
University of Illinois at Urbana–Champaign（伊利诺伊大学厄巴纳-香槟分校）；University of Chicago（芝加哥大学）
We develop in this paper a novel intrinsic classification algorithm -- multi-frequency class averaging (MFCA) -- for classifying noisy projection images obtained from three-dimensional cryo-electron microscopy (cryo-EM) by the similarity among their viewing directions. This new algorithm leverages multiple irreducible representations of the unitary group to introduce additional redundancy into the representation of the optimal in-plane rotational alignment, extending and outperforming the existing class averaging algorithm that uses only a single representation. The formal algebraic model and …
Institute of Statistical Science, Academia Sinica（中央研究院統計科學研究所）；Institute of Chemistry, Academia Sinica（中央研究院化學研究所）
Principal component analysis (PCA) is arguably the most widely used dimension-reduction method for vector-type data. When applied to a sample of images, PCA requires vectorization of the image data, which in turn entails solving an eigenvalue problem for the sample covariance matrix. We propose herein a two-stage dimension reduction (2SDR) method for image reconstruction from high-dimensional noisy image data. The first stage treats the image as a matrix, which is a tensor of order 2, and uses multilinear principal component analysis (MPCA) for matrix rank reduction and image denoising. The se…
Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where t…
The cryo-electron microscopy (Cryo-EM) becomes popular for macromolecular structure determination. However, the 2D images which Cryo-EM detects are of high noise and often mixed with multiple heterogeneous conformations or contamination, imposing a challenge for denoising. Traditional image denoising methods can not remove Cryo-EM image noise well when the signal-noise-ratio (SNR) of images is meager. Thus it is desired to develop new effective denoising techniques to facilitate further research such as 3D reconstruction, 2D conformation classification, and so on. In this paper, we approach th…
Recovering a Molecule's 3D Dynamics from Liquid-phase Electron Microscopy Movies
National Biomedical Imaging Center, Peking University（北京大学国家生物医学成像中心）；College of Future Technology, Peking University（北京大学未来技术学院）；College of Chemistry and Molecular Engineering, Peking University（北京大学化学与分子工程学院）；DP Technology, Ltd.（深度势能科技有限公司）
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly oriented two-dimensional projections. However, the imaged protein complexes may exhibit structural variability, which complicates reconstruction and is typically addressed using discrete clustering approaches that fail to capture the full range of protein dynamics. Here, we introduce …
Using cryogenic transmission electron microscopy, we revealed three dimensional (3D) structural details of the electrochemically plated lithium (Li) flakes and their solid electrolyte interphase (SEI), including the composite SEI skin-layer and SEI fossil pieces buried inside the Li matrix. As the SEI skin-layer is largely comprised of nanocrystalline LiF and Li2O in amorphous polymeric matrix, when complete Li stripping occurs, the compromised SEI three-dimensional framework buckles, forming nanoscale bends and wrinkles. We showed that the flexibility and resilience of the SEI skin-layer play…
Universidad Politécnica de Madrid（马德里理工大学）；Centre national de la recherche scientifique (CNRS)（法国国家科学研究中心）；Interdisciplinary Institute for Neuroscience (IINS)（跨学科神经科学研究所）；University of Bordeaux（波尔多大学）；Mechanobiology Institute（机械生物学研究所）；National University of Singapore（新加坡国立大学）
Microscopy images often suffer from high levels of noise, which can hinder further analysis and interpretation. Content-aware image restoration (CARE) methods have been proposed to address this issue, but they often require large amounts of training data and suffer from over-fitting. To overcome these challenges, we propose a novel framework for few-shot microscopy image denoising. Our approach combines a generative adversarial network (GAN) trained via contrastive learning (CL) with two structure preserving loss terms (Structural Similarity Index and Total Variation loss) to further improve t…
Multiple stains are usually used to highlight biological substances in biomedical image analysis. To decompose multiple stains for co-localization quantification, blind source separation is usually performed. Prior model-based stain separation methods usually rely on stains' spatial distributions over an image and may fail to solve the co-localization problem. With the advantage of machine learning, deep generative models are used for this purpose. Since prior knowledge of imaging models is ignored in purely data-driven solutions, these methods may be sub-optimal. In this study, a novel learni…
Institute of Imaging and Computer Vision, RWTH Aachen University（亚琛工业大学成像与计算机视觉研究所）
Recent developments in fluorescence microscopy allow capturing high-resolution 3D images over time for living model organisms. To be able to image even large specimens, techniques like multi-view light-sheet imaging record different orientations at each time point that can then be fused into a single high-quality volume. Based on measured point spread functions (PSF), deconvolution and content fusion are able to largely revert the inevitable degradation occurring during the imaging process. Classical multi-view deconvolution and fusion methods mainly use iterative procedures and content-based …
Duke University（杜克大学）；Duke University School of Medicine（杜克大学医学院）
Single-particle cryo-electron microscopy (cryo-EM) is an emerging imaging modality capable of visualizing proteins and macro-molecular complexes at near-atomic resolution. The low electron-doses used to prevent sample radiation damage, result in images where the power of the noise is 100 times greater than the power of the signal. To overcome the low-SNRs, hundreds of thousands of particle projections acquired over several days of data collection are averaged in 3D to determine the structure of interest. Meanwhile, recent image super-resolution (SR) techniques based on neural networks have sho…
Technische Universität München（慕尼黑工业大学）；Helmholtz Zentrum München（亥姆霍兹慕尼黑研究中心）；TranslaTUM Center for Translational Cancer Research（TranslaTUM转化癌症研究中心）；University of Zürich（苏黎世大学）
Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research. Yet, a massive lack of annotations prevents the broad use of deep learning to analyze such data. So far, existing generative models fail to mitigate this problem because of frequent labeling errors. In this paper, we introduce a novel generative method which leverages real anatomical information to generate realistic image-label pairs of tumours. We construct a dual-pathway generator, for the anatomical image and label, trained in a cycle-consistent setup, constrained …
A main task in cryo-electron microscopy single particle reconstruction is to find a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm for ab-initio reconstruction for molecules with tetrahedral or octahedral symmetry. The algorithm exploits the multiple common lines between each pair of projection-images as well as self common lines within each image. It is robust to noise in the input images as it integrates the information from all images at once. The applicability of the proposed algorithm…
We introduce a framework for recovering an image from its rotationally and translationally invariant features based on autocorrelation analysis. This work is an instance of the multi-target detection statistical model, which is mainly used to study the mathematical and computational properties of single-particle reconstruction using cryo-electron microscopy (cryo-EM) at low signal-to-noise ratios. We demonstrate with synthetic numerical experiments that an image can be reconstructed from rotationally and translationally invariant features and show that the reconstruction is robust to noise. Th…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied macromolecule, or a relatively small number of its conformations. This reduces the effectiveness of the technique for proteins with flexible regions, which are known to play a key role in protein function. Recent methods for capturing conformational heterogeneity in cryo-EM data model it in volume space, making recovery of continuous atomic structures challenging. He…
Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of bio-molecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3D refinement, which resolves a high-resolution 3D structure from an initial approximate volume by refining the estimation of the orientation of each projection. In this work, we propose a new approach that refines the projection angles on the continuum. We formulate the optimization problem over the density map and the orientations jointly. T…
