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We propose a framework to jointly determine the deformation parameters and reconstruct the unknown volume in electron cryotomography (CryoET). CryoET aims to reconstruct three-dimensional biological samples from two-dimensional projections.…

Image and Video Processing · Electrical Eng. & Systems 2023-10-17 Valentin Debarnot , Sidharth Gupta , Konik Kothari , Ivan Dokmanic

We introduce ICE-TIDE, a method for cryogenic electron tomography (cryo-ET) that simultaneously aligns observations and reconstructs a high-resolution volume. The alignment of tilt series in cryo-ET is a major problem limiting the…

Image and Video Processing · Electrical Eng. & Systems 2024-12-16 Valentin Debarnot , Vinith Kishore , Ricardo D. Righetto , Ivan Dokmanić

Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses…

Computer Vision and Pattern Recognition · Computer Science 2022-09-01 Axel Levy , Frédéric Poitevin , Julien Martel , Youssef Nashed , Ariana Peck , Nina Miolane , Daniel Ratner , Mike Dunne , Gordon Wetzstein

Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and…

Cryo-electron tomography (cryo-ET) enables 3D visualization of cellular structures. Accurate reconstruction of high-resolution volumes is complicated by the very low signal-to-noise ratio and a restricted range of sample tilts. Recent…

Image and Video Processing · Electrical Eng. & Systems 2026-03-03 Vinith Kishore , Valentin Debarnot , AmirEhsan Khorashadizadeh , Ricardo D. Righetto , Benjamin D. Engel , Ivan Dokmanić

Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient…

Biomolecules · Quantitative Biology 2021-06-29 Kai Yi , Jianye Pang , Yungeng Zhang , Xiangrui Zeng , Min Xu

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…

Image and Video Processing · Electrical Eng. & Systems 2021-01-12 Koby Bibas , Gili Weiss-Dicker , Dana Cohen , Noa Cahan , Hayit Greenspan

Cryo-electron microscopy (cryo-EM) allows for the high-resolution reconstruction of 3D structures of proteins and other biomolecules. Successful reconstruction of both shape and movement greatly helps understand the fundamental processes of…

Computer Vision and Pattern Recognition · Computer Science 2023-10-12 Xinhang Liu , Yan Zeng , Yifan Qin , Hao Li , Jiakai Zhang , Lan Xu , Jingyi Yu

Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting…

Signal Processing · Electrical Eng. & Systems 2025-09-03 Vinith Kishore , Valentin Debarnot , AmirEhsan Khorashadizadeh , Ivan Dokmanić

Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…

Quantitative Methods · Quantitative Biology 2018-05-16 Chang Liu , Xiangrui Zeng , Ruogu Lin , Xiaodan Liang , Zachary Freyberg , Eric Xing , Min Xu

Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded…

Quantitative Methods · Quantitative Biology 2021-08-04 Muyuan Chen , Wei Dai , Ying Sun , Darius Jonasch , Cynthia Y He , Michael F. Schmid , Wah Chiu , Steven J Ludtke

Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional…

Applications · Statistics 2013-12-02 Mikhail Langovoy , Michael Habeck , Bernhard Schoelkopf

Cryo-electron tomography (cryo-ET) has emerged as a powerful tool for studying the structural heterogeneity of proteins and their complexes, offering insights into macromolecular dynamics directly within cells. Driven by recent…

Biomolecules · Quantitative Biology 2025-07-01 Jackson Carrion , Joseph H. Davis

Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET…

Quantitative Methods · Quantitative Biology 2020-11-02 Xiangrui Zeng , Min Xu

Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information,…

Quantitative Methods · Quantitative Biology 2021-07-01 Muyuan Chen , James M. Bell , Xiaodong Shi , Stella Y. Sun , Zhao Wang , Steven J. Ludtke

Cryo-electron tomography (cryo-ET) enables in situ visualization of macromolecular structures, where subtomogram analysis tasks such as classification, alignment, and averaging are critical for structural determination. However, effective…

Computer Vision and Pattern Recognition · Computer Science 2025-10-07 Runmin Jiang , Wanyue Feng , Yuntian Yang , Shriya Pingulkar , Hong Wang , Xi Xiao , Xiaoyu Cao , Genpei Zhang , Xiao Wang , Xiaolong Wu , Tianyang Wang , Yang Liu , Xingjian Li , Min Xu

Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to…

Machine Learning · Statistics 2015-01-29 Ali Punjani , Marcus A. Brubaker

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and…

Quantitative Methods · Quantitative Biology 2021-11-18 Hmrishav Bandyopadhyay , Zihao Deng , Leiting Ding , Sinuo Liu , Mostofa Rafid Uddin , Xiangrui Zeng , Sima Behpour , Min Xu

Cryo-electron tomography (cryo-ET) provides direct 3D visualization of macromolecules inside the cell, enabling analysis of their in situ morphology. This morphology can be regarded as an SE(3)-invariant, denoised volumetric representation…

Computer Vision and Pattern Recognition · Computer Science 2026-01-06 Mostofa Rafid Uddin , Mahek Vora , Qifeng Wu , Muyuan Chen , Min Xu

Cryogenic electron tomography is a technique for imaging biological samples in 3D. A microscope collects a series of 2D projections of the sample, and the goal is to reconstruct the 3D density of the sample called the tomogram.…

Computer Vision and Pattern Recognition · Computer Science 2024-08-13 Simon Wiedemann , Reinhard Heckel
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