23 papers · ranked by Valyu relevance
Cédric MessaoudiI, Thomas Boudier, Carlos Oscar Sanchez Sorzano, Sergio Marco
'Sergio Marco'] Background Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or…
Shawn Zheng, Georg Wolff, Garrett Greenan, Zhen Chen + 5 more
AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion…
Muyuan Chen
Cryogenic electron tomography (CryoET) provides 3D views of vitrified cellular samples, and protein structures can be determined from the tomograms by averaging many copies of the same protein computationally. However, the resolution of these averaged structures, particularly for smaller proteins, is often constrained…
Ariana Peck, Yue Yu, Mohammadreza Paraan, Dari Kimanius + 14 more
A high throughput processing pipeline that performs comprehensive corrections is needed to realize the full potential of cryo-electron tomography and subtomogram averaging. The field’s fragmented software landscape remains a significant hurdle to this end. Here we present AreTomoLive, an automated real-time pipeline…
Euan Pyle, Giulia Zanetti
Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from…
Min Xu, Frank Alber
Background Cryo-electron tomography emerges as an important component for structural system biology. It not only allows the structural characterization of macromolecular complexes, but also the detection of their cellular localizations in near living conditions. However, the method is hampered by low resolution…
Yongchun Lü, Xiangrui Zeng, Xiaofang Zhao, Shirui Li + 3 more
'Xin Gao' 'Min Xu'] Background Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microscopy technology, the image quality of three-dimensional reconstruction of…
Norbert Lindow, Florian N. Brünig, Vincent J. Dercksen, Gunar Fabig + 5 more
We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively…
Azat Slyamov, Viktor Nikitin, Doğa Gürsoy, Rajmund Mokso + 1 more
Joint ptychography and tomography (JPT) is a recently developed framework that enables highresolution reconstruction of 3D volumes with significantly relaxed constraints on probe overlap at adjacent scan positions. In ptychographic X-ray computed tomography (PXCT) experiment scanning translations are controlled with…
Tristan van Leeuwen, Simon Maretzke, Kees Joost Batenburg
In tomographic reconstruction, the goal is to reconstruct an unknown object from a collection of line integrals. Given a complete sampling of such line integrals for various angles and directions, explicit inverse formulas exist to reconstruct the object. Given noisy and incomplete measurements, the inverse problem is…
Doğa Gürsoy, Young P. Hong, Kuan He, Karl Hujsak + 11 more
'Si Chen' 'Yue Li' 'Mingyuan Ge' 'Lisa M. Miller' 'Yong S. Chu' 'Vincent De Andrade' 'Kai He' 'Oliver Cossairt' 'Aggelos K. Katsaggelos' 'Chris Jacobsen'] As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the…
C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros + 3 more
Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images.…
Jose-Jesus Fernandez, Sam Li, Tanmay A.M. Bharat, David A. Agard
Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series…
Anthony Butler, Philip H. Butler, Stephen T. Bell, G. Chelkov + 8 more
The MARS scanner[1] is designed for the x-ray spectroscopic study of samples with the aid of computer tomography methods. Computer tomography allows the reconstruction of slices of an investigated sample using a set of shadow projections obtained for different angles. Projections in the MARS scanner are produced using…
Muyuan Chen, James M. Bell, Xiaodong Shi, Stella Sun + 2 more
'Steven J. Ludtke'] 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, the data processing is very labor intensive and results are…
Jasenko Zivanov, Joaquín Otón, Zunlong Ke, Andriko von Kügelgen + 8 more
We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D…
Britta Weber, Erin M. Tranfield, Johanna L. Höög, Daniel Baum + 5 more
'Claude Antony' 'Tony Hyman' 'Jean-Marc Verbavatz' 'Steffen Prohaska' 'Yanmin Yang'] Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to…
Yixiu Zhao, Xiangrui Zeng, Qiang Guo, Min Xu
Motivation: Cellular Electron CryoTomography (CECT) is an emerging 3D imaging technique that visualizes subcellular organization of single cells at sub-molecular resolution and in near-native state. CECT captures large numbers of macromolecular complexes of highly diverse structures and abundances. However, the…
Shenghao Wang, Kai Zhang, Zhili Wang, Kun Gao + 3 more
'Peiping Zhu' 'Ziyu Wu'] Abstract: X-ray computed tomography at the nanometer scale (nano-CT) offers a wide range of applications in scientific and industrial areas. Here we describe a reliable, user-friendly and fast software package based on LabVIEW that may allow to perform all procedures after the acquisition of…
Sagar Khavnekar, Philipp S. Erdmann, William Wan
Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular and macromolecular structures in native or near-native environments. While cryo-ET is amenable to a wide range of biological problems, these problems often have data processing…
Yael Harpaz, Yoel Shkolnisky
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…
Authors not listed
During charge/discharge cracking occurs in Nickel Manganese Cobalt (NMC) secondary particles. Secondary particles with cracks will have observably lower grey-levels in micro-CT datasets compared to an otherwise identical pristine particle. This is due to the ‘partial volume effect’ where voxels representative of space…
Authors not listed
In molecular machine learning, the choice of the representation of molecules can have a significant impact on model performance. However, understanding the root causes of these performance differences often proves challenging. One promising approach to explore model behavior is representational alignment, which…