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A user with 2,378 edits. Account created on 30 March 2009.
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14 April 2025

  • 10:2810:28, 14 April 2025 diff hist +82 Main Page →Image formation
  • 10:0010:00, 14 April 2025 diff hist +2,174 N 2025Bhandari Fast Created page with "== Citation == J. Bhandari, D. Kompaniiets, A. K. Singh, C. Bator, J. Porta, and B. Liu, “Efficient strategies and troubleshooting for single particle cryoEM data collection using EPU,” BMC Methods, vol. 2, no. 1, p. 3, 2025. == Abstract == Background CryoEM has gained popularity due to advancements in both hardware and software, making it possible to visualize biological molecular structures in detail. However, despite its growing use, cryoEM remains a costly tec..." current
  • 09:5909:59, 14 April 2025 diff hist +73 Main Page →Automated data collection
  • 09:4409:44, 14 April 2025 diff hist +1,212 N 2024Bai NUFT Created page with "== Citation == Z. Bai and J. Huang, “Non-uniform Fourier transform based image classification in single-particle Cryo-EM,” J. Structural Biology X, p. 100121, 2025. == Abstract == In the single-particle Cryo-EM projection image classification, it is a common practice to apply the Fourier transform to the images and extract rotation-invariant features in the frequency domain. However, this process involves interpolation, which can reduce the accuracy of the results..." current
  • 09:4409:44, 14 April 2025 diff hist +101 Main Page →2D Alignment
  • 09:0509:05, 14 April 2025 diff hist +2,589 N 2008Downing Twin Created page with "== Citation == K. H. Downing and R. M. Glaeser, “Restoration of weak phase-contrast images recorded with a high degree of defocus: the “twin image” problem associated with CTF correction.,” Ultramicroscopy, vol. 108, no. 9, pp. 921–928, Aug. 2008, doi: 10.1016/j.ultramic.2008.03.004. == Abstract == Relatively large values of objective-lens defocus must normally be used to produce detectable levels of image contrast for unstained biological specimens, which a..." current
  • 09:0409:04, 14 April 2025 diff hist +92 Main Page →Image formation
  • 08:5708:57, 14 April 2025 diff hist +1,291 N 2025Zhu Quality Created page with "== Citation == H. Zhu, G. Terashi, F. Farheen, T. Nakamura, and D. Kihara, “AI-based quality assessment methods for protein structure models from Cryo-EM,” Current Research in Structural Biology, p. 100164, 2025. == Abstract == Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, with an increasing number of structures being determined by cryo-EM each year, many at higher resolutions. However, challenges remain in accurately interpreting..." current
  • 08:5708:57, 14 April 2025 diff hist +86 Main Page →Books and reviews

10 April 2025

  • 08:4608:46, 10 April 2025 diff hist +2,020 N 2025Shah TomoCPT Created page with "== Citation == P. N. Shah, R. Sanchez-Garcia, and D. I. Stuart, “TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms,” Biological Crystallography, vol. 81, pp. 63–76, 2025. == Abstract == Cryo-electron tomography is a rapidly developing field for studying macromolecular complexes in their native environments and has the potential to revolutionize our understanding of protein function. However, fast and accurate id..." current
  • 08:4508:45, 10 April 2025 diff hist +76 Main Page →Subtomogram analysis
  • 08:3708:37, 10 April 2025 diff hist +1,466 N 2025Cao EMInfo Created page with "== Citation == H. Cao, J. He, T. Li, and S.-Y. Huang, “Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning,” J. Chemical Information and Modeling, 2025. == Abstract == With the resolution revolution of cryo-electron microscopy (cryo-EM) and the rapid development of image processing technology, cryo-EM has become an indispensable experimental method for determining the three-dimensional structures of biological macromolecu..." current
  • 08:3608:36, 10 April 2025 diff hist +113 Main Page →Segmentation

4 March 2025

19 February 2025

  • 07:4307:43, 19 February 2025 diff hist +1,645 N 2025Liu SpIsonet Created page with "== Citation == Y.-T. Liu, H. Fan, J. J. Hu, and Z. H. Zhou, “Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning,” Nature methods, vol. 22, pp. 113–123, 2025. == Abstract == While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the ‘preferred’ orientation problem) remains a complication for most specimens. Existing..." current
  • 07:4207:42, 19 February 2025 diff hist +124 Main Page →3D Reconstruction

18 February 2025

  • 09:1509:15, 18 February 2025 diff hist +2,280 N 2024Tang SimCryoCluster Created page with "== Citation == H. Tang, Y. Wang, J. Ouyang, and J. Wang, “Simcryocluster: a semantic similarity clustering method of cryo-EM images by adopting contrastive learning,” BMC bioinformatics, vol. 25, no. 1, p. 77, 2024. == Abstract == Background: Cryo-electron microscopy (Cryo-EM) plays an increasingly important role in the determination of the three-dimensional (3D) structure of macromolecules. In order to achieve 3D reconstruction results close to atomic resolution,..." current
  • 09:1409:14, 18 February 2025 diff hist +118 Main Page →2D Classification and clustering
  • 09:0409:04, 18 February 2025 diff hist +1,420 N 2024Li CryoStar Created page with "== Citation == Y. Li, Y. Zhou, J. Yuan, F. Ye, and Q. Gu, “CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction,” Nature Methods, pp. 1–9, 2024. == Abstract == Resolving conformational heterogeneity in cryogenic electron microscopy datasets remains an important challenge in structural biology. Previous methods have often been restricted to working exclusively on volumetric densities, neglecting the potential of incorpor..." current
  • 09:0209:02, 18 February 2025 diff hist +104 Main Page →3D Heterogeneity

11 February 2025

  • 14:2714:27, 11 February 2025 diff hist +1,479 N 2025Yan MPicker Created page with "== Citation == X. Yan et al., “MPicker: visualizing and picking membrane proteins for cryo-electron tomography,” Nature Communications, vol. 16, no. 1, p. 472, 2025. == Abstract == Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong co..." current
  • 14:2614:26, 11 February 2025 diff hist +83 Main Page →Subtomogram analysis

4 February 2025

  • 06:4406:44, 4 February 2025 diff hist +1,469 N 2024Kimanius Blush Created page with "== Citation == D. Kimanius et al., “Data-driven regularization lowers the size barrier of cryo-EM structure determination,” Nature Methods, pp. 1–6, 2024. == Abstract == Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is..." current
  • 06:4406:44, 4 February 2025 diff hist +74 Main Page →Sharpening of high resolution information
  • 06:4006:40, 4 February 2025 diff hist +1,830 N 2024Gyawali CryoSegNet Created page with "== Citation == R. Gyawali, A. Dhakal, L. Wang, and J. Cheng, “CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net,” Briefings in Bioinformatics, vol. 25, no. 4, 2024. == Abstract == Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determina-tion. However, existing methods trained on a limited amount of..." current
  • 06:3906:39, 4 February 2025 diff hist +73 Main Page →Automatic particle picking
  • 06:3306:33, 4 February 2025 diff hist +1,566 N 2024Almira TTM Created page with "== Citation == J. M. Almira, H. Phelippeau, and A. Martinez-Sanchez, “Fast normalized cross-correlation for template matching with rotations,” Journal of Applied Mathematics and Computing, vol. 70, no. 5, pp. 4937–4969, 2024. == Abstract == Normalized cross-correlation is the reference approach to carry out template matching on images. When it is computed in Fourier space, it can handle efficiently template translations but it cannot do so with template rotation..." current
  • 06:3206:32, 4 February 2025 diff hist +85 Main Page →Subtomogram analysis

3 February 2025

  • 07:4407:44, 3 February 2025 diff hist +1,592 N 2025Costa CryoSamba Created page with "== Citation == J. I. Costa-Filho, L. Theveny, M. de Sautu, and T. Kirchhausen, “CryoSamba: self-supervised deep volumetric denoising for cryo-electron tomography data,” J. Structural Biology, vol. 217, no. 1, p. 108163, 2025. == Abstract == Cryogenic electron tomography (cryo-ET) has rapidly advanced as a high-resolution imaging tool for visualizing subcellular structures in 3D with molecular detail. Direct image inspection remains challenging due to inherent low..." current
  • 07:4307:43, 3 February 2025 diff hist +71 Main Page →Noise reduction
  • 07:3707:37, 3 February 2025 diff hist +1,135 N 2025Sun PlasmaMembranes Created page with "== Citation == W. W. Sun et al., “Cryo-electron tomography pipeline for plasma membranes,” Nature Communications, vol. 16, no. 1, p. 855, 2025. == Abstract == Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suite..." current
  • 07:3707:37, 3 February 2025 diff hist +111 Main Page →Sample preparation
  • 07:2907:29, 3 February 2025 diff hist +1,489 N 2024Last Ais Created page with "== Citation == M. G. Last, L. Abendstein, L. M. Voortman, and T. H. Sharp, “Streamlining segmentation of cryo-electron tomography datasets with Ais,” Elife, vol. 13, p. RP98552, 2024. == Abstract == Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software..." current
  • 07:2807:28, 3 February 2025 diff hist +76 Main Page →Segmentation

31 January 2025

  • 13:0413:04, 31 January 2025 diff hist +1,605 N 2025deIsidro Misalignment Created page with "== Citation == F. de Isidro-Gómez, JL. Vilas, JM. Carazo, and COS. Sorzano, “Automatic detection of alignment errors in cryo-electron tomography,” J. Structural Biology, vol. 217, no. 1, p. 108153, 2025. == Abstract == Cryo-electron tomography is an imaging technique that allows the study of the three-dimensional structure of a wide range of biological samples, from entire cellular environments to purified specimens. This technique collects a series of images fro..." current
  • 12:5912:59, 31 January 2025 diff hist +82 Main Page →Image alignment

30 January 2025

  • 11:5911:59, 30 January 2025 diff hist +2,207 N 2022Kreutzberger Review Created page with "== Citation == M. A. Kreutzberger, R. R. Sonani, and E. H. Egelman, “Cryo-EM reconstruction of helical polymers: Beyond the simple cases,” Quarterly reviews of biophysics, vol. 57, p. e16, 2024. == Abstract == Helices are one of the most frequently encountered symmetries in biological assemblies. Helical symmetry has been exploited in electron microscopic studies as a limited number of filament images, in principle, can provide all the information needed to do a t..." current
  • 11:5811:58, 30 January 2025 diff hist +78 Main Page →Books and reviews

21 January 2025

20 January 2025

  • 06:3606:36, 20 January 2025 diff hist +1,302 N 2025Debarnot IceTide Created page with "== Citation == V. Debarnot, V. Kishore, R. D. Righetto, and I. Dokmanic, “Ice-tide: Implicit cryo-et imaging and deformation estimation,” IEEE Transactions on Computational Imaging, vol. 11, pp. 24–35, 2025. == Abstract == We introduce ICE-TIDE, amethod 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 resolution of..." current
  • 06:3506:35, 20 January 2025 diff hist +125 Main Page →3D reconstruction

17 January 2025

  • 17:2817:28, 17 January 2025 diff hist +1,580 N 2025Elferich CTFFind5 Created page with "== Citation == J. Elferich, L. Kong, X. Zottig, and N. Grigorieff, “CTFFIND5 provides improved insight into quality, tilt, and thickness of TEM samples,” eLife, vol. 13, p. RP97227, 2024. == Abstract == Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of..." current
  • 17:2517:25, 17 January 2025 diff hist +101 Main Page →CTF estimation and restoration
  • 17:2017:20, 17 January 2025 diff hist +1,381 N 2024Zhang Kam Created page with "== Citation == A. Zhang et al., “Moment-based metrics for molecules computable from cryogenic electron microscopy images,” Biological Imaging, vol. 4, p. e3, 2024. == Abstract == Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known..." current
  • 17:1817:18, 17 January 2025 diff hist +79 Main Page →3D Alignment

14 January 2025

  • 09:4709:47, 14 January 2025 diff hist +1,162 N 2024Sanchez Cesped Created page with "== Citation == R. Sanchez-Garcia, M. Saur, J. Vargas, C. Poelking, and C. M. Deane, “CESPED: A benchmark for supervised particle pose estimation in cryo-EM,” Physical Review Research, vol. 6, no. 2, p. 23245, 2024. == Abstract == Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a data set spec..." current
  • 09:4609:46, 14 January 2025 diff hist +99 Main Page →3D Alignment
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