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A user with 2,404 edits. Account created on 30 March 2009.
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20 June 2025

  • 09:5909:59, 20 June 2025 diff hist +1,341 N 2025Neiterman Frames Created page with "== Citation == E. H. Neiterman, A. Heimowitz, and G. Ben-Artzi, “A non-parametric approach to particle picking in all frames,” J. Structural Biology, p. 108201, 2025. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has significantly advanced macromolecular structure reconstruction. However, a key limitation is the conventional reliance on micrographs obtained by motion correction and averaging, which inherently loses the richness of information c..." current
  • 09:5809:58, 20 June 2025 diff hist +82 Main Page →Automatic particle picking
  • 09:4409:44, 20 June 2025 diff hist +1,717 N 2025Dickerson Damage Created page with "== Citation == J. L. Dickerson et al., “Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures,” Proc. Natl. Academy of Sciences, vol. 122, no. 17, p. e2421538122, 2025. == Abstract == The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been numerous attempts to reduce the effects of radiation damage by cooling the specimen beyond liquid-nitrogen te..." current
  • 09:4309:43, 20 June 2025 diff hist +96 Main Page →Image formation
  • 09:0109:01, 20 June 2025 diff hist +1,355 N 2025Kinman SIREN Created page with "== Citation == L. F. Kinman, M. V. Carreira, B. M. Powell, and J. H. Davis, “Automated model-free analysis of cryo-EM volume ensembles with SIREn,” Structure, vol. 33, no. 5, pp. 974–987, 2025. == Abstract == Cryogenic electron microscopy (cryo-EM) has the potential to capture snapshots of proteins in motion and generate hypotheses linking conformational states to biological function. This potential has been increasingly realized by the advent of machine learnin..." current
  • 09:0109:01, 20 June 2025 diff hist +96 Main Page →3D Heterogeneity

30 May 2025

  • 05:5105:51, 30 May 2025 diff hist +1,895 N 2025Mallet crAI Created page with "== Citation == V. Mallet, C. Rapisarda, H. Minoux, and M. Ovsjanikov, “Finding antibodies in cryo-EM maps with CrAI,” Bioinformatics, vol. 41, no. 5, p. btaf157, 2025. == Abstract == Motivation Therapeutic antibodies have emerged as a prominent class of new drugs due to their high specificity and their ability to bind to several protein targets. Once an initial antibody has been identified, its design and characteristics are refined using structural information, w..." current
  • 05:5005:50, 30 May 2025 diff hist +82 Main Page →Fitting and docking

16 May 2025

30 April 2025

  • 07:3307:33, 30 April 2025 diff hist +2,028 N 2020Zeng GumNet Created page with "== Citation == X. Zeng and M. Xu, “Gum-net: Unsupervised geometric matching for fast and accurate 3d subtomogram image alignment and averaging,” in Proc. of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020, pp. 4073–4084. == Abstract == We propose a Geometric unsupervised matching Net- work (Gum-Net) for finding the geometric correspondence between two images with application to 3D subtomogram alignment and averaging. Subtomogram alignmen..." current
  • 07:3207:32, 30 April 2025 diff hist +86 Main Page →Subtomogram analysis

23 April 2025

  • 07:1207:12, 23 April 2025 diff hist +1,479 N 2025Harar FakET Created page with "== Citation == P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “Faket: Simulating cryo-electron tomograms with neural style transfer,” Structure, vol. 33, no. 4, pp. 820–827, 2025. == Abstract == In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce th..." current
  • 07:0407:04, 23 April 2025 diff hist +103 Main Page →Software

21 April 2025

  • 07:0007:00, 21 April 2025 diff hist +1,472 N 2025Schoennenbeck CryoVIA Created page with "== Citation == P. Schönnenbeck, B. Junglas, and C. Sachse, “CryoVIA: An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs,” Structure, 2025. == Abstract == Imaging of lipid structures and associated protein complexes using cryoelectron microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in p..." current
  • 06:5906:59, 21 April 2025 diff hist +128 Main Page →Segmentation

16 April 2025

  • 10:4310:43, 16 April 2025 diff hist +1,827 N 2025Woollard InstaMap Created page with "== Citation == G. Woollard et al., “InstaMap: instant-NGP for cryo-EM density maps,” Biological Crystallography, vol. 81, no. 4, 2025. == Abstract == Despite the parallels between problems in computer vision and cryo-electron microscopy (cryo-EM), many state-of-the-art approaches from computer vision have yet to be adapted for cryo-EM. Within the computer-vision research community, implicits such as neural radiance fields (NeRFs) have enabled the detailed reconstr..." current
  • 10:4210:42, 16 April 2025 diff hist +93 Main Page →3D Reconstruction

15 April 2025

  • 15:2815:28, 15 April 2025 diff hist +1,226 N 2025Kapnulin Outlier Created page with "== Citation == L. Kapnulin, A. Heimowitz, and N. Sharon, “Outlier removal in cryo-EM via radial profiles,” J. Structural Biology, p. 108172, 2025. == Abstract == The process of particle picking, a crucial step in cryo-electron microscopy (cryo-EM) image analysis, often encounters challenges due to outliers, leading to inaccuracies in downstream processing. In response to this challenge, this research introduces an additional automated step to reduce the number of..." current
  • 15:2815:28, 15 April 2025 diff hist +87 Main Page →2D Alignment
  • 13:5813:58, 15 April 2025 diff hist +2,110 N 2025Chen GCTransNet Created page with "== Citation == C. Chen, Y. Yan, J. Wu, and W.-B. Gan, “GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers,” J. Structural Biology, p. 108170, 2025. == Abstract == Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mit..." current
  • 13:5513:55, 15 April 2025 diff hist +113 Main Page →Segmentation
  • 13:5313:53, 15 April 2025 diff hist +2,551 N 2025Haynes OptimalIce Created page with "== Citation == R. M. Haynes, J. Myers, C. S. López, J. Evans, O. Davulcu, and C. Yoshioka, “A strategic approach for efficient cryo-EM grid optimization using design of experiments,” J. Structural Biology, vol. 217, no. 1, p. 108068, 2025. == Abstract == In recent years, cryo-electron microscopy (cryo-EM) has become a practical and effective method of determining structures at previously unattainable resolutions due to advances in detection, automation, and data..." current
  • 13:5213:52, 15 April 2025 diff hist +93 Main Page →Sample preparation

14 April 2025

  • 10:2910:29, 14 April 2025 diff hist +1,265 N 2023Shi Compression Created page with "== Citation == H. Shi, C. Wu, and X. Zhang, “Addressing compressive deformation of proteins embedded in crystalline ice,” Structure, vol. 31, no. 2, pp. 213–220, 2023. == Abstract == For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, s..." current
  • 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
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