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3 February 2025
- 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
- 09:2509:25, 21 January 2025 diff hist −104 Main Page →3D Alignment Tag: Manual revert
- 09:2409:24, 21 January 2025 diff hist +104 Main Page →3D Alignment Tag: Reverted
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
3 January 2025
- 08:0208:02, 3 January 2025 diff hist +1,465 N 2023Lucas Baited Created page with "== Citation == B. A. Lucas, B. A. Himes, and N. Grigorieff, “Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias,” Elife, vol. 12, p. RP90486, 2023. == Abstract == Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and c..." current
- 08:0208:02, 3 January 2025 diff hist +86 Main Page →Automatic particle picking
- 07:5507:55, 3 January 2025 diff hist +1,442 N 2024Bhattacharjee TimeResolved Created page with "== Citation == S. Bhattacharjee et al., “Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling,” Cell, vol. 187, no. 3, pp. 782–796, 2024. == Abstract == The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-..." current
- 07:5407:54, 3 January 2025 diff hist +99 Main Page →Sample preparation
- 07:5007:50, 3 January 2025 diff hist +1,416 N 2024Tuijtel Lamellae Created page with "== Citation == M. W. Tuijtel et al., “Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging,” Science Advances, vol. 10, no. 17, p. eadk6285, 2024. == Abstract == Cryo–electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imagin..." current
- 07:4907:49, 3 January 2025 diff hist +87 Main Page →Sample preparation
- 07:4507:45, 3 January 2025 diff hist +1,890 N 2023Grassetti Graphene Created page with "== Citation == A. V. Grassetti, M. B. May, and J. H. Davis, “Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids (Video)| JoVE,” JoVE (Journal of Visualized Experiments), no. 201, p. e66023, 2023. == Abstract == In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to remove excess liquid and rapidly frozen in a roughly 20-100 nm thick layer..." current
- 07:4407:44, 3 January 2025 diff hist +91 Main Page →Sample preparation
27 December 2024
- 07:5807:58, 27 December 2024 diff hist +1,497 N 2023DiIorio AbInitio Created page with "== Citation == M. C. DiIorio and A. W. Kulczyk, “Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy,” Micromachines, vol. 14, no. 9, p. 1674, 2023. == Abstract == Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. Howe..." current
- 07:5707:57, 27 December 2024 diff hist +110 Main Page →Books and reviews
- 07:5307:53, 27 December 2024 diff hist +1,473 N 2023Langeberg RNAScaffold Created page with "== Citation == C. J. Langeberg and J. S. Kieft, “A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM,” Nucleic Acids Research, vol. 51, no. 20, pp. e100–e100, 2023. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins..." current
- 07:5207:52, 27 December 2024 diff hist +79 Main Page →Sample preparation
- 07:3707:37, 27 December 2024 diff hist +1,596 N 2023Riahi Transport Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re..." current
- 07:3607:36, 27 December 2024 diff hist +95 Main Page →3D Alignment
- 07:1907:19, 27 December 2024 diff hist +1,068 N 2024Singer Wasserstein Created page with "== Citation == A. Singer and R. Yang, “Alignment of density maps in Wasserstein distance,” Biological Imaging, vol. 4, p. e5, 2024. == Abstract == In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function en..." current
- 07:1807:18, 27 December 2024 diff hist +98 Main Page →3D Alignment
26 December 2024
- 11:0111:01, 26 December 2024 diff hist +1,531 N 2023Forsberg Filter Created page with "== Citation == B. O. Forsberg, P. N. Shah, and A. Burt, “A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps,” Nature Communications, vol. 14, no. 1, p. 5802, 2023. == Abstract == Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great eff..." current
- 11:0111:01, 26 December 2024 diff hist +84 Main Page →3D Heterogeneity
- 10:5010:50, 26 December 2024 diff hist +1,428 N 2023Dai CryoFEM Created page with "== Citation == X. Dai, L. Wu, S. Yoo, and Q. Liu, “Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps,” Briefings in Bioinformatics, vol. 24, no. 6, p. bbad405, 2023. == Abstract == Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity o..." current
- 10:4910:49, 26 December 2024 diff hist +103 Main Page →Fitting and docking
- 10:4410:44, 26 December 2024 diff hist +1,621 N 2023Afonine Varref Created page with "== Citation == P. V. Afonine, A. Gobet, L. Moissonnier, J. Martin, B. K. Poon, and V. Chaptal, “Conformational space exploration of cryo-EM structures by variability refinement,” Biochimica et Biophysica Acta (BBA)-Biomembranes, vol. 1865, no. 4, p. 184133, 2023. == Abstract == Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local..." current
- 10:4410:44, 26 December 2024 diff hist +98 Main Page →3D Heterogeneity
- 10:4010:40, 26 December 2024 diff hist +2,095 N 2023Yee Ot2Rec Created page with "== Citation == N. B.-y. Yee, E. M. Ho, M. Darrow, and M. Basham, “Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow,” Biophysical Journal, vol. 122, no. 3, p. 462a, 2023. == Abstract == Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With..." current
- 10:3810:38, 26 December 2024 diff hist +75 Main Page →Software
23 December 2024
- 20:1320:13, 23 December 2024 diff hist +2,019 N 2023Zhang Denoising Created page with "== Citation == D. Zhang et al., “Unsupervised Cryo-EM Images Denoising and Clustering based on Deep Convolutional Autoencoder and K-Means++,” IEEE Trans. Medical Imaging, vol. 42, pp. 1509–1521, 2023. == Abstract == Cryo-electron microscopy (cryo-EM) is a widely used structural determination technique. Because of the extremely low signal-to-noise ratio (SNR) of images captured by cryo-EM, clustering single-particle cryo-EM images with high accuracy is challengin..." current
- 20:0820:08, 23 December 2024 diff hist +118 Main Page →2D Preprocessing
- 20:0420:04, 23 December 2024 diff hist −5 2024Bendory Complexity No edit summary current
- 20:0320:03, 23 December 2024 diff hist +1,962 N 2024Bendory Complexity Created page with "== Citation == T. Bendory and D. Edidin, “The Sample Complexity of Sparse Multireference Alignment and Single-Particle Cryo-Electron Microscopy,” SIAM J. on Mathematics of Data Science, vol. 6, no. 2, pp. 254–282, 2024. == Abstract == Multireference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo–electron microscopy (cryo-EM) that ha..."
- 20:0320:03, 23 December 2024 diff hist +103 Main Page →2D Alignment
- 19:5819:58, 23 December 2024 diff hist +1,551 N 2024Liu DeepETPicker Created page with "== Citation == G. Liu, T. Niu, M. Qiu, Y. Zhu, F. Sun, and G. Yang, “DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning,” Nature Communications, vol. 15, no. 1, p. 2090, 2024. == Abstract == To solve three-dimensional structures of biological macromolecules in situ, large numbers of particles often need to be picked from cryo-electron tomograms. However, adoption of automated particle-picking meth..." current
- 19:5819:58, 23 December 2024 diff hist +94 Main Page →Subtomogram analysis
- 19:5419:54, 23 December 2024 diff hist +1,478 N 2023Rice TomoTwin Created page with "== Citation == G. Rice, T. Wagner, M. Stabrin, O. Sitsel, D. Prumbaum, and S. Raunser, “TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining,” Nature methods, vol. 20, no. 6, pp. 871–880, 2023. == Abstract == Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volu..." current