ArticleNature protocols2008
Image processing for electron microscopy single-particle analysis using XMIPP.
Article in Nature protocols, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 196 papers.
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Who cites it
196 citing papers in PubMed, 328 citations in OpenAlex.
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- High-throughput cryo-EM structure determination of amyloids.Faraday discussions · 2022Article
- Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates.Structure (London, England : 1993) · 2022Article
- Forty years in cryoEM of membrane proteins.Microscopy (Oxford, England) · 2022Article
- New tools for automated cryo-EM single-particle analysis in RELION-4.0.The Biochemical journal · 2021Article
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- A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments.Scientific reports · 2021Article
- Development of basic building blocks for cryo-EM: the emcore and emvis software libraries.Acta crystallographica. Section D, Structural biology · 2020Article
- Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.Nature plants · 2020Article
- CDAE: A Cascade of Denoising Autoencoders for Noise Reduction in the Clustering of Single-Particle Cryo-EM Images.Frontiers in genetics · 2020Article
- Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit.International journal of molecular sciences · 2019Review
- Coherent diffractive imaging of microtubules using an X-ray laser.Nature communications · 2019Article
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- Structural basis for adPEO-causing mutations in the mitochondrial TWINKLE helicase.Human molecular genetics · 2019Article
136 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.