Automatic particle selection from electron micrographs using machine learning techniques.

PubWeight™: 0.96‹?› | Rank: Top 15%

🔗 View Article (PMC 2777658)

Published in J Struct Biol on June 23, 2009

Authors

C O S Sorzano1, E Recarte, M Alcorlo, J R Bilbao-Castro, C San-Martín, R Marabini, J M Carazo

Author Affiliations

1: Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain. coss@cnb.csic.es

Articles cited by this

EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol (1999) 27.52

Automated molecular microscopy: the new Leginon system. J Struct Biol (2005) 10.00

XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol (2004) 4.95

Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc (2008) 4.90

Maximum-likelihood multi-reference refinement for electron microscopy images. J Mol Biol (2005) 3.00

FindEM--a fast, efficient program for automatic selection of particles from electron micrographs. J Struct Biol (2004) 2.74

Automated cryoEM data acquisition and analysis of 284742 particles of GroEL. J Struct Biol (2006) 2.15

Automatic particle selection: results of a comparative study. J Struct Biol (2004) 1.82

Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J Struct Biol (2005) 1.58

Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study. J Struct Biol (2004) 1.49

Classical detection theory and the cryo-EM particle selection problem. J Struct Biol (2004) 1.29

Detecting circular and rectangular particles based on geometric feature detection in electron micrographs. J Struct Biol (2004) 1.20

Detecting particles in cryo-EM micrographs using learned features. J Struct Biol (2004) 1.15

Automatic particle detection through efficient Hough transforms. IEEE Trans Med Imaging (2003) 1.12

Localization of the N-terminus of minor coat protein IIIa in the adenovirus capsid. J Mol Biol (2008) 1.06

Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J Struct Biol (2007) 1.04

Auto-accumulation method using simulated annealing enables fully automatic particle pickup completely free from a matching template or learning data. J Struct Biol (2004) 1.01

Automatic particle pickup method using a neural network has high accuracy by applying an initial weight derived from eigenimages: a new reference free method for single-particle analysis. J Struct Biol (2004) 0.98

Image segmentation for automatic particle identification in electron micrographs based on hidden Markov random field models and expectation maximization. J Struct Biol (2004) 0.94

Application of template matching technique to particle detection in electron micrographs. J Struct Biol (2004) 0.91

A binary segmentation approach for boxing ribosome particles in cryo EM micrographs. J Struct Biol (2004) 0.90

Accurate calculation of image moments. IEEE Trans Image Process (2007) 0.90

SLEUTH--a fast computer program for automatically detecting particles in electron microscope images. J Struct Biol (2004) 0.87

Model-based particle picking for cryo-electron microscopy. J Struct Biol (2004) 0.87

An approach to automated particle picking from electron micrographs based on reduced representation templates. J Struct Biol (2004) 0.86

A two step approach for semi-automated particle selection from low contrast cryo-electron micrographs. J Struct Biol (2004) 0.85

TYSON: robust searching, sorting, and selecting of single particles in electron micrographs. J Struct Biol (2004) 0.78

Articles by these authors

XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol (2004) 4.95

Nonsmooth nonnegative matrix factorization (nsNMF). IEEE Trans Pattern Anal Mach Intell (2006) 2.51

A clustering approach to multireference alignment of single-particle projections in electron microscopy. J Struct Biol (2010) 2.19

Sequence-related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures. Proc Natl Acad Sci U S A (2000) 1.98

Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli. J Microsc (1988) 1.88

3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy (1998) 1.78

Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. J Mol Evol (1997) 1.71

Integrating electron microscopy information into existing Distributed Annotation Systems. J Struct Biol (2007) 1.69

General morphology and capsid fine structure of African swine fever virus particles. Virology (1984) 1.52

Purification and organization of the gene 1 portal protein required for phage P22 DNA packaging. Biochemistry (1988) 1.50

Xmipp 3.0: an improved software suite for image processing in electron microscopy. J Struct Biol (2013) 1.47

Large T-antigen double hexamers imaged at the simian virus 40 origin of replication. Mol Cell Biol (2000) 1.42

A structural model for the Escherichia coli DnaB helicase based on electron microscopy data. J Struct Biol (1995) 1.39

A novel neural network technique for analysis and classification of EM single-particle images. J Struct Biol (2001) 1.37

Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions. J Mol Biol (1988) 1.34

Pattern recognition and classification of images of biological macromolecules using artificial neural networks. Biophys J (1994) 1.31

Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution. J Mol Biol (1986) 1.31

Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel. J Mol Biol (1997) 1.24

A multiresolution approach to orientation assignment in 3D electron microscopy of single particles. J Struct Biol (2004) 1.21

Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics (2009) 1.18

The RepA protein of plasmid RSF1010 is a replicative DNA helicase. J Biol Chem (1997) 1.15

Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC. Structure (1998) 1.15

Computer graphic display method for visualizing three-dimensional biological structures. Science (1986) 1.14

The effect of overabundant projection directions on 3D reconstruction algorithms. J Struct Biol (2001) 1.14

Three-dimensional structure of T3 connector purified from overexpressing bacteria. J Mol Biol (1992) 1.12

The three-dimensional structure of a DNA translocating machine at 10 A resolution. Structure (1999) 1.11

A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment. Ultramicroscopy (2003) 1.09

The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. EMBO J (2001) 1.07

Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J Struct Biol (2007) 1.04

Mapping and fuzzy classification of macromolecular images using self-organizing neural networks. Ultramicroscopy (2000) 1.02

Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy. Ultramicroscopy (2004) 1.02

Three-dimensional reconstruction of the ribosome from Escherichia coli. Biophys J (1989) 1.01

Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection. J Struct Biol (1997) 1.00

Three-dimensional reconstruction of bacteriophage phi 29 neck particles at 2 X 2 nm resolution. J Mol Biol (1985) 0.98

A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server. J Struct Biol (1999) 0.96

Three-dimensional reconstruction of the sevenfolded form of Bacillus subtilis Gro EL Chaperonin. J Struct Biol (1991) 0.94

Bacteriophage T3 gene 8 product oligomer structure. J Ultrastruct Mol Struct Res (1986) 0.93

Transfer function restoration in 3D electron microscopy via iterative data refinement. Phys Med Biol (2004) 0.91

Polymorphic quaternary organization of the Bacillus subtilis bacteriophage SPP1 replicative helicase (G40 P). J Mol Biol (1998) 0.91

Structural localization of the proteins of the head to tail connecting region of bacteriophage phi 29. Virology (1983) 0.91

Designing and executing scientific workflows with a programmable integrator. Bioinformatics (2004) 0.89

Two-step demodulation based on the Gram-Schmidt orthonormalization method. Opt Lett (2012) 0.89

FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. J Struct Biol (2012) 0.88

Structure of phage phi 29 connector protein assembled in vivo. Virology (1985) 0.88

Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs. J Struct Biol (2008) 0.87

A new non-crystallographic image-processing technique reveals the architecture of ribosomes. Trends Biochem Sci (1988) 0.87

The problem of identification of prognostic factors for persistent trophoblastic disease. Gynecol Oncol (1988) 0.86

Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections. J Microsc (1987) 0.86

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. Bioinformatics (2013) 0.85

Helicases as nucleic acid unwinding machines. Nat Struct Biol (2000) 0.85

Non-rigid consistent registration of 2D image sequences. Phys Med Biol (2010) 0.84

Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques. J Struct Biol (2013) 0.83

pH-controlled quaternary states of hexameric DnaB helicase. J Mol Biol (2000) 0.83

Two-step interferometry by a regularized optical flow algorithm. Opt Lett (2011) 0.82

Volumetric restrictions in single particle 3DEM reconstruction. Pattern Recognit (2008) 0.80

The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy. Eur Biophys J (2000) 0.78

Structural study of tetragonal-ordered aggregates of phage phi 29 necks. J Ultrastruct Res (1984) 0.77

Self-organizing tree growing network for classifying amino acids. Bioinformatics (1998) 0.77

FEMME database: topologic and geometric information of macromolecules. J Struct Biol (2003) 0.76

Self-organizing tree-growing network for the classification of protein sequences. Protein Sci (1998) 0.76

Correlation of topographic surface and volume data from three-dimensional electron microscopy. J Struct Biol (2001) 0.75

A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners. Phys Med Biol (2009) 0.75

On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures. Comput Appl Biosci (1994) 0.75

Shack-Hartmann centroid detection using the spiral phase transform. Appl Opt (2012) 0.75

Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy. J Struct Biol (1996) 0.75

Flow cytometric diagnosis of partial mole. Pathol Res Pract (1992) 0.75

An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data. Comput Appl Biosci (1995) 0.75

New phylogenetic venues opened by a novel implementation of the DNAml algorithm. Bioinformatics (1998) 0.75

Analysis of structural variability within two-dimensional biological crystals by a combination of patch averaging techniques and self organizing maps. Ultramicroscopy (1996) 0.75

Computational space reduction and parallelization of a new clustering approach for large groups of sequences. Bioinformatics (1998) 0.75