List of works - Javier Vargas

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.

scientific article published on 17 September 2017

A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

scientific article published on 12 June 2015

A new algorithm for high-resolution reconstruction of single particles by electron microscopy

scientific article published on 24 August 2018

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs ⬇️

scientific article published on August 19, 2013

A review of resolution measures and related aspects in 3D Electron Microscopy

scientific article published on 22 September 2016

A robust approach to ab initio cryo-electron microscopy initial volume determination

scientific article published on 27 September 2019

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.

scientific article published on 28 January 2015

Alignment of direct detection device micrographs using a robust Optical Flow approach.

scientific article published on 12 February 2015

Analysis of the principal component algorithm in phase-shifting interferometry.

scientific article

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ

scientific article

Automatic local resolution-based sharpening of cryo-EM maps

scientific article published on 01 February 2020

Blind estimation of DED camera gain in Electron Microscopy

scientific article published on 15 March 2018

CESPED: A benchmark for supervised particle pose estimation in cryo-EM

scientific article published on 4 June 2024

CTF Challenge: Result summary.

scientific article published on 23 April 2015

Calibration of a Shack-Hartmann wavefront sensor as an orthographic camera

scientific article published on 01 June 2010

Circular common-path point diffraction interferometer

scientific article published in October 2012

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.

scientific article

Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps

article

Deflectometric method for the measurement of user power for ophthalmic lenses

scientific article published on 01 September 2010

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions

scientific article published on 13 April 2016

Direct demodulation of closed-fringe interferograms based on active contours

scientific article published on 01 November 2010

Efficient initial volume determination from electron microscopy images of single particles

scientific article published on 27 June 2014

Fast and automatic identification of particle tilt pairs based on Delaunay triangulation.

scientific article published on 18 October 2016

Fast two-dimensional simultaneous phase unwrapping and low-pass filtering.

scientific article published in January 2012

Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope

scientific article

Imaging polarimeters based on liquid crystal variable retarders: an emergent technology for space instrumentation

Local analysis of strains and rotations for macromolecular electron microscopy maps

scientific article published on 18 April 2016

Local computational methods to improve the interpretability and analysis of cryo-EM maps

scientific article published on 13 May 2020

Local fringe density determination by adaptive filtering

scientific article published on 01 January 2011

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps

scientific article published on 26 January 2018

Multiplicative phase-shifting interferometry using optical flow.

scientific article published in August 2012

Multiresolution approach based on projection matrices

scientific article published on 01 March 2009

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy ⬇️

scientific article published on April 19, 2013

Optical inspection of liquid crystal variable retarder inhomogeneities

scientific article published in February 2010

Particle alignment reliability in single particle electron cryomicroscopy: a general approach

scientific article published on 22 February 2016

Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques ⬇️

scientific article published on August 6, 2013

Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap.

scientific article published on 30 August 2017

Phase-shifting interferometry based on induced vibrations

scientific article published in January 2011

Phase-shifting interferometry based on principal component analysis.

scientific article published in April 2011

Precise phase retrieval under harsh conditions by constructing new connected interferograms

scientific article published on 14 April 2016

Principal component analysis-based quantitative differential interference contrast microscopy

scientific article published on 01 January 2019

Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis.

scientific article published on 24 July 2017

Regularized least squares phase sampling interferometry ⬇️

scientific article published on March 14, 2011

Role of the filter phase in phase sampling interferometry.

scientific article published in October 2011

Scipion web tools: Easy to use cryo-EM image processing over the web.

scientific article published on 3 October 2017

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

scientific article published on 20 April 2016

Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.

scientific article published in January 2013

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function

scientific article published in April 2018

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function

scientific article published on 01 September 2018

Shack-Hartmann centroid detection using the spiral phase transform.

scientific article

Shack-Hartmann spot dislocation map determination using an optical flow method

scientific article published in January 2014

Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins

scientific article

Space-qualified liquid-crystal variable retarders for wide-field-of-view coronagraphs

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

scientific article published on 01 January 2019

The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

scientific article published on 17 January 2020

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data

scientific article

Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins

scientific article published on 16 September 2019

Two-step demodulation based on the Gram-Schmidt orthonormalization method

scientific article published on 01 February 2012

Two-step interferometry by a regularized optical flow algorithm.

scientific article published in September 2011

Two-step self-tuning phase-shifting interferometry

scientific article published on 01 January 2011

Windowed phase unwrapping using a first-order dynamic system following iso-phase contours

scientific article published on 01 November 2012

XTEND: Extending the depth of field in cryo soft X-ray tomography

scientific article published on 04 April 2017

Xmipp 3.0: an improved software suite for image processing in electron microscopy

scientific article

List of works by Javier Vargas

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.

A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

A new algorithm for high-resolution reconstruction of single particles by electron microscopy

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs ⬇️

A review of resolution measures and related aspects in 3D Electron Microscopy

A robust approach to ab initio cryo-electron microscopy initial volume determination

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.

Alignment of direct detection device micrographs using a robust Optical Flow approach.

Analysis of the principal component algorithm in phase-shifting interferometry.

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ

Automatic local resolution-based sharpening of cryo-EM maps

Blind estimation of DED camera gain in Electron Microscopy

CESPED: A benchmark for supervised particle pose estimation in cryo-EM

CTF Challenge: Result summary.

Calibration of a Shack-Hartmann wavefront sensor as an orthographic camera

Circular common-path point diffraction interferometer

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.

Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps

Deflectometric method for the measurement of user power for ophthalmic lenses

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions

Direct demodulation of closed-fringe interferograms based on active contours

Efficient initial volume determination from electron microscopy images of single particles

Fast and automatic identification of particle tilt pairs based on Delaunay triangulation.

Fast two-dimensional simultaneous phase unwrapping and low-pass filtering.

Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope

Imaging polarimeters based on liquid crystal variable retarders: an emergent technology for space instrumentation

Local analysis of strains and rotations for macromolecular electron microscopy maps

Local computational methods to improve the interpretability and analysis of cryo-EM maps

Local fringe density determination by adaptive filtering

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps

Multiplicative phase-shifting interferometry using optical flow.

Multiresolution approach based on projection matrices

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy ⬇️

Optical inspection of liquid crystal variable retarder inhomogeneities

Particle alignment reliability in single particle electron cryomicroscopy: a general approach

Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques ⬇️

Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap.

Phase-shifting interferometry based on induced vibrations

Phase-shifting interferometry based on principal component analysis.

Precise phase retrieval under harsh conditions by constructing new connected interferograms

Principal component analysis-based quantitative differential interference contrast microscopy

Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis.

Regularized least squares phase sampling interferometry ⬇️

Role of the filter phase in phase sampling interferometry.

Scipion web tools: Easy to use cryo-EM image processing over the web.

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function

Shack-Hartmann centroid detection using the spiral phase transform.

Shack-Hartmann spot dislocation map determination using an optical flow method

Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins

Space-qualified liquid-crystal variable retarders for wide-field-of-view coronagraphs

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data

Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins

Two-step demodulation based on the Gram-Schmidt orthonormalization method

Two-step interferometry by a regularized optical flow algorithm.

Two-step self-tuning phase-shifting interferometry

Windowed phase unwrapping using a first-order dynamic system following iso-phase contours

XTEND: Extending the depth of field in cryo soft X-ray tomography

Xmipp 3.0: an improved software suite for image processing in electron microscopy