Person: Vargas Balbuena, Javier
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First Name
Javier
Last Name
Vargas Balbuena
Affiliation
Universidad Complutense de Madrid
Faculty / Institute
Ciencias Físicas
Department
Óptica
Area
Optica
Identifiers
4 results
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Now showing 1 - 4 of 4
Item Two-step interferometry by a regularized optical flow algorithm(Optics Letters, 2011) Quiroga Mellado, Juan Antonio; Vargas Balbuena, Javier; Sánchez Sorzano, Carlos Óscar; Estrada, Julio César; Carazo García, José MaríaA two-step phase-shifting method, that can demodulate open-and closed-fringed patterns without local sign ambiguity is presented. The proposed method only requires a constant phase-shift between the two interferograms. This phase-shift does not need to be known and can take any value inside the range (0, 2 π), excluding the singular case where it corresponds to π. The proposed method is based on determining first the fringe direction map by a regularized optical flow algorithm. After that, we apply the spiral phase transform (SPT) to one of the fringe patterns and we determine its quadrature signal using the previously determined direction. The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results. A complete MATLAB software package is provided in [http://goo.gl/Snnz7].Item Fringe pattern denoising by image dimensionality reduction(Optics and Lassers in Engineering, 2013) Quiroga Mellado, Juan Antonio; Vargas Balbuena, Javier; Estrada, Julio César; Carazo García, José María; Sánchez Sorzano, Carlos ÓscarNoise is a key problem in fringe pattern processing, especially in single frame demodulation of interferograms. In this work, we propose to filter the pattern noise using a straightforward, fast and easy to implement denoising method, which is based on a dimensionality reduction approach, in the sense of image rank reduction. The proposed technique has been applied to simulated and experimental ESPI interferograms obtaining satisfactory results.Item DeepEMhancer: a deep learning solution for cryo-EM volume post-processing(Communications biology, 2021) Sánchez García, Rubén; Gómez Blanco, Josue; Cuervo, Ana; Carazo García, José María; Sorzano Sánchez, Óscar; Vargas Balbuena, JavierCryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on global B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to reduce noise levels and obtain more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase. Sanchez-Garcia et al. present DeepEMhancer, a deep learning-based method that can automatically perform post-processing of raw cryo-electron microscopy density maps. The authors report that DeepEMhancer globally improves local quality of density maps, and may represent a useful tool for novel structures where PDB models are not readily available.Item Two-step demodulation based on the Gram-Schmidt orthonormalization method(Optics Letters, 2012) Quiroga Mellado, Juan Antonio; Vargas Balbuena, Javier; Sánchez Sorzano, Carlos Óscar; Estrada, Julio C.; Carazo García, José MaríaThis Letter presents an efficient, fast, and straightforward two-step demodulating method based on a Gram-Schmidt (GS) orthonormalization approach. The phase-shift value has not to be known and can take any value inside the range (0, 2 π) excluding the singular case, where it corresponds to π. The proposed method is based on determining an orthonormalized interferogram basis from the two supplied interferograms using the GS method. We have applied the proposed method to simulated and experimental interferograms, obtaining satisfactory results. A complete MATLAB software package is provided at http://goo.gl/IZKF3.