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©2011 Optical Society of America, The presence of uncontrolled mechanical vibrations is typically the main precision-limiting factor of a phase-shifting interferometer. We present a method that instead of trying to insolate vibrations; it takes advantage of their presence to produce the different phase-steps. The method is based on spatial and time domain processing techniques to compute first the different unknown phase-steps and then reconstruct the phase from these tilt-shifted interferograms. In order to compensate the camera movement, it is needed to perform an affine registration process between the different interferograms. Simulated and experimental results demonstrate the effectiveness of the proposed technique without the use of any phase-shifter device, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2012 The Optical Society of America, Fringe patterns with a multiplicative phase shift among them appear in experimental techniques as photoelasticity and RGB shadow moiré, among others. These patterns cannot be processed using standard phase-shifting demodulation techniques. In this work, we propose to use a multiframe regularized optical flow algorithm to obtain the interesting modulating phase. The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2010 Optical Society of America., We demonstrate a method to calibrate a Shack-Hartmann sensor as an orthographic camera. This calibration method permits us to obtain the distance, the rotation matrix between the microlens array and CCD imaging planes, and the projection matrix, which models the projection of the incoming rays to the CCD imaging plane. The proposed calibration method introduces a very compact matrix notation and allows wavefront reconstruction without an explicit centroid search between the reference and distorted spot diagrams. We show a set of simulations in code V that prove the effectiveness of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© The 2011 Optical Society of America. This work was partially supported by the Spanish Ministry of Science and Technology under grant DPI2009-09023., In phase sampling interferometry, existing temporal analysis methods are sensitive to border effects and cannot deal with missing data. In this work we propose a quadrature filter that allows a reliable dynamic phase measurement for every sample, even in the cases involving few samples or missing data. The method is based on the use of a regularized least squares cost function that enforces the quadrature character of the filter. A comparison with existing techniques shows the effectiveness of the proposed method., Spanish Ministry of Science and Technology, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2011 Optical Society of America, An asynchronous phase-shifting method based on principal component analysis (PCA) is presented. No restrictions about the background, modulation, and phase shifts are necessary. The presented method is very fast and needs very low computational requirements, so it can be used with very large images and/or very large image sets. The method is based on obtaining two quadrature signals by the PCA algorithm. We have applied the proposed method to simulated and experimental interferograms, obtaining satisfactory results., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2010 Optical Society of America. We thank the Ministerio de Ciencia e Innovación of Spain for the financial support of this work given by project “Contribución española al instrumento MIRI del JWST: desarrollo del simulador criogénico del telescopio” with reference ESP2004-01049., In the optical quality measuring process of an optical system, including diamond-turning components, the use of a laser light source can produce an undesirable speckle effect in a Shack-Hartmann (SH) CCD sensor. This speckle noise can deteriorate the precision and accuracy of the wavefront sensor measurement. Here we present a SH centroid detection method founded on computer-based techniques and capable of measurement in the presence of strong speckle noise. The method extends the dynamic range imaging capabilities of the SH sensor through the use of a set of different CCD integration times. The resultant extended range spot map is normalized to accurately obtain the spot centroids. The proposed method has been applied to measure the optical quality of the main optical system (MOS) of the mid-infrared instrument telescope smulator. The wavefront at the exit of this optical system is affected by speckle noise when it is illuminated by a laser source and by air turbulence because it has a long back focal length (3017 mm). Using the proposed technique, the MOS wavefront error was measured and satisfactory results were obtained., Ministerio de Ciencia e Innovación of Spain, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2011 Optical Society of America, Any linear phase sampling algorithm can be described as a linear filter characterized by its frequency response. In traditional phase sampling interferometry the phase of the frequency response has been ignored because the impulse responses can be made real selecting the correct sample offset. However least squares methods and recursive filters can have a complex frequency response. In this paper, we derive the quadrature equations for a general phase sampling algorithm and describe the role of the filter phase., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2011 Optical Society of America, A two-step self-tuning phase-shifting method is presented. The phase-step between the two interferograms is not known when the experiment is performed. Our demodulating method finds, in a robust way, this unknown phase-step. Once the phase-step is estimated we proceed to phase demodulate the interferograms. Moreover our method only requires the fringe patterns to have a constant unknown phase-shift between them. As a consequence, this technique can be used to demodulate open and closed-fringed patterns without phase-sign ambiguity. The method may be regarded as a self-tuning quadrature filter, which determines the phase-shift between the two fringe patterns and finally estimates the demodulated phase map. The proposed technique has been tested with simulated and real interferograms obtaining satisfactory results., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2011 Elsevier Science B. V., We demonstrate a method to easily and quickly extend the dynamic range imaging capabilities of the camera in a typical interferometric approach. The camera dynamic range is usually low and limited to 256 gray levels. Also, it is well known that one may have over or under-exposed regions in the interferogram (due to non-uniform illumination) which makes these image regions not reliable. In our proposed method it is not necessary to obtain or use the non-linear camera response curve in order to extend the camera dynamic range. We obtain a sequence of differently exposed interferograms, typically five or six; after that, we compute the corresponding normalized fringe patterns and modulation maps using a typical normalization method. These normalized patterns are combined through a temporal weighted average using as weights the corresponding modulation maps. We show a set of experimental results that prove the effectiveness of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

©2004 IOP Publishing Ltd. One of the authors (G P) acknowledges support from project BFM2001-1356 of the Ministerio de Ciencia y Tecnología of Spain., We provide a simple theoretical study of beams non-uniformly polarized across their transverse sections which can be introduced in undergraduate optics courses. In order to generate such beams we propose to use a slightly convergent (or divergent) linearly and uniformly polarized beam impinging on an anisotropic uniaxial material with the beam propagation direction along the optic axis. Analytical expressions for the Jones vector, Stokes parameters, ellipticity and azimuth at each point of the transverse section, perpendicular to the propagation direction, are obtained at the output of this system. By means of these parameters a detailed description of the state of polarization across the transverse profile is given., Ministerio de Ciencia y Tecnología of Spain, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2010 Optical Society of America, We demonstrate a method to directly demodulate closed-fringe interferograms using a kind of active contour called a snake. This method can be used to demodulate a single closed-fringe interferogram when its background illumination and/or contrast terms have a spatial frequency similar to the spatial frequency of the equivalent normalized interferogram. Among other cases, this problematic usually appears in interferometry when spurious reflection appears in the interferogram. In these situations, typical Fourier-based methods are of no help. We show a set of simulations and experimental results that prove the effectiveness of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2012 Optical Society of America., In this work, we show a windowed phase-unwrapping technique that uses a first-order dynamic system and scans the phase following its iso-phase contours. In previous works, we have shown that low-pass first-order dynamic systems are very robust and useful in phase-unwrapping problems. However, it is well known that all phase-unwrapping methods have a minimum signal-to-noise ratio that they tolerate. This paper shows that scanning the phase within local windows and using a path following strategy, the first-order unwrapping method increases its tolerance to noise. In this way, using the improved approach, we can unwrap phase maps where the basic dynamic phase-unwrapping system fails. Tests and results are given, as well as the source code in order to show the performance of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2013 Elsevier Ltd. The authors would like to acknowledge economical support from the Spanish Ministry of Economy and Competitiveness through Grants ACI2009-1022, ACI2010-108 and BIO2010-16566, the Spanish Ministry of Science and Technology under Grant DPI2009-09023, and postdoctoral ‘‘Juan de la Cierva’’ grant with reference JCI-2011–10185. C.O.S. Sorzano is recipient of a Ramón y Cajal fellowship., Noise 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., Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science and Technology, Ramón y Cajal Fellowship, Juan de la Cierva Grants, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2010 Optical Society of America, We demonstrate a method to easily and quickly determine the local fringe density map of a fringe pattern. The method is based on an isotropic adaptive bandpass filter that is tuned at different frequencies. The modulation map after applying a specific bandpass frequencies filter presents a maximum response in the regions where the bandpass filter and fringe frequencies coincide. We show a set of simulations and experimental results that prove the effectiveness of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

This paper was published in Applied Optics and is made available as an electronic reprint with the permission of OSA. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. We thank the European Space Agency for economic support of this work given by the “Validation of liquid crystal variable retarders for solar orbiter polarization modulation package” project, reference number 22334/09/NL/SFe., Liquid crystal variable retarders (LCVRs) are starting to be widely used in optical systems because of their capacity to provide a controlled variable optical retardance between two orthogonal components of incident polarized light or to introduce a known phase shifting (PS) between coherent waves, both by means of an applied voltage. Typically, the retardance or PS introduced by an LCVR is not homogeneous across the aperture. On the one hand, the LCVR glass substrates present a global bend that causes an overall variation of the retardance or PS. On the other hand, in the manufacturing process of an LCVR, there sometimes appears a set of micro-air bubbles that causes local retardance or PS inhomogeneities. In this work, we present an interferometric technique based on a Mach-Zehnder interferometer that is insensitive to vibrations and capable of inspecting and characterizing the LCVR's retardance or PS inhomogeneities. The feasibility of the proposed method is demonstrated in the experimental results, where the LCVR retardance is measured with an error of about 0:2 rad. The thickness of possible micro-air bubbles is obtained with a resolution of about 50 nm., European Space Agency, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2011 The Optical Society Of America, We recently presented a new asynchronous demodulation method for phase-sampling interferometry. The method is based in the principal component analysis (PCA) technique. In the former work, the PCA method was derived heuristically. In this work, we present an in-depth analysis of the PCA demodulation method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2009 Optical Society of America. We thank the Ministerio de Ciencia y Tecnología of Spain for the financial support of this work given by project DPI2005-03891 and the Spanish Ministry of Education for support under a FPU grant., Active triangulation measurement systems with a rigid geometric configuration are inappropriate tor scanning large objects with low measuring tolerances. The reason is that the ratio between the depth recovery error and the lateral extension is a constant that depends on the geometric setup. As a consequence, measuring large areas with low depth recovery error requires the use of multiresolution techniques. We propose a multiresolution technique based on a camera-projector system previously calibrated. The method consists of changing the camera or projector's parameters in order to increase the system depth sensitivity A subpixel retroprojection error in the self-calibration process and a decrease of approximately one order of magnitude in the depth recovery error can be achieved using the proposed method., Ministerio de Ciencia y Tecnología of Spain, Spanish Ministry of Education, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2010 Optical Society of America. This work has been financially supported by the Spanish Ministry of Science and Technology through the project number DPI2009-09023. It has also benefited from the framework of the Spanish Optometry Network., This paper presents a deflectometric technique to measure the power of an ophthalmic lens as perceived by the user. It is based on a calibrated camera acting as a pinhole in order to measure ray deflection along the same path as the visual axis when the lens is held in front of the eye. We have analyzed numerically the accuracy of our technique, and it has been compared experimentally with a commercial "lens mapper" and with the real user power calculated from the measured topography of the lens surfaces to state the reliability and accuracy of the presented technique., Spanish Ministry of Science and Technology, Spanish Optometry Network, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

En este proyecto de innovación docente se han desarrollado una serie de videos cortos para fijar visualmente conceptos clave sobre instrumentación óptica. Estos videos están enfocados en la mejora de la compresión y análisis de los estudiantes de la asignatura Dispositivos de Instrumentación Óptica de cuarto curso del Grado en Físicas. Es decir, nuestro objetivo es proporcionar a los estudiantes con experiencias virtuales de laboratorio que les permitan entender de forma sencilla y rápida conceptos esenciales de la asignatura. También estos videos serán utilizados en el aula por los profesores como material docente de apoyo.

© The Royal Society of Chemistry 2022. We are thankful to Philip Baldwin, Dmitry Lyumkis, and Gabriel Lander for making their validation methods available (4.h and A.c). Javier Vargas and Jordi Burguet would like to thank the Spanish Ministry of Science and Innovation for financial support through the call 2019 Proyectos de I+D+i - RTI Tipo A (PID2019-108850RA-I00) and Arrate Muñoz Barrutia, PID2019-109820RB-I00, MCIN/AEI/10.13039/501100011033/, cofinanced by European Regional Development Fund (ERDF), "A way of making Europe.". The authors acknowledge the economic support from MICIN of the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in the area of Structural Biology, Grant PID2019-104757RB-I00 funded by MCIN/AEI/10.13039/501100011033/ and "ERDF A way of making Europe", by the European Union and Grant PRE2020 - 093527 funded by MCIN/AEI/ 10.13039/501100011033 and by "ESF Investing in your future". We also acknowledge support from "Comunidad Autonoma de Madrid" through Grant: S2017/BMD-3817, Instituto de Salud Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, "A way to make Europe"), and European Union (EU) and Horizon 2020 through grants: EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), HighResCells (ERC - 2018 - SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018 - Proposal: 857203), EOSC - Synergy (EINFRA-EOSC-5, Proposal: 857647), iNEXT-Discovery (Proposal: 871037), EnLaCES (H2020-MSCA-IF-2020, Proposal: 101024130)., The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded., Unión Europea. Horizonte 2020, Ministerio de Ciencia e Innovación (MICINN)/FEDER, Ministerio de Ciencia e Innovación (MICINN), Comunidad de Madrid, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© The Author(s) 2022. Artículo escrito por 20 autores. We thank Massimo Palmarini for CPT3 cells, Didier Trono for a generous gift of pMD2.G, Ron Vale for His10-PS-SNAPf vector, Goedele Maertens for sharing the luciferase assay protocol and critical reading of the manuscript, Massimo Pizzato for advice on RT assays and nucleofection, P. Walker and A. Purkiss for computer and software support, and M. Singer for help with tissue culture. This work was funded by US National Institutes of Health grants P50 AI150481 (P.C. and A.N.E.), R01 AI070042 (A.N.E.), and U54 AI150472 (D.L.); US National Science Foundation CAREER MCB-2048095, the Margaret T. Morris Foundation, and the Hearst Foundations (D.L.); the Spanish Ministry of Science and Innovation PID2019-108850RA-I00 (JV); and the Francis Crick Institute (P.C., H.Y., and I.A.T.), which receives its core funding from Cancer Research UK (FC001061, FC001221, FC001178), the UK Medical Research Council (FC001061, FC001221, FC001178), and the Wellcome Trust (FC001061, FC001221, and FC001178)., The authors determined high-resolution cryo-EM structures of the lentiviral intasome - the nucleoprotein complex that inserts viral DNA into a host chromosome - and show that the architecture comprising 16 integrase subunits is critical for its function. A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits(1). Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 angstrom resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the alpha-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes., Ministerio de Ciencia e Innovación (MICINN), Cancer Research UK/Medical Research Council (MRC)/Wellcome Trust, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

CRUE-CSIC (Acuerdos Transformativos 2022) ©2022 The Author(s). Published by Elsevier B.V. Authors want to acknowledge economical support from the Spanish Ministry of Science and Innovation through the call 2019 Proyectos de I + D + i - RTI Tipo A (PID2019-108850RA-I00)., Background and objective: Cryo-electron microscopy using single particle analysis is a powerful technique for obtaining 3D reconstructions of macromolecules in near native conditions. One of its major advances is its capacity to reveal conformations of dynamic molecular complexes. Most popular and successful current approaches to analyzing heterogeneous complexes are founded on Bayesian inference. However, these 3D classification methods require the tuning of specific parameters by the user and the use of complicated 3D re-classification procedures for samples affected by extensive heterogeneity. Thus, the success of these approaches highly depends on the user experience. We introduce a robust approach to identify many different conformations presented in a cryo-EM dataset based on Bayesian inference through Relion classification methods that does not require tuning of parameters and reclassification strategies. Methods: The algorithm allows both 2D and 3D classification and is based on a hierarchical clustering approach that runs automatically without requiring typical inputs, such as the number of conformations present in the dataset or the required classification iterations. This approach is applied to robustly determine the energy landscapes of macromolecules. Results: We tested the performance of the methods proposed here using four different datasets, comprising structurally homogeneous and highly heterogeneous cases. In all cases, the approach provided excellent results. The routines are publicly available as part of the CryoMethods plugin included in the Scipion package. Conclusions: Our results show that the proposed method can be used to align and classify homogeneous and heterogeneous datasets without requiring previous alignment information or any prior knowledge about the number of co-existing conformations. The approach can be used for both 2D and 3D autoclassification and only requires an initial volume. In addition, the approach is robust to the "att, Ministerio de Ciencia e Innovacion (MICIIN), Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2022 Optica Publishing Group. Funding. Ministerio de Ciencia e Innovación (PID2019-108850RA-I00)., We present an approach to enhance cryo-electron microscopy (cryo-EM) postprocessed maps based on a multiscale tubular filter. The method determines a tubularness measure locally by the analysis of the eigenvalues of the Hessian matrix. This information is used to enhance elongated local structures and to attenuate blob-like and plate-like structures. The approach, thus, introduces a priori information in the reconstructions to improve their interpretability and analysis at high-resolution. The proposed method has been tested with simulated and real cryo-EM maps including recent reconstructions of the SARS-CoV-2. Our results show that our methods can improve obtained reconstructions., Ministerio de Ciencia e Innovacion (MICINN), Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2022 Optica Publishing Group. Funding. Agencia Estatal de Investigación (PID2019-108850RA-I00)., This work proposes a new algorithm for demodulating fringe patterns using principal component analysis (PCA). The algorithm is based on the incremental implantation of the singular value decomposition (SVD) technique for computing the principal values associated with a set of fringe patterns. Instead of processing an entire set of interferograms, the proposed algorithm proceeds in an incremental way, processing sequentially one (as minimum) interferogram at a given time. The advantages of this procedure are twofold. Firstly, it is not necessary to store the whole set of images in memory, and, secondly, by computing a phase quality parameter, it is possible to determine the minimum number of images necessary to accurately demodulate a given set of interferograms. The proposed algorithm has been tested for synthetic and experimental in ter ferograms showing a good performance. (C) 2022 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement, Ministerio de Ciencia e Innovación (MICINN), Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© The Author(s) 2021. The authors would like to acknowledge economical support from: The Spanish Ministry of Science and Innovation through Grants: Proyectos de I+D+i - RTI Tipo A PID2019-108850RA-I00, SEV 2017-0712, PID2019-104757RB-I00/ AEI/10.13039/501100011033; the “Comunidad Autónoma de Madrid” through Grant S2017/BMD-3817; CSIC: PIE/COVID-19 number 202020E079; European Union (EU) and Horizon 2020 through grants EOSC Life (INFRAEOSC-04-2018, Proposal: 824087) and HighResCells (ERC - 2018- SyG, Proposal: 810057). J.V. acknowledges economical support from the Ramón y Cajal 2018 program (RYC2018-024087-I)., Cryo-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., Unión Europea. H2020, Ministerio de Ciencia e Innovación (MICINN), Comunidad de Madrid, Programa Ramón y Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

Received: 4 Dec 2020 / Revised: 3 Feb 2021 / Accepted: 10 Feb 2021 / Published: 14 May 2021. © 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement. Funding. Ministerio de Ciencia, Innovación y Universidades (PID2019-108850RA-I00, Ramón y Cajal 2018 program (RYC2018-024087-I))., We present an asynchronous phase-shifting demodulation approach based on the principal component analysis demodulation method that is robust to typical problems as turbulence, vibrations, and temporal instabilities of the optical setup. The method brings together a two-step and a phase-shifting asynchronous demodulation method to share their benefits while reducing their intrinsic limitations. Thus, the proposed approach is based on a two-fold process. First, the modulating phase is estimated from a two-step demodulation approach. Second, this information is used to compute weights to each phase-shifted pattern of the interferogram sequence, which are used in a novel weighted principal component demodulation approach. The proposed technique has been tested with simulated and real interferograms affected by turbulence and vibrations providing very satisfactory results in challenging cases., Ministerio de Ciencia, Innovación y Universidades (MICIU), Programa Ramón y Cajal, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2021 Elsevier Ltd. Authors want to acknowledge economical support from the Spanish Ministry of Science and Innovation through the call 2019 Proyectos de I+D+i - RTI Tipo A (PID2019-108850RA-I00). As well, authors acknowledge the support of the Consejo Nacional de Ciencia y Tecnologia (CONACYT) from Mexico. Disclosures. The authors declare no conflicts of interest., In this paper, we present a two steps phase-shifting fringe pattern demodulation method using the VU factorization. Compared with other methods, our proposal is robust to non-constant background illuminations and modulating terms (non-normalized fringes). We use the two given fringe patterns, and from these, we synthetically generate another two images that approach the background illumination in order to obtain a total set of four images. Such set is used in a matrix model that can be factorized using the VU factorization method to determine the modulating phase. Our proposal is able to recover the phase without 1) known phase shift, 2) normalized fringe patterns, and 3) any special non-linear pre-processing. Tests and results with an important representative diversity of interferograms, taken from different experiments, are shown to demonstrate the feasibility of this method., Ministerio de Ciencia e Innovación (MICIIN), Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2021 John Wiley & Sons A/S. The Brittle Bone Disease Consortium (1U54AR068069-0) is part of the National Center for Advancing Translational Sciences (NCATS) at the Rare Diseases Clinical Research Network (RDCRN), and it is funded through a collaboration between the Office of Rare Diseases Research (ORDR), NCATS, the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), the National Institute of Dental and Craniofacial Research (NIDCR), and the Eunice Kennedy Shriver National Institutes of Child Health and Development (NICHD). This article's authors are solely responsible for its content, and this article does not necessarily represent the National Institutes of Health's official views. The Brittle Bone Disease Consortium is also supported by the Osteogenesis Imperfecta Foundation. The authors also acknowledge the contributions of the following BBDC site coordinators: M. Abrahamson (OHSU), S. Alon (UCLA), M. Azamian and A. Turner (BCM), C. Brown (Nemours Alfred I. duPont Hospital), E. Carter and E. Yonko (HSS), A. Caudill (Chicago Shriners), K. Dobose (KKI), M. Durigova (Montreal Shriners Hospital for Children), A. Giles and E. Rajah (CNMC), M. Gross-King (Tampa Shriners), and E. Strudthoff (UNMC)., Objective Osteogenesis imperfecta (OI) is an autosomal dominant genetic disease that mainly affects the COL1A1/A2 genes. Individuals affected by OI types I, III, and IV have been reported to demonstrate characteristic facial manifestations of the disease. This study aimed to quantitatively assess OI patients' morphological characteristics. Materials and Methods This retrospective case-control study involved 306 individuals (145 male and 161 female). It used automatic facial annotation and statistical shape analysis to compare facial photographs of individuals affected by OI types I, III, and IV with a normocephalic control group. Four facial ratios were used to compare facial proportions. Additionally, we proposed a novel approach to facial analysis using 68 landmarks and statistical shape analysis to compare morphological features. A predictive model (PCALog) was trained to detect whether a subject was affected by OI, based on facial landmarks. Results Our findings correlate with previous reports of OI type III patients' facial characteristics being the most severely affected among the three types studied. Our novel approach facilitated an interpretation and comparison of morphological changes. Moreover, we successfully trained our PCALog model to automatically detect OI based on landmark features. Conclusion We found patients' facial manifestations of OI to be more pronounced at the level of the eyes and temples. Our morphological approach facilitates the comparison of various groups and should be considered for future craniofacial analysis studies. Machine learning models can be trained using facial landmarks to detect the presence of conditions that affect facial morphology., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2021 by the authors. Artículo firmado por más de 10 autores. The project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434). The fellowship code is LCF/BQ/DI18/11660021. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 713673. The work was supported by European Regional Development Fund-Project "CERIT Scientific Cloud" (No.CZ.02.1.01/0.0/0.0/16_013/0001802). The authors would like to acknowledge economic support from: The Spanish Ministry of Economy and Competitiveness through Grants PID2019-104757RB-I00 (AEI/FEDER, UE) and SEV 2017-0712, the “Comunidad Autónoma de Madrid” through Grant: S2017/BMD-3817. European Union (EU) and Horizon 2020 through grants: EOSC Life (Proposal: 824087), HighResCells (Proposal: 810057), IM-paCT (Proposal: 857203), EOSC-Synergy (Proposal: 857647) and iNEXT-Discovery (Proposal: 871037). Authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. J.V thanks economical support from the Spanish Ministry of Science and Innovation through the call 2019 Proyectos de I+D+i–RTI Tipo A (PID2019-108850RA-I00). We acknowledge the support of the French National Research Agency—ANR (ANR-11-BSV8-010-04, ANR-19-CE11-0008-01, and ANR-20-CE11-0020-03 to S.J.), the French National Center for Scientific Research and the Spanish National Research Council (CSIC2009FR0015 and PICS 2011 to S.J. and C.O.S.S.), and access to HPC resources of CINES and IDRIS granted by GENCI (2010-2016 project No. 072174, A0100710998, A0070710998, AP010712190, AD011012188 to S.J.)., Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package., Europea. Horizonte 2020, European Regional Development Fund-Project, Ministerio de Economía y Competitividad (MINECO)/FEDER, Ministerio de Ciencia e Innovación (MICINN), French National Research Agency (ANR), Comunidad de Madrid, Consejo Superior de Investigaciones Científicas (CSIC), Centre national de la recherche scientifique (CNRS), GENCI, Fundación La Caixa, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

Los métodos ópticos basados en triangulación activa han experimentado un gran avance en la pasada década y están comenzando a sustituir a los sensores tridimensionales basados en contacto en las diversas aplicaciones industriales de estos dispositivos. Estos métodos ópticos tienen propiedades que los hacen muy interesantes, como su gran velocidad, su capacidad de medida sin contacto y a campo completo y su bajo coste. No obstante, estos métodos presentan limitaciones prácticas cuando se está interesado en medir objetos extensos con gran precisión. En primer lugar los métodos de calibración para estos sistemas con los que se obtiene los resultados más precisos son muy difíciles de utilizar cuando se está interesado en calibrar un volumen de gran tamaño. Por otra parte, los sistemas de medida 3D basados en triangulación activa están caracterizados por tener una relación fija entre el área escaneada y la resolución en profundidad obtenida. Si se desea inspeccionar un área extensa se debe esperar obtener una resolución en profundidad pobre. Para obtener una medida 3D de un área extensa con alta resolución en profundidad es necesario realizar una medida en multiresolución. Finalmente, los métodos de triangulación activa estándares no son aplicables en el caso de que se desee inspeccionar una superficie no-cooperativa con una gran resolución espacial. Las superficies no-cooperativas se caracterizan por presentar una gran variación espacial de la reflectividad, de forma que existen regiones muy brillantes y muy oscuras. En la presenta memoria de tesis se presentan nuevos métodos de medida 3D mediante triangulación activa para resolver los problemas anteriormente mencionados. Por una parte, se introduce un nuevo método de calibración mixto para un sistema de triangulación activa que permite calibrar con gran precisión volúmenes de gran tamaño. Adicionalmente, se presentan dos nuevos métodos para la medida en multiresolución, uno local y otro global y finalmente se presenta

Los métodos ópticos basados en triangulación activa han experimentado un gran avance en la pasada década y están comenzando a sustituir a los sensores tridimensionales basados en contacto en las diversas aplicaciones industriales de estos dispositivos. Estos métodos ópticos tienen propiedades que los hacen muy interesantes, como su gran velocidad, su capacidad de medida sin contacto y a campo completo y su bajo coste. No obstante, estos métodos presentan limitaciones prácticas cuando se está interesado en medir objetos extensos con gran precisión. En primer lugar los métodos de calibración para estos sistemas con los que se obtiene los resultados más precisos son muy difíciles de utilizar cuando se está interesado en calibrar un volumen de gran tamaño. Por otra parte, los sistemas de medida 3D basados en triangulación activa están caracterizados por tener una relación fija entre el área escaneada y la resolución en profundidad obtenida. Si se desea inspeccionar un área extensa se debe esperar obtener una resolución en profundidad pobre. Para obtener una medida 3D de un área extensa con alta resolución en profundidad es necesario realizar una medida en multiresolución. Finalmente, los métodos de triangulación activa estándares no son aplicables en el caso de que se desee inspeccionar una superficie no-cooperativa con una gran resolución espacial. Las superficies no-cooperativas se caracterizan por presentar una gran variación espacial de la reflectividad, de forma que existen regiones muy brillantes y muy oscuras. En la presenta memoria de tesis se presentan nuevos métodos de medida 3D mediante triangulación activa para resolver los problemas anteriormente mencionados. Por una parte, se introduce un nuevo método de calibración mixto para un sistema de triangulación activa que permite calibrar con gran precisión volúmenes de gran tamaño. Adicionalmente, se presentan dos nuevos métodos para la medida en multiresolución, uno local y otro global y finalmente se presenta

© 2008 Society of Photo-Optical Instrumentation Engineers., 3-D triangulation measurement systems with a fixed geometrical configuration have practical limitations that make them inappropriate for a wide variety of applications. The reason is that the ratio between the depth recovery error and the lateral extension is a constant that depends on the geometrical setup. Therefore, with a fixed triangulation setup, there is a tradeoff between field of view and depth resolution. As a consequence, measuring large areas with low depth recovery error necessitates the use of multiresolution techniques. In this work, we propose a multiresolution technique based on a camera-projector system previously calibrated and a second auxiliary camera that can move freely. The method consists of making first a measurement with a large field of view (coarse measurement). Afterwards, the geometrical configuration of the 3-D rig is changed to acquire a small field of view (fine measurement) that is referred to the original reference system and calibration parameters by means of the auxiliary camera. Using this method, a multiresolution reconstruction is possible without any optimization, registration, or recalibration process. Experimental results, which show a decrease of approximately one order of magnitude in the depth recovery error between fine and coarse measures, demonstrate the feasibility of the proposed method., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2008 Society of Photo-Optical Instrumentation Engineers., The industry dealing with microchip inspection requires fast, flexible, repeatable, and stable 3-D measuring systems. The typical devices used for this purpose are coordinate measurement machines (CMMs). These systems have limitations such as high cost, low measurement speed, and small quantity of measured 3-D points. Now optical techniques are beginning to replace the typical touch probes because of their noncontact nature, their full-field measurement capability, their high measurement density, as well as their low cost and high measurement speed. However, typical properties of microchip devices, which include a strongly spatially varying reflectance, make impossible the direct use of the classical optical 3-D measurement techniques. We present a 3-D measurement technique capable of optically measuring these devices using a camera-projector system. The proposed method improves the dynamic range of the imaging system through the use of a set of gray-code (GC) and phase- shift (PS) measures with different CCD integration times. A set of extended-range GC and PS images are obtained and used to acquire a dense 3-D measure of the object. We measure the 3-D shape of an integrated circuit and obtained satisfactory results., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

Reliable inspection of large surfaces with low depth recovery error is needed in a wide variety of industrial applications, for example in external defect inspection in aeronautical surfaces. Active triangulation measurement systems with a rigid geometrical configuration are inappropriate for scanning large objects with low measuring tolerances due to the fixed ratio between the depth recovery error and the lateral extension. Therefore, with a rigid triangulation setup, if we are interested in defect inspection over extended surfaces then we have to assume errors proportional to the field of view that can preclude a precise local defect measurement. This problem can be solved by the use of multiresolution techniques. In this work we demonstrate the application of an active triangulation multiresolution method for defect inspection of large aeronautical panels. The technique is based on a standard camera-projector system used together with a second auxiliary camera that can move freely. The result is a global measurement with a superposed local measurement without any optimization, explicit registration or recalibration process. The presented results show that the depth recovery error of the local measurement permits the local defects measurement together with a wide-area inspection.

© 2007 Society of Photo-Optical Instrumentation Engineers., A novel calibration method for whole field three-dimensional shape measurement by means of fringe projection is presented. Standard calibration techniques, polynomial- and model-based, have practical limitations such as the difficulty of measuring large fields of view, the need to use precise z stages, and bad calibration results due to inaccurate calibration points. The proposed calibration procedure is a mixture of the two main standard techniques, sharing their benefits and avoiding their main problems. In the proposed method, an absolute phase is projected over marked planes placed at unknown positions. The corresponding absolute phase and marks positions are recovered for each plane location. Using Zhang's calibration method, internal camera parameters (also called intrinsic parameters) and the spatial position for each plane are computed. Later on, a polynomial fit of depth with respect to the phase is performed. To obtain the absolute position of an object point, the depth coordinate is obtained by means of the polynomial calibration and its absolute phase. Then the lateral coordinates are computed from the depth, the internal parameters, and the pixel coordinates of the imaged point. Experimental results comparing the proposed method with the standard polynomial- based calibration are shown, demonstrating the feasibility of the proposed technique., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

© 2006 Society of Photo-Optical Instrumentation Engineers., We present a high-speed 3-D spatiotemporal shape measurement technique by means of structured light. Current methods use a constant number of images that do not take into account the available temporal continuity of the measured object. That is, they focus on acquiring and processing as quickly as possible a fixed number of images to solve for the correspondence problem and later obtain the 3-D shape by triangulation. The number of images used imposes the use of some spatial support. The major contribution of our research is a new spatiotemporal scheme that, depending on the object's movement, adaptively uses the maximum number of projected images consistent with the local temporal continuity, therefore solving the correspondence problem with the minimum possible spatial support for each position. This is achieved by the use of a hybrid color pattern composed of an analog sinusoidal periodic code in the red channel and a digital binary spatial code in the blue channel that is cyclically displaced. No subpixel calculation is used and it is possible to implement error correction strategies that make the method fast and reliable, enabling dynamic online 3-D measurement of objects in movement., Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub