Extended object reconstruction in adaptive-optics imaging: the multiresolution approach

We propose the application of multiresolution transforms, such as wavelets (WT) and curvelets (CT), to the reconstruction of images of extended objects that have been acquired with adaptive optics (AO) systems. Such multichannel approaches normally make use of probabilistic tools in order to distinguish significant structures from noise and reconstruction residuals. Furthermore, we aim to check the historical assumption that image-reconstruction algorithms using static PSFs are not suitable for AO imaging. We convolve an image of Saturn taken with the Hubble Space Telescope (HST) with AO PSFs from the 5-m Hale telescope at the Palomar Observatory and add both shot and readout noise. Subsequently, we apply different approaches to the blurred and noisy data in order to recover the original object. The approaches include multi-frame blind deconvolution (with the algorithm IDAC), myopic deconvolution with regularization (with MISTRAL) and wavelets- or curvelets-based static PSF deconvolution (AWMLE and ACMLE algorithms). We used the mean squared error (MSE) and the structural similarity index (SSIM) to compare the results. We discuss the strengths and weaknesses of the two metrics. We found that CT produces better results than WT, as measured in terms of MSE and SSIM. Multichannel deconvolution with a static PSF produces results which are generally better than the results obtained with the myopic/blind approaches (for the images we tested) thus showing that the ability of a method to suppress the noise and to track the underlying iterative process is just as critical as the capability of the myopic/blind approaches to update the PSF.Comment: In revision in Astronomy & Astrophysics. 19 pages, 13 figure

Integración narrativa de códigos visuales en Pathé Frères (1905-1910)

Premio extraordinario de Trabajo Fin de Máster curso 2017/2018. Máster en Cinematografí

Towards Long-term and Archivable Reproducibility

Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term. A set of criteria is introduced to address this problem: Completeness (no execution requirement beyond a minimal Unix-like operating system, no administrator privileges, no network connection, and storage primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free software. As a proof of concept, we introduce "Maneage" (Managing data lineage), enabling cheap archiving, provenance extraction, and peer verification that been tested in several research publications. We show that longevity is a realistic requirement that does not sacrifice immediate or short-term reproducibility. The caveats (with proposed solutions) are then discussed and we conclude with the benefits for the various stakeholders. This paper is itself written with Maneage (project commit eeff5de).Comment: The downloadable source (on arXiv) includes the full/automatic reproduction info (scripts, config files and input data links). Supplementary datasets and source also available on Zenodo.3872248: https://doi.org/10.5281/zenodo.4291207 . v2: Referee points addressed, two appendices adde

Galaxy And Mass Assembly (GAMA): extended intragroup light in a group at <i>z</i> = 0.2 from deep Hyper Suprime-Cam images

We present a pilot study to assess the potential of Hyper Suprime-Cam Public Data Release 2 (HSC-PDR2) images for the analysis of extended faint structures within groups of galaxies. We examine the intragroup light (IGL) of the group 400138 (Mdyn = 1.3 ± 0.5 × 1013 M⊙, z ∼ 0.2) from the Galaxy And Mass Assembly (GAMA) survey using Hyper Suprime-Cam Subaru Strategic Program Public Data Release 2 (HSC-SSP PDR2) images in g, r, and i bands. We present the most extended IGL measurement to date, reaching down to μlimg=30.76 mag arcsec−2 (3σ; 10 × 10 arcsec2) at a semimajor axis of 275 kpc. The IGL shows mean colour values of g − i = 0.92, g − r = 0.60, and r − i = 0.32 (±0.01). The IGL stellar populations are younger (2–2.5 Gyr) and less metal rich ([Fe/H] ∼ −0.4) than those of the host group galaxies. We find a range of IGL fractions as a function of total group luminosity of ∼2−36 per cent depending on the definition of IGL, with larger fractions the bluer the observation wavelength. The early-type to late-type galaxy ratio suggests that 400138 is a more evolved group, dominated by early-type galaxies, and the IGL fraction agrees with that of other similarly evolved groups. These results are consistent with tidal stripping of the outer parts of Milky Way-like galaxies as the main driver of the IGL build-up. This is supported by the detection of substructure in the IGL towards the galaxy member 1660615 suggesting a recent interaction (<1 Gyr ago) of that galaxy with the core of the group

Galaxy And Mass Assembly (GAMA): extended intragroup light in a group at z = 0.2 from deep Hyper Suprime-Cam images

We present a pilot study to assess the potential of Hyper Suprime-Cam Public Data Release 2 (HSC-PDR2) images for the analysis of extended faint structures within groups of galaxies. We examine the intragroup light (IGL) of the group 400138 (Mdyn = 1.3 ± 0.5 × 1013 M⊙, z ∼ 0.2) from the Galaxy And Mass Assembly (GAMA) survey using Hyper Suprime-Cam Subaru Strategic Program Public Data Release 2 (HSC-SSP PDR2) images in g, r, and i bands. We present the most extended IGL measurement to date, reaching down to μglim=30.76 role= presentation style= box-sizing: border-box; margin: 0px; padding: 0px; border: 0px; font-variant: inherit; font-stretch: inherit; line-height: normal; font-family: inherit; vertical-align: baseline; display: inline; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; position: relative; \u3eμlimg=30.76μglim=30.76 mag arcsec−2 (3σ; 10 × 10 arcsec2) at a semimajor axis of 275 kpc. The IGL shows mean colour values of g − i = 0.92, g − r = 0.60, and r − i = 0.32 (±0.01). The IGL stellar populations are younger (2–2.5 Gyr) and less metal rich ([Fe/H] ∼ −0.4) than those of the host group galaxies. We find a range of IGL fractions as a function of total group luminosity of ∼2−36 per cent role= presentation style= box-sizing: border-box; margin: 0px; padding: 0px; border: 0px; font-variant: inherit; font-stretch: inherit; line-height: normal; font-family: inherit; vertical-align: baseline; display: inline; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; position: relative; \u3e∼2−36 per cent∼2−36 per cent depending on the definition of IGL, with larger fractions the bluer the observation wavelength. The early-type to late-type galaxy ratio suggests that 400138 is a more evolved group, dominated by early-type galaxies, and the IGL fraction agrees with that of other similarly evolved groups. These results are consistent with tidal stripping of the outer parts of Milky Way-like galaxies as the main driver of the IGL build-up. This is supported by the detection of substructure in the IGL towards the galaxy member 1660615 suggesting a recent interaction (\u3c1 Gyr ago) of that galaxy with the core of the group

Study of Adaptive Optics Images by means of Multiscalar Transforms

[eng] Adaptive optics (AO) systems are used to increase the spatial resolution achieved by ground-based telescopes, which are limited by the atmospheric motion of air layers above them. Therefore, the real cut-off frequency is extended closer to the theoretical diffraction limit of the telescope thus allowing more high-frequency information from the object to be present in the image. Nevertheless, although the goal of image reconstruction and deconvolution algorithms is basically the same (i.e., to recover a “real” diffracted limit image, free of noise, from the object), and since the correction of AO is not complete (i.e., the effective cut-off frequency achieved by AO is still below the theoretical diffraction limit), the simultaneous use of such deconvolution algorithms over dataset acquired with AO is possible and desirable to further enhance their contrast. On the other hand, multiresolution tools like the wavelet transform (WT) have been historically introduced into multiple deconvolution schemes improving their performance with respect to their non-wavelet counterparts. The ability of such transforms to separate image components depending on their frequency content results in solutions that are generally closer to the real object. On the other hand, AO community generally states that, due to the high variability of AO PSFs is necessary to update the PSF estimate during the reconstruction process. Hence, the use of blind and myopic deconvolution algorithms should be unavoidable and yields to better results than those obtained by the static-PSFs codes. Therefore, being the aforementioned paragraphs the current state-of-art of AO imaging, this thesis yields the following topics/goals: 1. The static-PSF algorithm AMWLE has been applied over binary systems simulated for the 3-m Shane telescope to evaluate the photometric accuracy of the reconstruction. Its performance is compared with the PSF-fitting algorithm StarFinder, commonly used by the AO community, as well as other algorithms like FITSTAR, PDF deconvolution and IDAC. Results shown that AWMLE is able to produce better results than StarFinder and FITSTAR, and very similar results with respect to the rest of codes, especially for high Strehl ratios (SR) and matched PSFs. 2. A new deconvolution algorithm called ACMLE, based on the curvelet transform (CT) and a maximum likelihood estimator (MLE), has been designed for the reconstruction of extended and/or elongated objects. ACMLE has been tested together with AMWLE and blind/myopic codes such as MISTRAL and IDAC over Saturn and galaxy simulated images for the 5-m. Hale telescope. It is shown that the performance in the presence of noise of the multiresolution static-PSF algorithms is better than myopic and blind algorithms, thus showing that the control of noise is as important as the update of the PSF estimate during the reconstruction process. 3. A unidimensional WT has been applied in the spectral deconvolution of integral field spectroscopy (IFS) datacubes for direct imaging of exoplanets with EPICS instrument, which will be installed at the forthcoming 39-m E-ELT telescope. When this approach is compared with the classical non-wavelet one, an improvement of 1 mag from angle separations equal to 73 mas is devised. Furthermore, detection of close-in planets, between 43 and 58 mas also benefit of the application of wavelets. The use of WT allows the APLC chronograph to obtain similar results with respect to the apodizer-only solution, especially with increasing Talbot length, thus showing that WT classify planet frequency components and chromatic aberrations in different scales. Preliminary results for HARMONI spectrograph are also shown. This thesis opens several lines of research that will be addressed in future: - The world of multiresolution transforms is extremely huge and has produced dozens of new mathematical tools. Among many other, it is worthwhile to mention the shearlet transform, which is an extension/improvement of CT, and the waveatom tool, which is intended to classify textures in the image. They should be studied and compared to establish their best performance and their best field of application over AO images. - Blind and myopic algorithms have proved their ability for large mismatches between the “real” PSF that has created the image and the PSF that is used as a first estimate in the reconstruction process. However, their performance in the presence of noise is highly affected. Hence, it is convenient to investigate if it is possible to introduce (and how to do it) multiresolution transforms into these algorithms to improve their behavior. - For the study of IFS datacubes, other father scaling functions with different shapes could be proposed, in particular, it can be considered a “dynamic” scaling function with the ability to modulate its shape according to the low frequency signal to be removed from the spaxel. This could potentially improved the final photometry of the detected faint source. Besides, the design of a dictionary of wavelets, which increase the decomposing resolution across the spaxel, instead of a single dyadic decomposition, can improve the photometric accuracy of detected planets as well as their spectral characterizations, taking full advantage of the information contained in the IFS datacubes

Anisoplanatic imaging through turbulence using principal component analysis

The performance of optical systems is highly degraded by atmospheric turbulence when observing both vertically (e.g., astronomy, remote sensing) or horizontally (e.g. long-range surveillance). This problem can be partially alleviated using adaptive optics (AO) but only for small fields of view (FOV), described by the isoplanatic angle, for which the turbulence-induced aberrations can be considered constant. Additionally, this problem can also be tackled using post-processing techniques such as deconvolution algorithms which take into account the variability of the point spread function (PSF) in anisoplanatic conditions. Variability of the PSF across the field of view in anisoplanatic imagery can be described using principal component analysis. Then, a certain number of variable PSFs can be used to create new basis functions, called principal components (PC), which can be considered constant across the FOV and, therefore, potentially be used to perform global deconvolution. Our approach is tested on simulated, single-conjugate AO data

Marginal blind deconvolution of adaptive-optics corrected images of satellites

Conventional blind deconvolution estimates jointly the PSF and the object being imaged, and therefore it is subject to degeneracies. Instead, we use a marginalized approach which has good statistical properties. We show results on AO-corrected observations of satellites. The method will be extended to anisoplanatic imaging

Méthode de reconstruction bayésienne conjointement super-résolue et sectionnée optiquement pour la microscopie par illumination structurée

International audienceStructured Illumination Microscopy (SIM) is an imaging technique for achieving both super-resolution (SR) and optical sectioning (OS) in wide-field microscopy. It consists in illuminating the sample with periodic patterns at different orientations and positions. The resulting images are then processed to reconstruct the observed object with SR and/or OS. In this work, we present BOSSA-SIM, a general-purpose SIM reconstruction method, applicable to moving objects such as encountered in in vivo retinal imaging, that enables SR and OS jointly in a fully unsupervised Bayesian framework. By modeling a 2-layer object composed of an in-focus layer and a defocused layer, we show that BOSSA-SIM is able to jointly reconstruct them so as to get a super-resolved and optically sectioned in-focus layer. The achieved performance, assessed quantitatively by simulations for several noise levels, compares favorably with a state-of-the-art method. Finally, we validate our method on open-access experimental microscopy data.La microscopie par illumination structurée (SIM en anglais) est une technique d’imagerie plein champ permettant d’obtenir super-résolution (SR) et sectionnement optique (SO). Elle consiste à illuminer l’échantillon avec des motifs périodiques à différentes orientations et positions. Les images résultantes sont ensuite traitées numériquement pour reconstruire l’objet observé avec SR et/ou SO. Dans cet article, nous présentons BOSSA-SIM, une méthode de reconstruction SIM adaptée aux objets mobiles tels que ceux rencontrés en imagerie rétinienne in vivo, qui permet de réaliser conjointement SR et SO dans un cadre bayésien non supervisé. En modélisant un objet à deux couches composé d’une couche focalisée et d‘une couche défocalisée, nous montrons que BOSSA-SIM est capable de les reconstruire conjointement de manière à obtenir une couche focalisée super-résolue et sectionnée optiquement. Les performances atteintes, évaluées quantitativement par simulations pour différents niveaux de bruit, se comparent favorablement avec une méthode SIM à l’état de l’art. Finalement, nous validons notre méthode sur des données expérimentales de microscopie en libre accès

Vers une reconstruction super-résolue et sectionnée optiquement pour l’imagerie rétinienne par illumination structurée

International audienceStructured Illumination Microscopy (SIM) is an imaging technique for achieving both super-resolution (SR) and optical sectioning (OS) in wide-field microscopy using dedicated reconstruction algorithms. In this communication we focus on the very promising application of SIM to in vivo retinal imaging, which could benefit the study of the retinal 3D structure and function in the living eye. The SIM approaches commonly used in microscopy require a static object and are thus not suitable for in vivo retinal imaging due to uncontrolled eye movements. The few approaches developped with retinal imaging in mind only achieve SR.We propose a reconstruction method approach, tailored for retinal imaging, which achieves SR and OS jointly. It is based on a multi-layer model of the image formation process which takes into account the object shifts. The mean idea of our method is to reconstruct a 2-layer object composed of the super-resolved optical section of the object and a layer into which the object’s defocused contribution are rejected. Our proposed approach is validated by simulations and on experimental microscopy data.La microscopie par illumination structurée (SIM en anglais) est une technique d’imagerie utilisée en microscopie plein champ qui permet d’obtenir super-résolution (SR) et sectionnement optique (SO) grâce à des algorithmes de reconstruction dédiés. Dans cette communication, nous nous intéressons à l’application de la SIM à l’imagerie rétinienne in-vivo qui offre de nouvelles possibilités pour l’étude des structures et fonctions rétiniennes. Les méthodes de reconstruction SIM couramment utilisées en microscopie supposent un objet statique et donc ne conviennent pas au cas de l’imagerie rétinienne in-vivo à cause des mouvements oculaires. Les quelques approches proposées pour l’imagerie rétinienne ne permettent de réaliser que de la SR.Nous proposons une méthode de reconstruction adaptée à l’imagerie rétinienne qui réalise SR et SO conjointement. Elle repose sur un modèle physique multi-couches de la formation d’images, qui prend en compte les mouvements de l’objet. L’idée originale de notre approche est de reconstruire un objet bi-couche comprenant la section optique super-résolue de l’objet et une tranche où sont rejetées toutes les contributions défocalisées de l’objet. Nous validons la méthode proposée par simulations et sur des données expérimentales de microscopie