Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to complex and unstructured geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for unstructured geometries using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L$_1$ regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.Comment: 24 pages, 11 figures. Reviced version includes revised figures and improved clarit

Characterization of a Strain of Fukuyoa paulensis (Dinophyceae) from the Western Mediterranean Sea

17 páginas, 8 figuras, 4 tablasA single cell of the dinoflagellate genus Fukuyoa was isolated from the island of Formentera (Balearic Islands, west Mediterranean Sea), cultured, and characterized by morphological and molecular methods and toxin analyses. This is the first report of the Gambierdiscus lineage (genera Fukuyoa and Gambierdiscus) from the western Mediterranean Sea, which is cooler than its eastern basin. Molecular analyses revealed that the Mediterranean strain belongs to F. paulensis and that it bears LSU rDNA sequences identical to New Zealand, Australian, and Brazilian strains. It also shared an identical sequence of the more variable ITS-rDNA with the Brazilian strain. Toxin analyses showed the presence of maitotoxin, 54-deoxyCTX1B, and gambieric acid A. This is the first observation of the two latter compounds in a Fukuyoa strain. Therefore, both Gambierdiscus and Fukuyoa should be considered when as contributing to ciguatera fish poisoning. Different strains of Fukuyoa form a complex of morphologically cryptic lineages where F. paulensis stands as the most distantly related nominal species. The comparison of the ITS2 secondary structures revealed the absence of CBCs among strains. The study of the morphological and molecular traits depicted an unresolved taxonomic scenario impacted by the low strains samplingFinancial support for this research was provided by the Basque Government (project IT699-13). A grant from the University of the Basque Country (UPV/EHU) to H. David also supported this studyPeer reviewe

Multi-laboratory performance assessment of diffuse optics instruments: the BitMap exercise

SIGNIFICANCE: Multi-laboratory initiatives are essential in performance assessment and standardization-crucial for bringing biophotonics to mature clinical use-to establish protocols and develop reference tissue phantoms that all will allow universal instrument comparison. AIM: The largest multi-laboratory comparison of performance assessment in near-infrared diffuse optics is presented, involving 28 instruments and 12 institutions on a total of eight experiments based on three consolidated protocols (BIP, MEDPHOT, and NEUROPT) as implemented on three kits of tissue phantoms. A total of 20 synthetic indicators were extracted from the dataset, some of them defined here anew. APPROACH: The exercise stems from the Innovative Training Network BitMap funded by the European Commission and expanded to include other European laboratories. A large variety of diffuse optics instruments were considered, based on different approaches (time domain/frequency domain/continuous wave), at various stages of maturity and designed for different applications (e.g., oximetry, spectroscopy, and imaging). RESULTS: This study highlights a substantial difference in hardware performances (e.g., nine decades in responsivity, four decades in dark count rate, and one decade in temporal resolution). Agreement in the estimates of homogeneous optical properties was within 12% of the median value for half of the systems, with a temporal stability of <5  %   over 1 h, and day-to-day reproducibility of <3  %  . Other tests encompassed linearity, crosstalk, uncertainty, and detection of optical inhomogeneities. CONCLUSIONS: This extensive multi-laboratory exercise provides a detailed assessment of near-infrared Diffuse optical instruments and can be used for reference grading. The dataset-available soon in an open data repository-can be evaluated in multiple ways, for instance, to compare different analysis tools or study the impact of hardware implementations

Time-resolved multispectral optical tomography for reconstruction of depth- resolved changes in oxy- and deoxyhemoglobin

Dans cette thèse, j'ai développé de nouvelles techniques pour la tomographie optique diffuse. Dans la première partie, j'ai développé une méthode pour calculer des nouveaux types de données pour la tomographie optique diffuse. Avec cette nouvelle méthode, un plus grand ensemble de types de données peut être calculé et le bruit est moins corrélé. Les résultats montrent qu'une meilleure résolution en profondeur est obtenue par rapport à l'état de la technique. De plus, la quantification de l'absorption est améliorée de manière significative. Dans la deuxième partie, j'ai développé une méthode de régularisation par variation totale pour la tomographie optique diffuse sur des mailles irrégulières. Après, j'ai réalisé des expériences d'activation du cortex moteur cérébral chez des sujets adultes avec la collaboration de Politecnico di Milano. Des algorithmes précédemment développés ont été appliqués à ces mesures pour obtenir des reconstructions hémodynamiques en série chronologique du cortex moteur. Enfin, j'ai coordonné le plus grand jeu de données ouvert en optique diffuse composé des mesures effectuées dans le réseau BitMap.In this thesis I developed new techniques for diffuse optical tomography. In the first part, I developed a novel method to compute datatypes for diffuse optical tomography. With this new method a larger set of datatypes can be computed and noise is less correlated. Results show that better resolution in depth is obtained in comparison with the state-of-the-art. Moreover, quantification of absorption is improved significantly. In the second part, I developed total variation regularization method for diffuse optical tomography in irregular meshes. After, I performed brain motor cortex activation experiments in adult subjects with the collaboration of Politecnico di Milano. Previously developed algorithms were applied to that measurements obtaining time-series hemodynamic reconstructions of motor cortex. Finally, I coordinated the largest open dataset in diffuse optics composed by the measurements done within the BitMap network

Real-Time Dual-Wavelength Time-Resolved Diffuse Optical Tomography System for Functional Brain Imaging Based on Probe-Hosted Silicon Photomultipliers

Near-infrared diffuse optical tomography is a non-invasive photonics-based imaging technology suited to functional brain imaging applications. Recent developments have proved that it is possible to build a compact time-domain diffuse optical tomography system based on silicon photomultipliers (SiPM) detectors. The system presented in this paper was equipped with the same eight SiPM probe-hosted detectors, but was upgraded with six injection fibers to shine the sample at several points. Moreover, an automatic switch was included enabling a complete measurement to be performed in less than one second. Further, the system was provided with a dual-wavelength (670 n m and 820 n m ) light source to quantify the oxy- and deoxy-hemoglobin concentration evolution in the tissue. This novel system was challenged against a solid phantom experiment, and two in-vivo tests, namely arm occlusion and motor cortex brain activation. The results show that the tomographic system makes it possible to follow the evolution of brain activation over time with a 1 s -resolution

Tomographie optique multispectrale résolue en temps pour la reconstruction de changements en profondeur de l’oxy- et de la déoxyhémoglobine

In this thesis I developed new techniques for diffuse optical tomography. In the first part, I developed a novel method to compute datatypes for diffuse optical tomography. With this new method a larger set of datatypes can be computed and noise is less correlated. Results show that better resolution in depth is obtained in comparison with the state-of-the-art. Moreover, quantification of absorption is improved significantly. In the second part, I developed total variation regularization method for diffuse optical tomography in irregular meshes. After, I performed brain motor cortex activation experiments in adult subjects with the collaboration of Politecnico di Milano. Previously developed algorithms were applied to that measurements obtaining time-series hemodynamic reconstructions of motor cortex. Finally, I coordinated the largest open dataset in diffuse optics composed by the measurements done within the BitMap network.Dans cette thèse, j'ai développé de nouvelles techniques pour la tomographie optique diffuse. Dans la première partie, j'ai développé une méthode pour calculer des nouveaux types de données pour la tomographie optique diffuse. Avec cette nouvelle méthode, un plus grand ensemble de types de données peut être calculé et le bruit est moins corrélé. Les résultats montrent qu'une meilleure résolution en profondeur est obtenue par rapport à l'état de la technique. De plus, la quantification de l'absorption est améliorée de manière significative. Dans la deuxième partie, j'ai développé une méthode de régularisation par variation totale pour la tomographie optique diffuse sur des mailles irrégulières. Après, j'ai réalisé des expériences d'activation du cortex moteur cérébral chez des sujets adultes avec la collaboration de Politecnico di Milano. Des algorithmes précédemment développés ont été appliqués à ces mesures pour obtenir des reconstructions hémodynamiques en série chronologique du cortex moteur. Enfin, j'ai coordonné le plus grand jeu de données ouvert en optique diffuse composé des mesures effectuées dans le réseau BitMap

Improving Localization of Deep Inclusions in Time-Resolved Diffuse Optical Tomography

Time-resolved diffuse optical tomography is a technique used to recover the optical properties of an unknown diffusive medium by solving an ill-posed inverse problem. In time-domain, reconstructions based on datatypes are used for their computational efficiency. In practice, most used datatypes are temporal windows and Fourier transform. Nevertheless, neither theoretical nor numerical studies assessing different datatypes have been clearly expressed. In this paper, we propose an overview and a new process to compute efficiently a long set of temporal windows in order to perform diffuse optical tomography. We did a theoretical comparison of these large set of temporal windows. We also did simulations in a reflectance geometry with a spherical inclusion at different depths. The results are presented in terms of inclusion localization and its absorption coefficient recovery. We show that (1) the new windows computed with the developed method improve inclusion localization for inclusions at deep layers, (2) inclusion absorption quantification is improved at all depths and, (3) in some cases these windows can be equivalent to frequency based reconstruction at GHz order

Tomographie optique multispectrale résolue en temps pour la reconstruction de changements en profondeur de l’oxy- et de la déoxyhémoglobine

Noninvasive and continuous monitoring of patients are key features in the future of medical imaging. Biophotonics is a field that is attracting a lot of interest because its technology is intrinsically noninvasive and potentially miniaturizable and wearable. Regarding the imaging of human tissue using photonics, it has been proven that near-infrared diffuse optical tomography (DOT) permits to probe noninvasively and in depth the human tissue by reconstructing parameters of the composition of biological tissues such as the concentrations of oxygenated and deoxygenated hemoglobin in the blood. In this thesis, I describe the novel improvements I developed in the field of time-resolved DOT algorithms. First, I introduce a novel method to compute datatypes for tomographic reconstruction of time-resolved measurements. The results show that with this new approach the noise of datatypes are decorrelated and resolution in depth of reconstructions is improved significantly for inclusions deeper than 2.5 centimeters. After, I describe two different approaches to perform total variation regularization for DOT reconstruction on irregular meshes. The knowledge developed in previous parts was applied to in-vivo experiments on human subjects. In collaboration with Politecnico di Milano, I tested a time-resolved tomographic system with two probes of three source fibers and four silicon photomultiplier detectors each. Arm occlusion experiments were performed to validate the technology. After, I did motor cortex activation experiments on three different subjects. The results show that it is possible to monitor with one-second resolution the motor cortex activation and that spatial and in depth information can also be retrieved. Finally, I introduce the reader to the effort that is being done at BitMap network to push the standardization of diffuse optics field. I describe the work I did to build an open dataset with the measurements performed at twenty-eight instruments from eight different European institutions using three validated European protocols.La surveillance non invasive et continue des patients est un élément clé de l'avenir de l'imagerie médicale. La biophotonique est un domaine qui suscite beaucoup d'intérêt, car sa technologie est intrinsèquement non invasive, potentiellement miniaturisable et portable. En ce qui concerne l'imagerie de tissus humains en photonique, il a été prouvé que la tomographie optique diffuse dans le proche infrarouge (DOT) permettait de sonder de manière non invasive et en profondeur les tissus humains en reconstruisant des paramètres de la composition des tissus biologiques, tels que les concentrations en hémoglobine oxygénée et désoxygénée du sang. Dans cette thèse, je décris les nouvelles améliorations que j'ai développées dans le domaine des algorithmes DOT sur des acquisitions résolues en temps.Premièrement, je présente une nouvelle méthode de calcul des types de données pour la reconstruction tomographique de mesures résolues en temps. Les résultats montrent qu'avec cette nouvelle approche, le bruit des nouveaux types de données est décorrelé et la résolution en profondeur des reconstructions est améliorée de manière significative pour les inclusions plus profondes que 2,5 centimètres. Ensuite, je décris deux approches différentes pour effectuer la régularisation ((variation totale))pour la reconstruction DOT sur des maillages irréguliers. Les connaissances développées dans les parties précédentes ont été appliquées à des expériences in vivo sur des sujets humains. En collaboration avec Politecnico di Milano, j'ai testé un système tomographique à résolution temporelle avec deux sondes de trois sources et quatre détecteurs (photomultiplicateurs en silicium). Des expériences d'occlusion de bras ont été réalisées pour valider la technologie. Après, j'ai fait des expériences d'activation du cortex moteur sur trois sujets différents. Les résultats montrent qu'il est possible de surveiller l'activation du cortex moteur avec une résolution d'une seconde et que des informations spatiales et en profondeur peuvent également être récupérées. Enfin, je présente au lecteur les efforts déployés par le réseau BitMap pour pousser la normalisation du domaine de l'optique diffuse. Je décris le travail que j'ai effectué pour construire un jeu de données public avec les mesures effectuées sur 28 instruments de huit institutions européennes différentes à l'aide de trois protocoles européens valides