Reconstruction par acquisition compressée en imagerie ultrasonore médicale 3D et Doppler

This thesis is dedicated to the application of the novel compressed sensing theory to the acquisition and reconstruction of 3D US images and Doppler signals. In 3D US imaging, one of the major difficulties concerns the number of RF lines that has to be acquired to cover the complete volume. The acquisition of each line takes an incompressible time due to the finite velocity of the ultrasound wave. One possible solution for increasing the frame rate consists in reducing the acquisition time by skipping some RF lines. The reconstruction of the missing information in post processing is then a typical application of compressed sensing. Another excellent candidate for this theory is the Doppler duplex imaging that implies alternating two modes of emission, one for B-mode imaging and the other for flow estimation. Regarding 3D imaging, we propose a compressed sensing framework using learned overcomplete dictionaries. Such dictionaries allow for much sparser representations of the signals since they are optimized for a particular class of images such as US images.We also focus on the measurement sensing setup and propose a line-wise sampling of entire RF lines which allows to decrease the amount of data and is feasible in a relatively simple setting of the 3D US equipment. The algorithm was validated on 3D simulated and experimental data. For the Doppler application, we proposed a CS based framework for randomly interleaving Doppler and US emissions. The proposed method reconstructs the Doppler signal using a block sparse Bayesian learning algorithm that exploits the correlation structure within a signal and has the ability of recovering partially sparse signals as long as they are correlated. This method is validated on simulated and experimental Doppler data.DL’objectif de cette thèse est le développement de techniques adaptées à l’application de la théorie de l’acquisition compressée en imagerie ultrasonore 3D et Doppler. En imagerie ultrasonore 3D une des principales difficultés concerne le temps d’acquisition très long lié au nombre de lignes RF à acquérir pour couvrir l’ensemble du volume. Afin d’augmenter la cadence d’imagerie une solution possible consiste à choisir aléatoirement des lignes RF qui ne seront pas acquises. La reconstruction des données manquantes est une application typique de l’acquisition compressée. Une autre application d’intérêt correspond aux acquisitions Doppler duplex où des stratégies d’entrelacement des acquisitions sont nécessaires et conduisent donc à une réduction de la quantité de données disponibles. Dans ce contexte, nous avons réalisé de nouveaux développements permettant l’application de l’acquisition compressée à ces deux modalités d’acquisition ultrasonore. Dans un premier temps, nous avons proposé d’utiliser des dictionnaires redondants construits à partir des signaux d’intérêt pour la reconstruction d’images 3D ultrasonores. Une attention particulière a aussi été apportée à la configuration du système d’acquisition et nous avons choisi de nous concentrer sur un échantillonnage des lignes RF entières, réalisable en pratique de façon relativement simple. Cette méthode est validée sur données 3D simulées et expérimentales. Dans un deuxième temps, nous proposons une méthode qui permet d’alterner de manière aléatoire les émissions Doppler et les émissions destinées à l’imagerie mode-B. La technique est basée sur une approche bayésienne qui exploite la corrélation et la parcimonie des blocs du signal. L’algorithme est validé sur des données Doppler simulées et expérimentales

Ergodic encoding for single-element ultrasound imaging in vivo

Conventional ultrasound imaging relies on the computation of geometric time delay from multiple sensors to detect the position of a scatterer. In this paper, we present Ergodic Relay Ultrasound Imaging (ERUI), a method that utilizes an ergodic cavity down to a single ultrasonic sensor for ultrasound imaging. With the proposed method, the ergodic cavity creates a unique temporal signature that encodes the position of a scatterer. When compared to standard approaches, ERUI enables the generation of images of comparable quality while utilizing fewer detector elements. Our results suggest that ERUI has the potential to achieve image resolution similar to that of traditional imaging techniques, shifting the complexity from hardware to sofware. The demonstrated feasibility offers a promising path towards ultrasound probes with reduced costs and complexity for more portable scanning devices.Comment: 5 pages, 4 figures, Lette

Learning Sub-Sampling and Signal Recovery with Applications in Ultrasound Imaging

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data

Efficient algorithms and data structures for compressive sensing

Wegen der kontinuierlich anwachsenden Anzahl von Sensoren, und den stetig wachsenden Datenmengen, die jene produzieren, stößt die konventielle Art Signale zu verarbeiten, beruhend auf dem Nyquist-Kriterium, auf immer mehr Hindernisse und Probleme. Die kürzlich entwickelte Theorie des Compressive Sensing (CS) formuliert das Versprechen einige dieser Hindernisse zu beseitigen, indem hier allgemeinere Signalaufnahme und -rekonstruktionsverfahren zum Einsatz kommen können. Dies erlaubt, dass hierbei einzelne Abtastwerte komplexer strukturierte Informationen über das Signal enthalten können als dies bei konventiellem Nyquistsampling der Fall ist. Gleichzeitig verändert sich die Signalrekonstruktion notwendigerweise zu einem nicht-linearen Vorgang und ebenso müssen viele Hardwarekonzepte für praktische Anwendungen neu überdacht werden. Das heißt, dass man zwischen der Menge an Information, die man über Signale gewinnen kann, und dem Aufwand für das Design und Betreiben eines Signalverarbeitungssystems abwägen kann und muss. Die hier vorgestellte Arbeit trägt dazu bei, dass bei diesem Abwägen CS mehr begünstigt werden kann, indem neue Resultate vorgestellt werden, die es erlauben, dass CS einfacher in der Praxis Anwendung finden kann, wobei die zu erwartende Leistungsfähigkeit des Systems theoretisch fundiert ist. Beispielsweise spielt das Konzept der Sparsity eine zentrale Rolle, weshalb diese Arbeit eine Methode präsentiert, womit der Grad der Sparsity eines Vektors mittels einer einzelnen Beobachtung geschätzt werden kann. Wir zeigen auf, dass dieser Ansatz für Sparsity Order Estimation zu einem niedrigeren Rekonstruktionsfehler führt, wenn man diesen mit einer Rekonstruktion vergleicht, welcher die Sparsity des Vektors unbekannt ist. Um die Modellierung von Signalen und deren Rekonstruktion effizienter zu gestalten, stellen wir das Konzept von der matrixfreien Darstellung linearer Operatoren vor. Für die einfachere Anwendung dieser Darstellung präsentieren wir eine freie Softwarearchitektur und demonstrieren deren Vorzüge, wenn sie für die Rekonstruktion in einem CS-System genutzt wird. Konkret wird der Nutzen dieser Bibliothek, einerseits für das Ermitteln von Defektpositionen in Prüfkörpern mittels Ultraschall, und andererseits für das Schätzen von Streuern in einem Funkkanal aus Ultrabreitbanddaten, demonstriert. Darüber hinaus stellen wir für die Verarbeitung der Ultraschalldaten eine Rekonstruktionspipeline vor, welche Daten verarbeitet, die im Frequenzbereich Unterabtastung erfahren haben. Wir beschreiben effiziente Algorithmen, die bei der Modellierung und der Rekonstruktion zum Einsatz kommen und wir leiten asymptotische Resultate für die benötigte Anzahl von Messwerten, sowie die zu erwartenden Lokalisierungsgenauigkeiten der Defekte her. Wir zeigen auf, dass das vorgestellte System starke Kompression zulässt, ohne die Bildgebung und Defektlokalisierung maßgeblich zu beeinträchtigen. Für die Lokalisierung von Streuern mittels Ultrabreitbandradaren stellen wir ein CS-System vor, welches auf einem Random Demodulators basiert. Im Vergleich zu existierenden Messverfahren ist die hieraus resultierende Schätzung der Kanalimpulsantwort robuster gegen die Effekte von zeitvarianten Funkkanälen. Um den inhärenten Modellfehler, den gitterbasiertes CS begehen muss, zu beseitigen, zeigen wir auf wie Atomic Norm Minimierung es erlaubt ohne die Einschränkung auf ein endliches und diskretes Gitter R-dimensionale spektrale Komponenten aus komprimierten Beobachtungen zu schätzen. Hierzu leiten wir eine R-dimensionale Variante des ADMM her, welcher dazu in der Lage ist die Signalkovarianz in diesem allgemeinen Szenario zu schätzen. Weiterhin zeigen wir, wie dieser Ansatz zur Richtungsschätzung mit realistischen Antennenarraygeometrien genutzt werden kann. In diesem Zusammenhang präsentieren wir auch eine Methode, welche mittels Stochastic gradient descent Messmatrizen ermitteln kann, die sich gut für Parameterschätzung eignen. Die hieraus resultierenden Kompressionsverfahren haben die Eigenschaft, dass die Schätzgenauigkeit über den gesamten Parameterraum ein möglichst uniformes Verhalten zeigt. Zuletzt zeigen wir auf, dass die Kombination des ADMM und des Stochastic Gradient descent das Design eines CS-Systems ermöglicht, welches in diesem gitterfreien Szenario wünschenswerte Eigenschaften hat.Along with the ever increasing number of sensors, which are also generating rapidly growing amounts of data, the traditional paradigm of sampling adhering the Nyquist criterion is facing an equally increasing number of obstacles. The rather recent theory of Compressive Sensing (CS) promises to alleviate some of these drawbacks by proposing to generalize the sampling and reconstruction schemes such that the acquired samples can contain more complex information about the signal than Nyquist samples. The proposed measurement process is more complex and the reconstruction algorithms necessarily need to be nonlinear. Additionally, the hardware design process needs to be revisited as well in order to account for this new acquisition scheme. Hence, one can identify a trade-off between information that is contained in individual samples of a signal and effort during development and operation of the sensing system. This thesis addresses the necessary steps to shift the mentioned trade-off more to the favor of CS. We do so by providing new results that make CS easier to deploy in practice while also maintaining the performance indicated by theoretical results. The sparsity order of a signal plays a central role in any CS system. Hence, we present a method to estimate this crucial quantity prior to recovery from a single snapshot. As we show, this proposed Sparsity Order Estimation method allows to improve the reconstruction error compared to an unguided reconstruction. During the development of the theory we notice that the matrix-free view on the involved linear mappings offers a lot of possibilities to render the reconstruction and modeling stage much more efficient. Hence, we present an open source software architecture to construct these matrix-free representations and showcase its ease of use and performance when used for sparse recovery to detect defects from ultrasound data as well as estimating scatterers in a radio channel using ultra-wideband impulse responses. For the former of these two applications, we present a complete reconstruction pipeline when the ultrasound data is compressed by means of sub-sampling in the frequency domain. Here, we present the algorithms for the forward model, the reconstruction stage and we give asymptotic bounds for the number of measurements and the expected reconstruction error. We show that our proposed system allows significant compression levels without substantially deteriorating the imaging quality. For the second application, we develop a sampling scheme to acquire the channel Impulse Response (IR) based on a Random Demodulator that allows to capture enough information in the recorded samples to reliably estimate the IR when exploiting sparsity. Compared to the state of the art, this in turn allows to improve the robustness to the effects of time-variant radar channels while also outperforming state of the art methods based on Nyquist sampling in terms of reconstruction error. In order to circumvent the inherent model mismatch of early grid-based compressive sensing theory, we make use of the Atomic Norm Minimization framework and show how it can be used for the estimation of the signal covariance with R-dimensional parameters from multiple compressive snapshots. To this end, we derive a variant of the ADMM that can estimate this covariance in a very general setting and we show how to use this for direction finding with realistic antenna geometries. In this context we also present a method based on a Stochastic gradient descent iteration scheme to find compression schemes that are well suited for parameter estimation, since the resulting sub-sampling has a uniform effect on the whole parameter space. Finally, we show numerically that the combination of these two approaches yields a well performing grid-free CS pipeline

Deep data compression for approximate ultrasonic image formation

In many ultrasonic imaging systems, data acquisition and image formation are performed on separate computing devices. Data transmission is becoming a bottleneck, thus, efficient data compression is essential. Compression rates can be improved by considering the fact that many image formation methods rely on approximations of wave-matter interactions, and only use the corresponding part of the data. Tailored data compression could exploit this, but extracting the useful part of the data efficiently is not always trivial. In this work, we tackle this problem using deep neural networks, optimized to preserve the image quality of a particular image formation method. The Delay-And-Sum (DAS) algorithm is examined which is used in reflectivity-based ultrasonic imaging. We propose a novel encoder-decoder architecture with vector quantization and formulate image formation as a network layer for end-to-end training. Experiments demonstrate that our proposed data compression tailored for a specific image formation method obtains significantly better results as opposed to compression agnostic to subsequent imaging. We maintain high image quality at much higher compression rates than the theoretical lossless compression rate derived from the rank of the linear imaging operator. This demonstrates the great potential of deep ultrasonic data compression tailored for a specific image formation method.Comment: IEEE International Ultrasonics Symposium 202

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1

Enhanced ultrasound image reconstruction using a compressive blind deconvolution approach

Compressive deconvolution, combining compressive sampling and image deconvolution, represents an interesting possibility to reconstruct enhanced ultrasound images from compressed measurements. The model of compressive deconvolution includes, in addition to the measurement matrix, a 2D convolution operator carrying the information on the system point spread function which is usually unkown in practice. In this paper, we propose a novel alternating minimization-based optimization scheme to invert the resulting linear model, to jointly reconstruct enhanced ultrasound images and estimate the point spread function. The performance of the method is evaluated on both Shepp-Logan phantom and simulated ultrasound data