819 research outputs found

    Synthetic Aperture Radar (SAR) Meets Deep Learning

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    This reprint focuses on the application of the combination of synthetic aperture radars and depth learning technology. It aims to further promote the development of SAR image intelligent interpretation technology. A synthetic aperture radar (SAR) is an important active microwave imaging sensor, whose all-day and all-weather working capacity give it an important place in the remote sensing community. Since the United States launched the first SAR satellite, SAR has received much attention in the remote sensing community, e.g., in geological exploration, topographic mapping, disaster forecast, and traffic monitoring. It is valuable and meaningful, therefore, to study SAR-based remote sensing applications. In recent years, deep learning represented by convolution neural networks has promoted significant progress in the computer vision community, e.g., in face recognition, the driverless field and Internet of things (IoT). Deep learning can enable computational models with multiple processing layers to learn data representations with multiple-level abstractions. This can greatly improve the performance of various applications. This reprint provides a platform for researchers to handle the above significant challenges and present their innovative and cutting-edge research results when applying deep learning to SAR in various manuscript types, e.g., articles, letters, reviews and technical reports

    Development of Quantitative Bone SPECT Analysis Methods for Metastatic Bone Disease

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    Prostate cancer is one of the most prevalent types of cancer in males in the United States. Bone is a common site of metastases for metastatic prostate cancer. However, bone metastases are often considered “unmeasurable” using standard anatomic imaging and the RECIST 1.1 criteria. As a result, response to therapy is often suboptimally evaluated by visual interpretation of planar bone scintigraphy with response criteria related to the presence or absence of new lesions. With the commercial availability of quantitative single-photon emission computed tomography (SPECT) methods, it is now feasible to establish quantitative metrics of therapy response by skeletal metastases. Quantitative bone SPECT (QBSPECT) may provide the ability to estimate bone lesion uptake, volume, and the number of lesions more accurately than planar imaging. However, the accuracy of activity quantification in QBSPECT relies heavily on the precision with which bone metastases and bone structures are delineated. In this research, we aim at developing automated image segmentation methods for fast and accurate delineation of bone and bone metastases in QBSPECT. To begin, we developed registration methods to generate a dataset of realistic and anatomically-varying computerized phantoms for use in QBSPECT simulations. Using these simulations, we develop supervised computer-automated segmentation methods to minimize intra- and inter-observer variations in delineating bone metastases. This project provides accurate segmentation techniques for QBSPECT and paves the way for the development of QBSPECT methods for assessing bone metastases’ therapy response

    Evaluering av maskinlæringsmetoder for automatisk tumorsegmentering

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    The definition of target volumes and organs at risk (OARs) is a critical part of radiotherapy planning. In routine practice, this is typically done manually by clinical experts who contour the structures in medical images prior to dosimetric planning. This is a time-consuming and labor-intensive task. Moreover, manual contouring is inherently a subjective task and substantial contour variability can occur, potentially impacting on radiotherapy treatment and image-derived biomarkers. Automatic segmentation (auto-segmentation) of target volumes and OARs has the potential to save time and resources while reducing contouring variability. Recently, auto-segmentation of OARs using machine learning methods has been integrated into the clinical workflow by several institutions and such tools have been made commercially available by major vendors. The use of machine learning methods for auto-segmentation of target volumes including the gross tumor volume (GTV) is less mature at present but is the focus of extensive ongoing research. The primary aim of this thesis was to investigate the use of machine learning methods for auto-segmentation of the GTV in medical images. Manual GTV contours constituted the ground truth in the analyses. Volumetric overlap and distance-based metrics were used to quantify auto-segmentation performance. Four different image datasets were evaluated. The first dataset, analyzed in papers I–II, consisted of positron emission tomography (PET) and contrast-enhanced computed tomography (ceCT) images of 197 patients with head and neck cancer (HNC). The ceCT images of this dataset were also included in paper IV. Two datasets were analyzed separately in paper III, namely (i) PET, ceCT, and low-dose CT (ldCT) images of 86 patients with anal cancer (AC), and (ii) PET, ceCT, ldCT, and T2 and diffusion-weighted (T2W and DW, respectively) MR images of a subset (n = 36) of the aforementioned AC patients. The last dataset consisted of ceCT images of 36 canine patients with HNC and was analyzed in paper IV. In paper I, three approaches to auto-segmentation of the GTV in patients with HNC were evaluated and compared, namely conventional PET thresholding, classical machine learning algorithms, and deep learning using a 2-dimensional (2D) U-Net convolutional neural network (CNN). For the latter two approaches the effect of imaging modality on auto-segmentation performance was also assessed. Deep learning based on multimodality PET/ceCT image input resulted in superior agreement with the manual ground truth contours, as quantified by geometric overlap and distance-based performance evaluation metrics calculated on a per patient basis. Moreover, only deep learning provided adequate performance for segmentation based solely on ceCT images. For segmentation based on PET-only, all three approaches provided adequate segmentation performance, though deep learning ranked first, followed by classical machine learning, and PET thresholding. In paper II, deep learning-based auto-segmentation of the GTV in patients with HNC using a 2D U-Net architecture was evaluated more thoroughly by introducing new structure-based performance evaluation metrics and including qualitative expert evaluation of the resulting auto-segmentation quality. As in paper I, multimodal PET/ceCT image input provided superior segmentation performance, compared to the single modality CNN models. The structure-based metrics showed quantitatively that the PET signal was vital for the sensitivity of the CNN models, as the superior PET/ceCT-based model identified 86 % of all malignant GTV structures whereas the ceCT-based model only identified 53 % of these structures. Furthermore, the majority of the qualitatively evaluated auto-segmentations (~ 90 %) generated by the best PET/ceCT-based CNN were given a quality score corresponding to substantial clinical value. Based on papers I and II, deep learning with multimodality PET/ceCT image input would be the recommended approach for auto-segmentation of the GTV in human patients with HNC. In paper III, deep learning-based auto-segmentation of the GTV in patients with AC was evaluated for the first time, using a 2D U-Net architecture. Furthermore, an extensive comparison of the impact of different single modality and multimodality combinations of PET, ceCT, ldCT, T2W, and/or DW image input on quantitative auto-segmentation performance was conducted. For both the 86-patient and 36-patient datasets, the models based on PET/ceCT provided the highest mean overlap with the manual ground truth contours. For this task, however, comparable auto-segmentation quality was obtained for solely ceCT-based CNN models. The CNN model based solely on T2W images also obtained acceptable auto-segmentation performance and was ranked as the second-best single modality model for the 36-patient dataset. These results indicate that deep learning could prove a versatile future tool for auto-segmentation of the GTV in patients with AC. Paper IV investigated for the first time the applicability of deep learning-based auto-segmentation of the GTV in canine patients with HNC, using a 3-dimensional (3D) U-Net architecture and ceCT image input. A transfer learning approach where CNN models were pre-trained on the human HNC data and subsequently fine-tuned on canine data was compared to training models from scratch on canine data. These two approaches resulted in similar auto-segmentation performances, which on average was comparable to the overlap metrics obtained for ceCT-based auto-segmentation in human HNC patients. Auto-segmentation in canine HNC patients appeared particularly promising for nasal cavity tumors, as the average overlap with manual contours was 25 % higher for this subgroup, compared to the average for all included tumor sites. In conclusion, deep learning with CNNs provided high-quality GTV autosegmentations for all datasets included in this thesis. In all cases, the best-performing deep learning models resulted in an average overlap with manual contours which was comparable to the reported interobserver agreements between human experts performing manual GTV contouring for the given cancer type and imaging modality. Based on these findings, further investigation of deep learning-based auto-segmentation of the GTV in the given diagnoses would be highly warranted.Definisjon av målvolum og risikoorganer er en kritisk del av planleggingen av strålebehandling. I praksis gjøres dette vanligvis manuelt av kliniske eksperter som tegner inn strukturenes konturer i medisinske bilder før dosimetrisk planlegging. Dette er en tids- og arbeidskrevende oppgave. Manuell inntegning er også subjektiv, og betydelig variasjon i inntegnede konturer kan forekomme. Slik variasjon kan potensielt påvirke strålebehandlingen og bildebaserte biomarkører. Automatisk segmentering (auto-segmentering) av målvolum og risikoorganer kan potensielt spare tid og ressurser samtidig som konturvariasjonen reduseres. Autosegmentering av risikoorganer ved hjelp av maskinlæringsmetoder har nylig blitt implementert som del av den kliniske arbeidsflyten ved flere helseinstitusjoner, og slike verktøy er kommersielt tilgjengelige hos store leverandører av medisinsk teknologi. Auto-segmentering av målvolum inkludert tumorvolumet gross tumor volume (GTV) ved hjelp av maskinlæringsmetoder er per i dag mindre teknologisk modent, men dette området er fokus for omfattende pågående forskning. Hovedmålet med denne avhandlingen var å undersøke bruken av maskinlæringsmetoder for auto-segmentering av GTV i medisinske bilder. Manuelle GTVinntegninger utgjorde grunnsannheten (the ground truth) i analysene. Mål på volumetrisk overlapp og avstand mellom sanne og predikerte konturer ble brukt til å kvantifisere kvaliteten til de automatisk genererte GTV-konturene. Fire forskjellige bildedatasett ble evaluert. Det første datasettet, analysert i artikkel I–II, bestod av positronemisjonstomografi (PET) og kontrastforsterkede computertomografi (ceCT) bilder av 197 pasienter med hode/halskreft. ceCT-bildene i dette datasettet ble også inkludert i artikkel IV. To datasett ble analysert separat i artikkel III, nemlig (i) PET, ceCT og lavdose CT (ldCT) bilder av 86 pasienter med analkreft, og (ii) PET, ceCT, ldCT og T2- og diffusjonsvektet (henholdsvis T2W og DW) MR-bilder av en undergruppe (n = 36) av de ovennevnte analkreftpasientene. Det siste datasettet, som bestod av ceCT-bilder av 36 hunder med hode/halskreft, ble analysert i artikkel IV

    Deep Representation Learning with Limited Data for Biomedical Image Synthesis, Segmentation, and Detection

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    Biomedical imaging requires accurate expert annotation and interpretation that can aid medical staff and clinicians in automating differential diagnosis and solving underlying health conditions. With the advent of Deep learning, it has become a standard for reaching expert-level performance in non-invasive biomedical imaging tasks by training with large image datasets. However, with the need for large publicly available datasets, training a deep learning model to learn intrinsic representations becomes harder. Representation learning with limited data has introduced new learning techniques, such as Generative Adversarial Networks, Semi-supervised Learning, and Self-supervised Learning, that can be applied to various biomedical applications. For example, ophthalmologists use color funduscopy (CF) and fluorescein angiography (FA) to diagnose retinal degenerative diseases. However, fluorescein angiography requires injecting a dye, which can create adverse reactions in the patients. So, to alleviate this, a non-invasive technique needs to be developed that can translate fluorescein angiography from fundus images. Similarly, color funduscopy and optical coherence tomography (OCT) are also utilized to semantically segment the vasculature and fluid build-up in spatial and volumetric retinal imaging, which can help with the future prognosis of diseases. Although many automated techniques have been proposed for medical image segmentation, the main drawback is the model's precision in pixel-wise predictions. Another critical challenge in the biomedical imaging field is accurately segmenting and quantifying dynamic behaviors of calcium signals in cells. Calcium imaging is a widely utilized approach to studying subcellular calcium activity and cell function; however, large datasets have yielded a profound need for fast, accurate, and standardized analyses of calcium signals. For example, image sequences from calcium signals in colonic pacemaker cells ICC (Interstitial cells of Cajal) suffer from motion artifacts and high periodic and sensor noise, making it difficult to accurately segment and quantify calcium signal events. Moreover, it is time-consuming and tedious to annotate such a large volume of calcium image stacks or videos and extract their associated spatiotemporal maps. To address these problems, we propose various deep representation learning architectures that utilize limited labels and annotations to address the critical challenges in these biomedical applications. To this end, we detail our proposed semi-supervised, generative adversarial networks and transformer-based architectures for individual learning tasks such as retinal image-to-image translation, vessel and fluid segmentation from fundus and OCT images, breast micro-mass segmentation, and sub-cellular calcium events tracking from videos and spatiotemporal map quantification. We also illustrate two multi-modal multi-task learning frameworks with applications that can be extended to other domains of biomedical applications. The main idea is to incorporate each of these as individual modules to our proposed multi-modal frameworks to solve the existing challenges with 1) Fluorescein angiography synthesis, 2) Retinal vessel and fluid segmentation, 3) Breast micro-mass segmentation, and 4) Dynamic quantification of calcium imaging datasets

    2022 Review of Data-Driven Plasma Science

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    Data-driven science and technology offer transformative tools and methods to science. This review article highlights the latest development and progress in the interdisciplinary field of data-driven plasma science (DDPS), i.e., plasma science whose progress is driven strongly by data and data analyses. Plasma is considered to be the most ubiquitous form of observable matter in the universe. Data associated with plasmas can, therefore, cover extremely large spatial and temporal scales, and often provide essential information for other scientific disciplines. Thanks to the latest technological developments, plasma experiments, observations, and computation now produce a large amount of data that can no longer be analyzed or interpreted manually. This trend now necessitates a highly sophisticated use of high-performance computers for data analyses, making artificial intelligence and machine learning vital components of DDPS. This article contains seven primary sections, in addition to the introduction and summary. Following an overview of fundamental data-driven science, five other sections cover widely studied topics of plasma science and technologies, i.e., basic plasma physics and laboratory experiments, magnetic confinement fusion, inertial confinement fusion and high-energy-density physics, space and astronomical plasmas, and plasma technologies for industrial and other applications. The final section before the summary discusses plasma-related databases that could significantly contribute to DDPS. Each primary section starts with a brief introduction to the topic, discusses the state-of-the-art developments in the use of data and/or data-scientific approaches, and presents the summary and outlook. Despite the recent impressive signs of progress, the DDPS is still in its infancy. This article attempts to offer a broad perspective on the development of this field and identify where further innovations are required

    Lung Imaging and Function Assessment using Non-Contrast-Enhanced Magnetic Resonance Imaging

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    Measurement of pulmonary ventilation and perfusion has significant clinical value for the diagnosis and monitoring of prevalent lung diseases. To this end, non-contrast-enhanced MRI techniques have emerged as a promising alternative to scintigraphical measurements, computed tomography, and contrast-enhanced MRI. Although these techniques allow the acquisition of both structural and functional information in the same scan session, they are prone to robustness issues related to imaging artifacts and post-processing techniques, limiting their clinical utilization. In this work, new acquisition and post-processing techniques were introduced for improving the robustness of non-contrast-enhanced MRI based functional lung imaging. Furthermore, pulmonary functional maps were acquired in 2-year-old congenital diaphragmatic hernia (CDH) patients to demonstrate the feasibility of non-contrast-enhanced MRI methods for functional lung imaging. In the first study, a multi-acquisition framework was developed to improve robustness against field inhomogeneity artifacts. This method was evaluated at 1.5T and 3T field strengths via acquisitions obtained from healthy volunteers. The results demonstrate that the proposed acquisition framework significantly improved ventilation map homogeneity p<0.05. In the second study, a post-processing method based on dynamic mode decomposition (DMD) was developed to accurately identify dominant spatiotemporal patterns in the acquisitions. This method was demonstrated on digital lung phantoms and in vivo acquisitions. The findings indicate that the proposed method led to a significant reduction in dispersion of estimated ventilation and perfusion map amplitudes across different number of measurements when compared with competing methods p<0.05. In the third study, the free-breathing non-contrast-enhanced dynamic acquisitions were obtained from 2-year-old patients after CDH repair, and then processed using the DMD to obtain pulmonary functional maps. Afterwards, functional differences between ipsilateral and contralateral lungs were assessed and compared with results obtained using contrast-enhanced MRI measurements. The results demonstrate that pulmonary ventilation and perfusion maps can be generated from dynamic acquisitions successfully without the need for ionizing radiation or contrast agents. Furthermore, lung perfusion parameters obtained with DMD MRI correlate very strongly with parameters obtained using dynamic contrast-enhanced MRI. In conclusion, the presented work improves the robustness and accuracy of non-contrast-enhanced functional lung imaging using MRI. Overall, the methods introduced in this work may serve as a valuable tool in the clinical adaptation of non-contrast-enhanced imaging methods and may be used for longitudinal assessments of pulmonary functional changes

    Nuevas contribuciones a la teoría y aplicación del procesado de señal sobre grafos

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    [ES] El procesado de señal sobre grafos es un campo emergente de técnicas que combinan conceptos de dos áreas muy consolidadas: el procesado de señal y la teoría de grafos. Desde la perspectiva del procesado de señal puede obtenerse una definición de la señal mucho más general asignando cada valor de la misma a un vértice de un grafo. Las señales convencionales pueden considerarse casos particulares en los que los valores de cada muestra se asignan a una cuadrícula uniforme (temporal o espacial). Desde la perspectiva de la teoría de grafos, se pueden definir nuevas transformaciones del grafo de forma que se extiendan los conceptos clásicos del procesado de la señal como el filtrado, la predicción y el análisis espectral. Además, el procesado de señales sobre grafos está encontrando nuevas aplicaciones en las áreas de detección y clasificación debido a su flexibilidad para modelar dependencias generales entre variables. En esta tesis se realizan nuevas contribuciones al procesado de señales sobre grafos. En primer lugar, se plantea el problema de estimación de la matriz Laplaciana asociada a un grafo, que determina la relación entre nodos. Los métodos convencionales se basan en la matriz de precisión, donde se asume implícitamente Gaussianidad. En esta tesis se proponen nuevos métodos para estimar la matriz Laplaciana a partir de las correlaciones parciales asumiendo respectivamente dos modelos no Gaussianos diferentes en el espacio de las observaciones: mezclas gaussianas y análisis de componentes independientes. Los métodos propuestos han sido probados con datos simulados y con datos reales en algunas aplicaciones biomédicas seleccionadas. Se demuestra que pueden obtenerse mejores estimaciones de la matriz Laplaciana con los nuevos métodos propuestos en los casos en que la Gaussianidad no es una suposición correcta. También se ha considerado la generación de señales sintéticas en escenarios donde la escasez de señales reales puede ser un problema. Los modelos sobre grafos permiten modelos de dependencia por pares más generales entre muestras de señal. Así, se propone un nuevo método basado en la Transformada de Fourier Compleja sobre Grafos y en el concepto de subrogación. Se ha aplicado en el desafiante problema del reconocimiento de gestos con las manos. Se ha demostrado que la extensión del conjunto de entrenamiento original con réplicas sustitutas generadas con los métodos sobre grafos, mejora significativamente la precisión del clasificador de gestos con las manos.[CAT] El processament de senyal sobre grafs és un camp emergent de tècniques que combinen conceptes de dues àrees molt consolidades: el processament de senyal i la teoria de grafs. Des de la perspectiva del processament de senyal pot obtindre's una definició del senyal molt més general assignant cada valor de la mateixa a un vèrtex d'un graf. Els senyals convencionals poden considerar-se casos particulars en els quals els valors de la mostra s'assignen a una quadrícula uniforme (temporal o espacial). Des de la perspectiva de la teoria de grafs, es poden definir noves transformacions del graf de manera que s'estenguen els conceptes clàssics del processament del senyal com el filtrat, la predicció i l'anàlisi espectral. A més, el processament de senyals sobre grafs està trobant noves aplicacions en les àrees de detecció i classificació a causa de la seua flexibilitat per a modelar dependències generals entre variables. En aquesta tesi es donen noves contribucions al processament de senyals sobre grafs. En primer lloc, es planteja el problema d'estimació de la matriu Laplaciana associada a un graf, que determina la relació entre nodes. Els mètodes convencionals es basen en la matriu de precisió, on s'assumeix implícitament la gaussianitat. En aquesta tesi es proposen nous mètodes per a estimar la matriu Laplaciana a partir de les correlacions parcials assumint respectivament dos models no gaussians diferents en l'espai d'observació: mescles gaussianes i anàlisis de components independents. Els mètodes proposats han sigut provats amb dades simulades i amb dades reals en algunes aplicacions biomèdiques seleccionades. Es demostra que poden obtindre's millors estimacions de la matriu Laplaciana amb els nous mètodes proposats en els casos en què la gaussianitat no és una suposició correcta. També s'ha considerat el problema de generar senyals sintètics en escenaris on l'escassetat de senyals reals pot ser un problema. Els models sobre grafs permeten models de dependència per parells més generals entre mostres de senyal. Així, es proposa un nou mètode basat en la Transformada de Fourier Complexa sobre Grafs i en el concepte de subrogació. S'ha aplicat en el desafiador problema del reconeixement de gestos amb les mans. S'ha demostrat que l'extensió del conjunt d'entrenament original amb rèpliques substitutes generades amb mètodes sobre grafs, millora significativament la precisió del classificador de gestos amb les mans.[EN] Graph signal processing appears as an emerging field of techniques that combine concepts from two highly consolidated areas: signal processing and graph theory. From the perspective of signal processing, it is possible to achieve a more general signal definition by assigning each value of the signal to a vertex of a graph. Conventional signals can be considered particular cases where the sample values are assigned to a uniform (temporal or spatial) grid. From the perspective of graph theory, new transformations of the graph can be defined in such a way that they extend the classical concepts of signal processing such as filtering, prediction and spectral analysis. Furthermore, graph signal processing is finding new applications in detection and classification areas due to its flexibility to model general dependencies between variables. In this thesis, new contributions are given to graph signal processing. Firstly, it is considered the problem of estimating the Laplacian matrix associated with a graph, which determines the relationship between nodes. Conventional methods are based on the precision matrix, where Gaussianity is implicitly assumed. In this thesis, new methods to estimate the Laplacian matrix from the partial correlations are proposed respectively assuming two different non-Gaussian models in the observation space: Gaussian Mixtures and Independent Component Analysis. The proposed methods have been tested with simulated data and with real data in some selected biomedical applications. It is demonstrate that better estimates of the Laplacian matrix can be obtained with the new proposed methods in cases where Gaussianity is not a correct assumption. The problem of generating synthetic signal in scenarios where real signals scarcity can be an issue has also been considered. Graph models allow more general pairwise dependence models between signal samples. Thus a new method based on the Complex Graph Fourier Transform and on the concept of subrogation is proposed. It has been applied in the challenging problem of hand gesture recognition. It has been demonstrated that extending the original training set with graph surrogate replicas, significantly improves the accuracy of the hand gesture classifier.Belda Valls, J. (2022). Nuevas contribuciones a la teoría y aplicación del procesado de señal sobre grafos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/19133

    A goal-driven unsupervised image segmentation method combining graph-based processing and Markov random fields

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    Image segmentation is the process of partitioning a digital image into a set of homogeneous regions (according to some homogeneity criterion) to facilitate a subsequent higher-level analysis. In this context, the present paper proposes an unsupervised and graph-based method of image segmentation, which is driven by an application goal, namely, the generation of image segments associated with a user-defined and application-specific goal. A graph, together with a random grid of source elements, is defined on top of the input image. From each source satisfying a goal-driven predicate, called seed, a propagation algorithm assigns a cost to each pixel on the basis of similarity and topological connectivity, measuring the degree of association with the reference seed. Then, the set of most significant regions is automatically extracted and used to estimate a statistical model for each region. Finally, the segmentation problem is expressed in a Bayesian framework in terms of probabilistic Markov random field (MRF) graphical modeling. An ad hoc energy function is defined based on parametric models, a seed-specific spatial feature, a background-specific potential, and local-contextual information. This energy function is minimized through graph cuts and, more specifically, the alpha-beta swap algorithm, yielding the final goal-driven segmentation based on the maximum a posteriori (MAP) decision rule. The proposed method does not require deep a priori knowledge (e.g., labelled datasets), as it only requires the choice of a goal-driven predicate and a suited parametric model for the data. In the experimental validation with both magnetic resonance (MR) and synthetic aperture radar (SAR) images, the method demonstrates robustness, versatility, and applicability to different domains, thus allowing for further analyses guided by the generated product
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