Quantification of the volumetric benefit of image-guided radiotherapy (IGRT) in prostate cancer: margins and presence probability map

International audiencePURPOSE: To quantify the prostate and seminal vesicles (SV) anatomic variations in order to choose appropriate margins including intrapelvic anatomic variations. To quantify volumetric benefit of image-guided radiotherapy (IGRT). PATIENTS AND METHODS: Twenty patients, receiving a total dose of 70 Gy in the prostate, had a planning CT scan and eight weekly CT scans during treatment. Prostate and SV were manually contoured. Each weekly CT scan was registered to the planning CT scan according to three modalities: radiopaque skin marks, pelvis bone or prostate. For each patient, prostate and SV displacements were quantified. 3D maps of prostate and SV presence probability were established. Volumes including minimal presence probabilities were compared between the three modalities of registration. RESULTS: For the prostate intrapelvic displacements, systematic and random variations and maximal displacements for the entire population were: 5mm, 2.7 mm and 16.5mm in anteroposterior axis; 2.7 mm, 2.4mm and 11.4mm in superoinferior axis and 0.5mm, 0.8mm and 3.3mm laterally. Margins according to van Herk recipe (to cover the prostate for 90% of the patients with the 95% isodose) were: 8mm, 8.3mm and 1.9 mm, respectively. The 100% prostate presence probability volumes correspond to 37%, 50% and 61% according to the registration modality. For the SV, these volumes correspond to 8%, 14% and 18% of the SV volume. CONCLUSIONS: Without IGRT, 5mm prostate posterior margins are insufficient and should be at least 8mm, to account for intrapelvic anatomic variations. Prostate registration almost doubles the 100% presence probability volume compared to skin registration. Deformation of SV will require either to increase dramatically margins (simple) or new planning (not realistic)

Cuckoo Search Algorithm with Lévy Flights for Global-Support Parametric Surface Approximation in Reverse Engineering

This paper concerns several important topics of the Symmetry journal, namely, computer-aided design, computational geometry, computer graphics, visualization, and pattern recognition. We also take advantage of the symmetric structure of the tensor-product surfaces, where the parametric variables u and v play a symmetric role in shape reconstruction. In this paper we address the general problem of global-support parametric surface approximation from clouds of data points for reverse engineering applications. Given a set of measured data points, the approximation is formulated as a nonlinear continuous least-squares optimization problem. Then, a recent metaheuristics called Cuckoo Search Algorithm (CSA) is applied to compute all relevant free variables of this minimization problem (namely, the data parameters and the surface poles). The method includes the iterative generation of new solutions by using the Lévy flights to promote the diversity of solutions and prevent stagnation. A critical advantage of this method is its simplicity: the CSA requires only two parameters, many fewer than any other metaheuristic approach, so the parameter tuning becomes a very easy task. The method is also simple to understand and easy to implement. Our approach has been applied to a benchmark of three illustrative sets of noisy data points corresponding to surfaces exhibiting several challenging features. Our experimental results show that the method performs very well even for the cases of noisy and unorganized data points. Therefore, the method can be directly used for real-world applications for reverse engineering without further pre/post-processing. Comparative work with the most classical mathematical techniques for this problem as well as a recent modification of the CSA called Improved CSA (ICSA) is also reported. Two nonparametric statistical tests show that our method outperforms the classical mathematical techniques and provides equivalent results to ICSA for all instances in our benchmark.This research work has received funding from the project PDE-GIR (Partial Differential Equations for Geometric modelling, Image processing, and shape Reconstruction) of the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant agreement No. 778035, the Spanish Ministry of Economy and Competitiveness (Computer Science National Program) under Grant #TIN2017-89275-R of the Agencia Estatal de Investigación and European Funds FEDER (AEI/FEDER, UE), and the project #JU12, jointly supported by public body SODERCAN of the Regional Government of Cantabria and European Funds FEDER (SODERCAN/FEDER UE). We also thank Toho University, Nihon University, and the Symmetry 2018, 10, 58 23 of 25 University of Cantabria for their support to conduct this research wor

Geometric representation of neuroanatomical data observed in mouse brain at cellular and gross levels

This dissertation studies two problems related to geometric representation of neuroanatomical data: (i) spatial representation and organization of individual neurons, and (ii) reconstruction of three-dimensional neuroanatomical regions from sparse two-dimensional drawings. This work has been motivated by nearby development of new technology, Knife-Edge Scanning Microscopy (KESM), that images a whole mouse brain at cellular level in less than a month. A method is introduced to represent neuronal data observed in the mammalian brain at the cellular level using geometric primitives and spatial indexing. A data representation scheme is defined that captures the geometry of individual neurons using traditional geometric primitives, points and cross-sectional areas along a trajectory. This representation captures inferred synapses as directed links between primitives and spatially indexes observed neurons based on the locations of their cell bodies. This method provides a set of rules for acquisition, representation, and indexing of KESMgenerated data. Neuroanatomical data observed at the gross level provides the underlying regional framework for neuronal circuits. Accumulated expert knowledge on neuroanatomical organization is usually given as a series of sparse two-dimensional contours. A data structure and an algorithm are described to reconstruct separating surfaces among multiple regions from these sparse cross-sectional contours. A topology graph is defined for each region that describes the topological skeleton of the region’s boundary surface and that shows between which contours the surface patches should be generated. A graph-directed triangulation algorithm is provided to reconstruct surface patches between contours. This graph-directed triangulation algorithm combined together with a piecewise parametric curve fitting technique ensures that abutting or shared surface patches are precisely coincident. This method overcomes limitations in i) traditional surfaces-from-contours algorithms that assume binary, not multiple, regionalization of space, and in ii) few existing separating surfaces algorithms that assume conversion of input into a regular volumetric grid, which is not possible with sparse inter-planar resolution

Reconstruction of 3D Neuronal Structures from Densely Packed Electron Microscopy Data Stacks

The goal of fully decoding how the brain works requires a detailed wiring diagram of the brain network that reveals the complete connectivity matrix. Recent advances in high-throughput 3D electron microscopy (EM) image acquisition techniques have made it possible to obtain high-resolution 3D imaging data that allows researchers to follow axons and dendrites and to identify pre-synaptic and post-synaptic sites, enabling the reconstruction of detailed neural circuits of the nervous system at the level of synapses. However, these massive data sets pose unique challenges to structural reconstruction because the inevitable staining noise, incomplete boundaries, and inhomogeneous staining intensities increase difficulty of 3D reconstruction and visualization. In this dissertation, a new set of algorithms are provided for reconstruction of neuronal morphology from stacks of serial EM images. These algorithms include (1) segmentation algorithms for obtaining the full geometry of neural circuits, (2) interactive segmentation tools for manual correction of erroneous segmentations, and (3) a validation method for obtaining a topologically correct segmentation when a set of segmentation alternatives are available. Experimental results obtained by using EM images containing densely packed cells demonstrate that (1) the proposed segmentation methods can successfully reconstruct full anatomical structures from EM images, (2) the editing tools provide a way for the user to easily and quickly refine incorrect segmentations, (3) and the validation method is effective in combining multiple segmentation results. The algorithms presented in this dissertation are expected to contribute to the reconstruction of the connectome and to open new directions in the development of reconstruction methods

Physically-based simulation of ice formation

The geometric and optical complexity of ice has been a constant source of wonder and inspiration for scientists and artists. It is a defining seasonal characteristic, so modeling it convincingly is a crucial component of any synthetic winter scene. Like wind and fire, it is also considered elemental, so it has found considerable use as a dramatic tool in visual effects. However, its complex appearance makes it difficult for an artist to model by hand, so physically-based simulation methods are necessary. In this dissertation, I present several methods for visually simulating ice formation. A general description of ice formation has been known for over a hundred years and is referred to as the Stefan Problem. There is no known general solution to the Stefan Problem, but several numerical methods have successfully simulated many of its features. I will focus on three such methods in this dissertation: phase field methods, diffusion limited aggregation, and level set methods. Many different variants of the Stefan problem exist, and each presents unique challenges. Phase field methods excel at simulating the Stefan problem with surface tension anisotropy. Surface tension gives snowflakes their characteristic six arms, so phase field methods provide a way of simulating medium scale detail such as frost and snowflakes. However, phase field methods track the ice as an implicit surface, so it tends to smear away small-scale detail. In order to restore this detail, I present a hybrid method that combines phase fields with diffusion limited aggregation (DLA). DLA is a fractal growth algorithm that simulates the quasi-steady state, zero surface tension Stefan problem, and does not suffer from smearing problems. I demonstrate that combining these two algorithms can produce visual features that neither method could capture alone. Finally, I present a method of simulating icicle formation. Icicle formation corresponds to the thin-film, quasi-steady state Stefan problem, and neither phase fields nor DLA are directly applicable. I instead use level set methods, an alternate implicit front tracking strategy. I derive the necessary velocity equations for level set simulation, and also propose an efficient method of simulating ripple formation across the surface of the icicles

Radiothérapie guidée par l'image du cancer de la prostate (vers l'intégration des déformations anatomiques)

Ce travail de thèse porte sur la quantification et la prise en compte des variations anatomiques en cours de radiothérapie guidée par l'image pour le cancer de la prostate. Nous proposons tout d'abord une approche basée population pour quantifier et analyser les incertitudes géométriques, notamment à travers des matrices de probabilité de présence de la cible en cours de traitement. Nous proposons ensuite une méthode d'optimisation des marges suivant des critères de couverture géométrique de la cible tumorale. Cette méthode permet d'obtenir des marges objectives associées aux différents types d'incertitudes géométriques et aux différentes modalités de repositionnement du patient. Dans un second temps, nous proposons une méthode d'estimation de la dose cumulée reçue localement par les tissus pendant un traitement de radiothérapie de la prostate. Cette méthode repose notamment sur une étape de recalage d'images de façon à estimer les déformations des organes entre les séances de traitement et la planification. Différentes méthodes de recalage sont proposées, suivant les informations disponibles (délinéations ou points homologues) pour contraindre la déformation estimée. De façon à évaluer les méthodes proposées au regard de l'objectif de cumul de dose, nous proposons ensuite la génération et l'utilisation d'un fantôme numérique reposant sur un modèle biomécanique des organes considérés. Les résultats de l'approche sont présentés sur ce fantôme numérique et sur données réelles. Nous montrons ainsi que l'apport de contraintes géométriques permet d'améliorer significativement la précision du cumul et que la méthode reposant sur la sélection de contraintes ponctuelles présente un bon compromis entre niveau d'interaction et précision du résultat. Enfin, nous abordons la question de l'analyse de données de populations de patients dans le but de mieux comprendre les relations entre dose délivrée localement et effets cliniques. Grâce au recalage déformable d'une population de patients sur une référence anatomique, les régions dont la dose est significativement liée aux événements de récidive sont identifiées. Il s'agit d'une étude exploratoire visant à terme à mieux exploiter l'information portée par l'intégralité de la distribution de dose, et ce en fonction du profil du cancer.This work deals with the quantification and the compensation of anatomical deformations during image-guided radiotherapy of prostate cancer. Firstly, we propose a population-based approach to quantify the geometrical uncertainties by means of coverage probability matrices of the target tumor during the treatment. We then propose a margins optimization method based on geometrical coverage criteria of the tumor target. This method provides rationnal margins models associated to the different geometrical uncertainties and patient repositioning protocols. Secondly, we propose a method to estimate the locally accumulated dose during the treatment. This method relies on a deformable image registration process in order to estimate the organ deformations between each treatment fraction and the planning. Different registration methods are proposed, using different level of user interactions (landmarks specification or delineations) to constrain the deformation estimation. In order to evaluate the performance of the proposed methods, we then describe the generation of a numerical phantom based on a biomechanical model. The results are presented for the numerical phantom and real clinical cases. We show that the benefit brought by the manual placement of some landmarks to constrain the registration represents a good compromise between the required interaction level and the dose estimation accuracy. Finally, we address the issue of the analysis of population data in order to better understand the relationship between the locally delivered dose and clinical effects. With deformable image registration of a population of patients on an anatomical template, regions whose dose is significantly associated with recurrence events are identified. This last part is an exploratory study aiming to better use the information carried by the entire distribution dose, and according to the cancer profile.RENNES1-Bibl. électronique (352382106) / SudocSudocFranceF

Hardware accelerated volume texturing.

The emergence of volume graphics, a sub field in computer graphics, has been evident for the last 15 years. Growing from scientific visualization problems, volume graphics has established itself as an important field in general computer graphics. However, the general graphics fraternity still favour the established surface graphics techniques. This is due to well founded and established techniques and a complete pipeline through software onto display hardware. This enables real-time applications to be constructed with ease and used by a wide range of end users due to the readily available graphics hardware adopted by many computer manufacturers. Volume graphics has traditionally been restricted to high-end systems due to the complexity involved with rendering volume datasets. Either specialised graphics hardware or powerful computers were required to generate images, many of these not in real-time. Although there have been specialised hardware solutions to the volume rendering problem, the adoption of the volume dataset as a primitive relies on end-users with commodity hardware being able to display images at interactive rates. The recent emergence of programmable consumer level graphics hardware is now allowing these platforms to compute volume rendering at interactive rates. Most of the work in this field is directed towards scientific visualisation. The work in this thesis addresses the issues in providing real-time volume graphics techniques to the general graphics community using commodity graphics hardware. Real-time texturing of volumetric data is explored as an important set of techniques in delivering volume datasets as a general graphics primitive. The main contributions of this work are; The introduction of efficient acceleration techniques; Interactive display of amorphous phenomena modelled outside an object defined in a volume dataset; Interactive procedural texture synthesis for volume data; 2D texturing techniques and extensions for volume data in real-time; A flexible surface detail mapping algorithm that removes many previous restrictions Parts of this work have been presented at the 4th International Workshop on Volume Graphics and also published in Volume Graphics 2005

A New Approach to the Construction of Surfaces from Contour Data

This paper presents a new approach to the construction of a surface from a stack of contour slices. Unlike most existing methods, this new approach handles ambiguous conditions consistently without employing an algorithm to establish a correspondence between vertices on one contour and those on the next. It is easy to implement and fast to compute, requiring only basic geometric properties, namely closedness and simplicity, to be available with contour data. The advantages of this new approach have also been demonstrated with solutions to a few classical problems from the literature and some practical problems in medical imaging. It can also be applied to geographical surveying and keyframe animations