CAPES / Este trabalho apresenta a adaptação do código Geant4 para conversão de imagens DICOM (Digital Imaging and Communications in Medicine) de crânio, obtidas em tomografia convencional (CT), em um phantom antropomórfico virtual. O trabalho foi baseado no exemplo médico denominado “Código Dicom”, disponibilizado pelos desenvolvedores do código Geant4. Durante a execução do trabalho foram feitas reestruturações no exemplo “Código Dicom” para a conversão direta de imagens tomográficas em um phantom virtual. Foram retirados do código todos os passos referentes aos eventos físicos nucleares. Foi reformulado o arquivo DicomHandler.cc para não realizar a compressão dos pixels da imagem de CT. Em seguida foi realizada a conversão direta de imagens tomográficas, de um phantom físico de polietileno (PEAD) com núcleo central de acrílico e de um crânio real humano, em phantoms virtuais para o código Geant4. Os resultados demonstraram que com este código é possível a reconstrução de áreas anatômicas com geometrias complexas, partindo do uso de imagens tomográficas reais. / This work presents the adaptation of the Geant4 code for converting DICOM (Digital Imaging and Communications in Medicine) images of a skull, obtained in conventional tomography (CT), into a virtual anthropomorphic phantom. The work was based on the medical example named "Dicom Code" provided by the developers of the code Geant4. During the execution, restructurings using the "Dicom Code" example were made to achieve the direct conversion of tomographic images into a virtual phantom. All the steps referring to nuclear physical events were removed. The file DicomHandler.cc was reformulated in order to avoid the pixels compression of the CT image. The CT images of a physical polyethylene (PEAD) phantom with acrylic core and a real human skull were then converted into virtual phantoms for the code Geant4. The results showed that with this code, it may be possible the reconstruction of anatomical areas with complex geometries, based on the use of real tomographic images.

Este trabalho apresenta o desenvolvimento de um estimulador galvânico vestibular para ser usado em experimentos de imageamento por ressonância magnética funcional (fMRI). Em experiências de fMRI é necessário a produção de estímulos somatossensoriais no paciente. Os estímulos devem ser sincronizados com a sequência de pulsos da fMRI. O estimulador foi dividido em circuitos analógicos (colocados dentro da sala do magneto) e circuitos digitais (sala de comando do sistema de MRI). A comunicação entre os circuitos é feita através de fibra óptica. Experimentos de fMRI realizados com voluntários demonstraram que o estimulador proposto é capaz de manter a sincronização com sistema de fMRI e pode ser usado para localizar as áreas do cérebro que são ativados pelo sistema vestibular. / This work presents the development of a galvanic vestibular stimulator to be used in functional magnetic resonance imaging experiments (fMRI). In fMRI experiments it is required the production of somatosensory stimuli in the patient must be sincronized with the fMRI pulse sequence. The stimulator circuits were divided in analog circuits (placed within the magnet room) and digital circuits (placed in the MRI command room). The communication between the circuits is made through optical fiber. fMRI experiments performed with volunteers demonstrated that the proposed stimulator is able to keep the sincronization with the MRI system and can be used to locate the brain areas that are activated by the vestibular system.

CAPES / Este trabalho apresenta a adaptação do código Geant4 para conversão de imagens DICOM (Digital Imaging and Communications in Medicine) de crânio, obtidas em tomografia convencional (CT), em um phantom antropomórfico virtual. O trabalho foi baseado no exemplo médico denominado “Código Dicom”, disponibilizado pelos desenvolvedores do código Geant4. Durante a execução do trabalho foram feitas reestruturações no exemplo “Código Dicom” para a conversão direta de imagens tomográficas em um phantom virtual. Foram retirados do código todos os passos referentes aos eventos físicos nucleares. Foi reformulado o arquivo DicomHandler.cc para não realizar a compressão dos pixels da imagem de CT. Em seguida foi realizada a conversão direta de imagens tomográficas, de um phantom físico de polietileno (PEAD) com núcleo central de acrílico e de um crânio real humano, em phantoms virtuais para o código Geant4. Os resultados demonstraram que com este código é possível a reconstrução de áreas anatômicas com geometrias complexas, partindo do uso de imagens tomográficas reais. / This work presents the adaptation of the Geant4 code for converting DICOM (Digital Imaging and Communications in Medicine) images of a skull, obtained in conventional tomography (CT), into a virtual anthropomorphic phantom. The work was based on the medical example named "Dicom Code" provided by the developers of the code Geant4. During the execution, restructurings using the "Dicom Code" example were made to achieve the direct conversion of tomographic images into a virtual phantom. All the steps referring to nuclear physical events were removed. The file DicomHandler.cc was reformulated in order to avoid the pixels compression of the CT image. The CT images of a physical polyethylene (PEAD) phantom with acrylic core and a real human skull were then converted into virtual phantoms for the code Geant4. The results showed that with this code, it may be possible the reconstruction of anatomical areas with complex geometries, based on the use of real tomographic images.

Made available in DSpace on 2014-10-09T12:41:04Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:10:03Z (GMT). No. of bitstreams: 1 04674.pdf: 2960498 bytes, checksum: 31da12ce5904c3db2729e9982663d7fe (MD5) / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2014-11-10T10:59:52Z No. of bitstreams: 0 / Made available in DSpace on 2014-11-10T10:59:52Z (GMT). No. of bitstreams: 0 / Sendo o método mais preciso para estimar a dose absorvida em radioterapia, o Método de Monte Carlo (MMC) tem sido amplamente utilizado no planejamento de tratamento radioterápico. No entanto, a sua eciência pode ser melhorada para aplicações clínicas de rotina. Nesta dissertação é apresentado o código CUBMC, um código de Monte Carlo que simula o transporte de fótons para cálculo de dose, desenvolvido na plataforma CUDA (Compute Unified Device Architecture). A simulação de eventos físicos é baseada no algoritmo presente no código PENELOPE, e as tabelas de seção de choque utilizadas são geradas pela rotina MATERIAL, também presente no código PENELOPE. Os fótons são transportados em objetos simuladores descritos por voxels. Existem duas abordagens distintas utilizadas para a simulação. A primeira delas obriga o fóton a realizar uma parada toda vez que cruza a fronteira de um voxel, a segunda e pelo Método de Woodcock, onde o fóton ignora a existência de fronteiras e é transportado em um meio homogêneo fictício. O código CUBMC tem como objetivo ser uma opção de código simulador que, ao utilizar a capacidade de processamento paralelo de unidades de processamento gráfico (GPU), apresente alto desempenho em máquinas compactas e de baixo custo, podendo assim ser aplicado em casos clínicos e incorporado a sistemas de planejamento de tratamento em radioterapia. / Dissertação (Mestrado em Tecnologia Nuclear) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Submitted by Pedro Silva Filho (pfsilva@ipen.br) on 2017-11-16T18:08:36Z No. of bitstreams: 0 / Made available in DSpace on 2017-11-16T18:08:36Z (GMT). No. of bitstreams: 0 / O propósito de um objeto simulador é representar a alteração do campo de radiação provocada pela absorção e espalhamento em um dado tecido ou órgão de interesse. Suas características geométricas e de composição devem estar próximos o máximo possível aos valores associados ao seu análogo natural. Estruturas anatômicas podem ser transformadas em objetos virtuais 3D por técnicas de imageamento médico (p. ex. Tomografia Computadorizada) e impressas por prototipagem rápida utilizando materiais como, por exemplo, o ácido poliláctico. Sua produção para pacientes específicos requer o preenchimento de requisitos como a acurácia geométrica com a anatomia do individuo e a equivalência ao tecido, de modo que se possa realizar medidas utilizáveis, e ser insensível aos efeitos da radiação. O objetivo desse trabalho foi avaliar o comportamento de materiais impressos 3D quando expostos a feixes de fótons diversos, com ênfase para a qualidade de radiotherapia (6 MV), visando a sua aplicação na dosimetria clínica. Para isso foram usados 30 dosímetros termoluminescentes de LiF:Mg,Ti. Foi analisada também a equivalência entre o PMMA e o PLA impresso para a resposta termoluminescente de 30 dosímetros de CaSO4:Dy. As irradiações com feixes de fótons com qualidade de radioterapia foram simuladas com o uso do sistema de planejamento Eclipse™, com o Anisotropic Analytical Algorithm e o Acuros&reg XB Advanced Dose Calculation algorithm. Além do uso do Eclipse™ e dos testes dosimétricos, foram realizadas simulações computacionais utilizando o código MCNP5. As simulações com o código MCNP5 foram realizadas para calcular o coeficiente de atenuação de placas impressas expostas a diversas qualidades de raios X de radiodiagnóstico e para desenvolver um modelo computacional de placas impressas 3D. / Dissertação (Mestrado em Tecnologia Nuclear) / IPEN/D / Instituto de Pesquisas Energéticas e Nucleares - IPEN-CNEN/SP

Dans le domaine de la radiobiologie, les dommages causés à l'ADN nucléaire sont largement étudiés puisque l’ADN est considéré la cible la plus sensible dans la cellule. En plus de l’ADN, les mitochondries commencent à attirer l'attention comme des cibles sensibles, car elles contrôlent de nombreuses fonctions importantes pour la survie de la cellule. Ce sont des organites à double membranes principalement chargées de la production d'énergie ainsi que la régulation réactive des espèces d'oxygène, la signalisation cellulaire et le contrôle de l'apoptose. Certaines expériences ont montré qu'après exposition aux rayonnements ionisants, les teneurs mitochondriales sont modifiées et leurs fonctions sont affectées. C'est pourquoi nous sommes intéressés par l'étude des effets des rayonnements ionisants sur les mitochondries. À l'échelle microscopique, les simulations Monte-Carlo sont utiles pour reproduire les traces de particules ionisantes pour une étude approfondie. Par conséquent, nous avons produit des fantômes 3D de mitochondries à partir d'images microscopiques de cellules fibroblastiques. Ces fantômes ont été transformés de façon à être téléchargés dans Geant4 sous forme de mailles tessélisées et tétraédriques remplies d'eau représentant la géométrie réaliste de ces organites. Les simulations numériques ont été effectuées afin de calculer les dépôts d’énergie induits par des photons de 250 keV à l'intérieur de ces fantômes. Les processus électromagnétiques Geant4-DNA sont utilisés pour simuler les traces des électrons secondaires produits. Étant donné que les dommages groupés sont plus difficiles à réparer par les cellules, un algorithme spécifique est utilisé pour étudier le regroupement spatial des dégâts potentiels des rayonnements. En radiothérapie, il est difficile de donner une dose efficace aux sites de la tumeur sans affecter les tissus environnants sains. L'utilisation de nanoparticules d'or comme radio-sensibilisateurs semble être prometteuse. Leur coefficient d'absorption élevé augmente la probabilité d’interaction des photons et induit une dose tumorale plus importante lorsque ces particules sont absorbés de manière préférentielle dans les tumeurs. Puisque l'or a un nombre atomique élevé, les électrons Auger sont produits en abondance. Ces électrons ont une portée plus faible que les photoélectrons, ce qui leur permet de déposer la majeure partie de leur énergie près de la nanoparticule, ce qui augmente la dose locale. Nous avons étudié l'effet radio-sensibilisant des nanoparticules d'or sur le fantôme des mitochondries. L'efficacité de cette méthode dépend du nombre, de la taille et de la répartition spatiale des nanoparticules d'or. Après exposition aux rayonnements ionisants, des espèces réactives d'oxygène sont produites dans le milieu biologique qui contient une quantité d'eau abondante. Dans cette étude, nous simulons les espèces chimiques produites à l'intérieur du fantôme des mitochondries et leur regroupement est estimé. La distribution spatiale des produits chimiques et leur évolution avec le temps et par la suite analysée au moyen d’algorithme spécifique de traitement de données. / In the field of radiobiology, damage to nuclear DNA is extensively studied since it is considered as a sensitive target inside cells. Mitochondria are starting to get some attention as sensitive targets as well since they control many functions important to the cell’s survival. They are double membraned organelles mainly in charge of energy production as well as reactive oxygen species regulation, cell signaling and apoptosis control. Some experiments have shown that after exposure to ionizing radiation the mitochondrial contents are altered and their functions are affected. That is why we are interested in studying the effects of ionizing radiation on mitochondria. At the microscopic scale, Monte Carlo simulations are helpful in reproducing the tracks of ionizing particles for a close study. Therefore, we produced 3D phantoms of mitochondria starting from microscopic images of fibroblast cells. These phantoms are easily uploaded into Geant4 as tessellated and tetrahedral meshes filled with water representing the realistic geometry of these organelles. Microdosimetric analysis is performed to deposited energy by 250keV photons inside these phantoms. The Geant4-DNA electromagnetic processes are used to simulate the tracking of the produced secondary electrons. Since clustered damages are harder to repair by cells, a clustering algorithm is used to study the spatial clustering of potential radiation damages. In radiotherapy, it is a challenge to deliver an efficient dose to the tumor sites without affecting healthy surrounding tissues. The use of gold nanoparticles as radio-sensitizers seems to be promising. Their high photon absorption coefficient compared to tissues deposit a larger dose when they are preferentially absorbed in tumors. Since gold has a high atomic number, Auger electrons are produced abundantly. These electrons have lower range than photoelectrons enabling them to deposit most of their energy near the nanoparticle and thus increasing the local dose. We studied the radio-sensitizing effect of gold nanoparticles on the mitochondria phantom. The effectiveness of this method is dependent on the number, size and spatial distribution of gold nanoparticles. After exposure to ionizing radiation, reactive oxygen species are produced in the biological material that contains abundant amount of water. In this study, we simulate the chemical species produced inside the mitochondria phantom and their clustering is estimated. We take advantage of the Geant4-DNA chemistry processes libraries that is recently included in the Geant4.10.1 release to simulate the spatial distribution of the chemicals and their evolution with time.

L'objectif de cette thèse concerne l'association de deux techniques de mesure dans le cadre de la caractérisation in vivo de la peau. La première, nommée Spectroscopie de Réflectance Diffuse (DRS), permet la caractérisation des paramètres optiques de la peau analysée et quantifie les phénomènes d'absorption et de diffusion de la lumière. La deuxième est la microspectroscopie Raman. Elle fournit une identification chimique des composés analysés sans marquage. L'objet de cette thèse est d'évaluer l'effet de l'interaction lumière-matière sur les capacités de localisation et de quantification de la microspectroscopie Raman, lesquelles sont dégradées dans un milieu diffusant tel que la peau. Une approche in vivo bimodale (DRS et Raman) est proposée pour la caractérisation biochimique quantitative des tissus cutanés avec l'idée d'établir un protocole de correction des spectres Raman acquis, en exploitant les propriétés optiques fournies par la DRS. Elle est décomposée en trois axes de travail complémentaires : le développement d'une instrumentation DRS permettant la mesure des spectres de réflectance diffuse et le calcul des propriétés optiques dans la zone sondée par la spectroscopie Raman ; le développement de fantômes optiques permettant une compréhension expérimentale des phénomènes d'absorption, de diffusion élastique et de diffusion Raman; le développement d'un protocole de correction des spectres Raman à partir des propriétés optiques obtenues par DRS. / This thesis relates to the combination of two in vivo skin characterization techniques. On the one hand, Diffuse Reflectance Spectroscopy (DRS) enables skin optical properties characterization by quantifying light absorption and light elastic scattering. On the other hand, Raman microspectroscopy provides information on molecular compositions of tissues with no need of labeling. Localization and quantification functions of Raman microspectroscopy are both distorted in scattering media such as skin. Therefore, the aim of this thesis was to assess the effect of light-matter interactions on these functions. A bimodal method is proposed to achieve quantitative biochemical characterization of cutaneous tissues in vivo. The main idea is to develop a procedure of Raman spectra correction based on the quantified optical properties provided by DRS. This work was divided in three complementary approaches: the development of a system enabling diffuse reflectance and optical properties measurements in the same zone as Raman microspectroscopy; the fabrication of optical phantoms improving our knowledge on absorption, elastic scattering and Raman scattering phenomena; and the development of a Raman spectra correction model as function of the skin optical properties given by DRS measurements.

The thesis deals with LSCI (Laser Speckle Contrast Imaging), an optical method utilizing laser speckle contrast for the estimation of blood flow changes. LSCI is non-invasive and technically not demanding approach, capabilities of which have not yet been fully exploited. The literature review part contains detailed description of the operating principle, imaging techniques, potential for medical applications with considering the limiting factors. The main aim of the thesis is to design and construct a complete LSCI system including appropriate phantoms able to simulate blood flow through the tissue. Imaging algorithms for the obtained data evaluation were implemented in Matlab® development enviroment. Finally, the created system was tested using different acquisition parameters as well as varying the image processing schemes. The resulting qualitative flow images were subsequently discussed and confronted with the theoretical assumptions.

Medical micromotors have the potential to lead to a paradigm shift in future biomedicine, as they may perform active drug delivery, microsurgery, tissue engineering, or assisted fertilization in a minimally invasive manner. However, the translation to clinical treatment is challenging, as many applications of single or few micromotors require real-time tracking and control at high spatiotemporal resolution in deep tissue. Although optical techniques are a popular choice for this task, absorption and strong light scattering lead to a pronounced decrease of the signal-to-noise ratio with increasing penetration depth. Here, a highly reflective micromotor is introduced which reflects more than tenfold the light intensity of simple gold particles and can be precisely navigated by external magnetic fields. A customized optical IR imaging setup and an image correlation technique are implemented to track single micromotors in real-time and label-free underneath phantom and ex vivo mouse skull tissues. As a potential application, the micromotors speed is recorded when moving through different viscous fluids to determine the viscosity of diverse physiological fluids toward remote cardiovascular disease diagnosis. Moreover, the micromotors are loaded with a model drug to demonstrate their cargotransport capability. The proposed reflective micromotor is suitable as theranostic tool for sub-skin or organ-on-a-chip applications.