Recorte volumétrico usando técnicas de interação 2D e 3D

A visualização de conjuntos de dados volumétricos é comum em diversas áreas de aplicação e há já alguns anos os diversos aspectos envolvidos nessas técnicas vêm sendo pesquisados. No entanto, apesar dos avanços das técnicas de visualização de volumes, a interação com grandes volumes de dados ainda apresenta desafios devido a questões de percepção (ou isolamento) de estruturas internas e desempenho computacional. O suporte do hardware gráfico para visualização baseada em texturas permite o desenvolvimento de técnicas eficientes de rendering que podem ser combinadas com ferramentas de recorte interativas para possibilitar a inspeção de conjuntos de dados tridimensionais. Muitos estudos abordam a otimização do desempenho de ferramentas de recorte, mas muito poucos tratam das metáforas de interação utilizadas por essas ferramentas. O objetivo deste trabalho é desenvolver ferramentas interativas, intuitivas e fáceis de usar para o recorte de imagens volumétricas. Inicialmente, é apresentado um estudo sobre as principais técnicas de visualização direta de volumes e como é feita a exploração desses volumes utilizando-se recorte volumétrico. Nesse estudo é identificada a solução que melhor se enquadra no presente trabalho para garantir a interatividade necessária. Após, são apresentadas diversas técnicas de interação existentes, suas metáforas e taxonomias, para determinar as possíveis técnicas de interação mais fáceis de serem utilizadas por ferramentas de recorte. A partir desse embasamento, este trabalho apresenta o desenvolvimento de três ferramentas de recorte genéricas implementadas usando-se duas metáforas de interação distintas que são freqüentemente utilizadas por usuários de aplicativos 3D: apontador virtual e mão virtual. A taxa de interação dessas ferramentas é obtida através de programas de fragmentos especiais executados diretamente no hardware gráfico. Estes programas especificam regiões dentro do volume a serem descartadas durante o rendering, com base em predicados geométricos. Primeiramente, o desempenho, precisão e preferência (por parte dos usuários) das ferramentas de recorte volumétrico são avaliados para comparar as metáforas de interação empregadas. Após, é avaliada a interação utilizando-se diferentes dispositivos de entrada para a manipulação do volume e ferramentas. A utilização das duas mãos ao mesmo tempo para essa manipulação também é testada. Os resultados destes experimentos de avaliação são apresentados e discutidos.

Computed tomographic-dacryocystography (CT-DCG) of the normal canine nasolacrimal drainage system with three-dimensional reconstruction

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Uso de renderização volumétrica e realidade virtual para problemas de percolação na engenharia

In the recovering process of oil, rock heterogeneity has a huge impact on how fluids move in the field, defining how much oil can be recovered. In order to study this variability, percolation theory, which describes phenomena involving geometry and connectivity are the bases, is a very useful model. Result of percolation is tridimensional data and have no physical meaning until visualized in form of images or animations. Although a lot of powerful and sophisticated visualization tools have been developed, they focus on generation of planar 2D images. In order to interpret data as they would be in the real world, virtual reality techniques using stereo images could be used. In this work we propose an interactive and helpful tool, named ZSweepVR, based on virtual reality techniques that allows a better comprehension of volumetric data generated by simulation of dynamic percolation. The developed system has the ability to render images using two different techniques: surface rendering and volume rendering. Surface rendering is accomplished by OpenGL directives and volume rendering is accomplished by the Zsweep direct volume rendering engine. In the case of volumetric rendering, we implemented an algorithm to generate stereo images. We also propose enhancements in the original percolation algorithm in order to get a better performance. We applied our developed tools to a mature field database, obtaining satisfactory results. The use of stereoscopic and volumetric images brought valuable contributions for the interpretation and clustering formation analysis in percolation, what certainly could lead to better decisions about the exploration and recovery process in oil fields

Contributo dei sistemi di fusione d'immagine mediante ecografia combinata con TAC e o RMN nella diagnosi del piccolo epatocarcinoma (< 2 cm) in pazienti con epatopatia cronica

L’ecografia è la metodica diagnostica più utilizzata come screening e follow-up nei pazienti epatopatici con o senza lesioni focali e questo grazie alle sue peculiari caratteristiche, che sono date dall’essere real-time, maneggevole, priva di radiazioni ionizzanti e con bassi costi. Tuttavia tale metodica se confrontata con la TC o la RMN, può avere importanti limiti, quali l’impossibilità di visualizzare piccole lesioni localizzate in aree anatomicamente “difficili” o in pazienti obesi, che sono già state identificate con altre tecniche, come la TC o la RMN. Per superare queste limitazioni sono stati introdotti dei sistemi di “fusione d’immagine” che consentono di sincronizzare in tempo reale una metodica real time con bassa risoluzione spaziale come l’ecografia ed una statica ad alta risoluzione come la TC o la RMN. Ciò si ottiene creando attorno al paziente un piccolo campo elettromagnetico costituito da un generatore e da un rilevatore applicato al trasduttore ecografico ed introducendo in un computer abbinato all’ecografo il “volume rendering” dell’addome del paziente ottenuto mediante TC multistrato o RM. Il preciso “ appaiamento spaziale “ delle due metodiche si ottiene individuando in entrambe lo stesso piano assiale di riferimento e almeno 3-4 punti anatomici interni. Tale sistema di fusione d’immagine potrebbe essere molto utile in campo epatologico nella diagnostica non invasiva del piccolo epatocarcinoma, che secondo le ultime linee guida, nei noduli di dimensioni fra 1 e 2 cm, richiede una concordanza nel comportamento contrastografico della lesione in almeno due tecniche d’immagine. Lo scopo del nostro lavoro è stato pertanto quello di valutare, in pazienti epatopatici, il contributo che tale sistema può dare nell’identificazione e caratterizzazione di lesioni inferiori a 20 mm, che erano già state identificate alla TC o alla RMN come noduli sospetti per HCC, ma che non erano stati visualizzati in ecografia convenzionale. L’eventuale re-identificazione con l’ecografia convenzionale dei noduli sospetti per essere HCC, può permettere di evitare, alla luce dei criteri diagnostici non invasivi un’ ulteriore tecnica d’immagine ed eventualmente la biopsia. Pazienti e Metodi: 17 pazienti cirrotici (12 Maschi; 5 Femmine), con età media di 68.9 +/- 6.2 (SD) anni, in cui la TC e la RMN con mezzo di contrasto avevano identificato 20 nuove lesioni focali epatiche, inferiori a 20 mm (13,6 +/- 3,6 mm), sospette per essere epatocarcinomi (HCC), ma non identificate all’ecografia basale (eseguita in cieco rispetto alla TC o alla RMN) sono stati sottoposti ad ecografia senza e con mezzo di contrasto, focalizzata su una zona bersaglio identificata tramite il sistema di fusione d’immagini, che visualizza simultaneamente le immagini della TC e della RMN ricostruite in modalità bidimensionale ( 2D), tridimensionale ( 3 D) e real-time. La diagnosi finale era stata stabilita attraverso la presenza di una concordanza diagnostica, secondo le linee guida internazionali o attraverso un follow-up nei casi di discordanza. Risultati: Una diagnosi non invasiva di HCC è stata raggiunta in 15/20 lesioni, inizialmente sospettate di essere HCC. Il sistema di fusione ha identificato e mostrato un comportamento contrastografico tipico in 12/15 noduli di HCC ( 80%) mentre 3/15 HCC (20%) non sono stati identificati con il sistema di fusione d’immagine. Le rimanenti 5/20 lesioni non sono state visualizzate attraverso i sistemi di fusione d’immagine ed infine giudicate come falsi positivi della TC e della RMN, poiché sono scomparse nei successivi mesi di follow-up e rispettivamente dopo tre, sei, nove, dodici e quindici mesi. Conclusioni: I nostri risultati preliminari mostrano che la combinazione del sistema di fusione dell’immagine associata all’ecografia senza e con mezzo di contrasto (CEUS), migliora il potenziale dell’ecografia nell’identificazione e caratterizzazione dell’HCC su fegato cirrotico, permettendo il raggiungimento di una diagnosi, secondo criteri non invasivi e slatentizzazndo casi di falsi positivi della TC e della RMN.

Analyse zur Auswirkung der irreversiblen Wavelet-Kompression (JPEG2000) auf CT-Bildverarbeitungs- und Darstellungsalgorithmen

Der technische Fortschritt konfrontiert die medizinische Bildgebung wie keine andere Sparte der Medizin mit einem rasanten Anstieg zu speichernder Daten. Anschaffung, Wartung und Ausbau der nötigen Infrastruktur entwickeln sich zunehmend zu einem ökonomischen Faktor. Ein Verfahren, welches diesem Trend etwas entgegensetzten könnte ist die irreversible Bilddatenkompression. Sie ist seit über 10 Jahren Gegenstand vieler Studien, deren Ergebnisse sich wiederum in Empfehlungen zum Einsatz irreversibler Kompression mehrerer nationaler und internationaler Organisation, wie CAR, DRG, RCR und ESR wiederspiegeln. Tenor dieser Empfehlungen ist, dass der Einsatz von moderater irreversibler Bilddatenkompression sicher und sinnvoll ist. Teil dieser Empfehlungen sind auch Angaben über das Maß an Kompression, ausgedrückt in Kompressionsraten, welche je nach Untersuchung und anatomischer Region als sicher anwendbar gelten und keinen diagnostisch relevanten Verlust der komprimierten Bilder erzeugen.rnVerschiedene Kompressionsalgorithmen wurden vorgeschlagen. Letztendlich haben sich vor allem die beiden weit verbreiteten Algorithmen JPEG und JPEG2000 bewährt. Letzterer erfährt in letzter Zeit zunehmen Anwendung, aufgrund seiner einfacheren Handhabung und seiner umfangreichen Zusatzfunktionen.rnAufgrund rechtlich-ethischer Bedenken hat die irreversible Kompression keine breite praktische Anwendung finden können. Dafür verantwortlich ist unter anderem auch die Unklarheit, wie sich irreversible Kompression auf Nach- und Weiterverarbeitung (sog. Postprocessing) medizinischer Bilder, wie Segmentierung, Volumetrie oder 3D-Darstellung, auswirkt. Bisherige Studien zu diesem Thema umfassen vier verschiedene Postprocessing-Algorithmen. Die untersuchten Algorithmen zeigten sich bei verlustbehafteter Kompression im Bereich der erwähnten, publizierten Kompressionsraten weitgehend unbeeinflusst. Lediglich die computergestützte Messung von Stenosegraden in der digitalen Koronarangiographie kollidiert mit den in Großbritannien geltenden Empfehlungen. Die Verwendung unterschiedlicher Kompressionsalgorithmen schränkt die allgemeinernAussagekraft dieser Studienergebnisse außerdem ein.rnZur Erweiterung der Studienlage wurden vier weitere Nach- und Weiterverarbeitungsalgorithmen auf ihre Kompressionstoleranz untersucht. Dabei wurden die Kompressionsraten von 8:1, 10:1 und 15:1 verwendet, welche um die empfohlenen Kompressionsraten von CAR, DRG, RCR und ESR liegen und so ein praxisnahes Setting bieten. Als Kompressionsalgorithmus wurde JPEG2000 verwendet, aufgrund seiner zunehmenden Nutzung in Studien sowie seiner bereits erwähnten Vorzüge in Sachen Handhabung und Zusatzfunktionen. Die vier Algorithmen umfassten das 3D-Volume rendering von CT-Angiographien der Becken-Bein-Gefäße, die Computer-assistierte Detektion von Lungenrundherden, die automatisierte Volumetrie von Leberrundherden und die funktionelle Bestimmung der Ejektionsfraktion in computertomographischen Aufnahmen des Herzens.rnAlle vier Algorithmen zeigten keinen Einfluss durch irreversibler Bilddatenkompression in denrngewählten Kompressionsraten (8:1, 10:1 und 15:1). Zusammen mit der bestehenden Literatur deuten die Ergebnisse an, dass moderate irreversible Kompression im Rahmen aktueller Empfehlungen keinen Einfluss auf Nach- und Weiterverarbeitung medizinischer Bilder hat. Eine explizitere Vorhersage zu einem bestimmten, noch nicht untersuchten Algorithmus ist jedoch aufgrund der unterschiedlichen Funktionsweisen und Programmierungen nicht sicher möglich.rnSofern ein Postprocessing Algorithmus auf komprimiertes Bildmaterial angewendet werden soll, muss dieser zunächst auf seine Kompressionstoleranz getestet werden. Dabei muss der Test eine rechtlich-ethische Grundlage für den Einsatz des Algorithmus bei komprimiertem Bildmaterial schaffen. Es sind vor allem zwei Optionen denkbar, die Testung institutsintern, eventuell unter Zuhilfenahme von vorgefertigten Bibliotheken, oder die Testung durch den Hersteller des Algorithmus.

Getting in touch-3D printing in Forensic Imaging

With the increasing use of medical imaging in forensics, as well as the technological advances in rapid prototyping, we suggest combining these techniques to generate displays of forensic findings. We used computed tomography (CT), CT angiography, magnetic resonance imaging (MRI) and surface scanning with photogrammetry in conjunction with segmentation techniques to generate 3D polygon meshes. Based on these data sets, a 3D printer created colored models of the anatomical structures. Using this technique, we could create models of bone fractures, vessels, cardiac infarctions, ruptured organs as well as bitemark wounds. The final models are anatomically accurate, fully colored representations of bones, vessels and soft tissue, and they demonstrate radiologically visible pathologies. The models are more easily understood by laypersons than volume rendering or 2D reconstructions. Therefore, they are suitable for presentations in courtrooms and for educational purposes.

Importance of 3D-CT imaging in single-bullet cranioencephalic gunshot wounds

PURPOSE: The aim of this paper is to demonstrate that computed tomography (CT) and three-dimensional (3D) CT imaging techniques can be useful tools for evaluating gunshot wounds of the skull in forensic medicine. Three purposes can be achieved: (1) identifying and recognising the bullet entrance wound - and exit wound, if present; (2) recognising the bullet's intracranial course by studying damage to bone and brain tissue; (3) suggesting hypotheses as to the dynamics of the event. MATERIALS AND METHODS: Ten cadavers of people who died of a fatal head injury caused by a single gunshot were imaged with total-body CT prior to conventional autoptic examination. Three-dimensional-CT reconstructions were obtained with the volume-rendering technique, and data were analysed by two independent observers and compared with autopsy results. RESULTS: In our experience, CT analysis and volumetric reconstruction techniques allowed the identification of the bullet entrance and exit wounds and intracranial trajectory, as well as helping to formulate a hypothesis on the extracranial trajectory to corroborate circumstantial evidence. CONCLUSIONS: CT imaging techniques are excellent tools for addressing the most important questions of forensic medicine in the case of gunshot wounds of the skull, with results as good as (or sometimes better than) traditional autoptic methods.

Extended CT scale overcomes restoration caused streak artifacts for dental identification in CT--3D color encoded automatic discrimination of dental restorations

OBJECTIVE: Besides DNA, dental radiographs play a major role in the identification of victims in mass casualties or in corpses with major postmortem alterations. Computed tomography (CT) is increasingly applied in forensic investigations and is used to scan the dentition of deceased persons within minutes. We investigated different restoration materials concerning their radiopacity in CT for dental identification purposes. METHODS: Extracted teeth with different filling materials (composite, amalgam, ceramic, temporary fillings) were CT scanned. Radiopacities of the filling materials were analyzed in extended CT scale images. RESULTS: Radiopacity values ranged from 6000-8500HU (temporary fillings), 4500-17000HU (composite fillings) and >30710HU (Amalgam and Gold). The values were used to define presets for a 3D colored volume rendering software. CONCLUSIONS: The effects of filling material caused streak artifacts could be distinctively reduced for the assessment of the dental status and a postprocessing algorithm was introduced that allows for 3D color encoded visualization and discrimination of different dental restorations based on postmortem CT data.

Grey-matter abnormalities in boys with Tourette syndrome: magnetic resonance imaging study using optimised voxel-based morphometry

The genesis of Tourette syndrome is still unknown, but a core role for the pathways of cortico-striatal-thalamic-cortical circuitry (CSTC) is supposed. Volume-rendering magnetic resonance imaging data-sets were analysed in 14 boys with Tourette syndrome and 15 age-matched controls using optimised voxel-based morphometry. Locally increased grey-matter volumes (corrected P < 0.001) were found bilaterally in the ventral putamen. Regional decreases in grey matter were observed in the left hippocampal gyrus. This unbiased analysis confirmed an association between striatal abnormalities and Tourette syndrome, and the hippocampal volume alterations indicate an involvement of temporolimbic pathways of the CSTC in the syndrome.

Ultra-high-resolution dual-source CT for forensic dental visualization-discrimination of ceramic and composite fillings

Dental identification is the most valuable method to identify human remains in single cases with major postmortem alterations as well as in mass casualties because of its practicability and demanding reliability. Computed tomography (CT) has been investigated as a supportive tool for forensic identification and has proven to be valuable. It can also scan the dentition of a deceased within minutes. In the present study, we investigated currently used restorative materials using ultra-high-resolution dual-source CT and the extended CT scale for the purpose of a color-encoded, in scale, and artifact-free visualization in 3D volume rendering. In 122 human molars, 220 cavities with 2-, 3-, 4- and 5-mm diameter were prepared. With presently used filling materials (different composites, temporary filling materials, ceramic, and liner), these cavities were restored in six teeth for each material and cavity size (exception amalgam n = 1). The teeth were CT scanned and images reconstructed using an extended CT scale. Filling materials were analyzed in terms of resulting Hounsfield units (HU) and filling size representation within the images. Varying restorative materials showed distinctively differing radiopacities allowing for CT-data-based discrimination. Particularly, ceramic and composite fillings could be differentiated. The HU values were used to generate an updated volume-rendering preset for postmortem extended CT scale data of the dentition to easily visualize the position of restorations, the shape (in scale), and the material used which is color encoded in 3D. The results provide the scientific background for the application of 3D volume rendering to visualize the human dentition for forensic identification purposes.

Heparin and cancer revisited: Mechanistic connections involving platelets, P-selectin, carcinoma mucins, and tumor metastasis

Independent studies indicate that expression of sialylated fucosylated mucins by human carcinomas portends a poor prognosis because of enhanced metastatic spread of tumor cells, that carcinoma metastasis in mice is facilitated by formation of tumor cell complexes with blood platelets, and that metastasis can be attenuated by a background of P-selectin deficiency or by treatment with heparin. The effects of heparin are not primarily due to its anticoagulant action. Other explanations have been suggested but not proven. Here, we bring together all these unexplained and seemingly disparate observations, showing that heparin treatment attenuates tumor metastasis in mice by inhibiting P-selectin-mediated interactions of platelets with carcinoma cell-surface mucin ligands. Selective removal of tumor mucin P-selectin ligands, a single heparin dose, or a background of P-selectin deficiency each reduces tumor cell-platelet interactions in vitro and in vivo. Although each of these maneuvers reduced the in vivo interactions for only a few hours, all markedly reduce long-term organ colonization by tumor cells. Three-dimensional reconstructions by using volume-rendering software show that each situation interferes with formation of the platelet “cloak” around tumor cells while permitting an increased interaction of monocytes (macrophage precursors) with the malignant cells. Finally, we show that human P-selectin is even more sensitive to heparin than mouse P-selectin, giving significant inhibition at concentrations that are in the clinically acceptable range. We suggest that heparin therapy for metastasis prevention in humans be revisited, with these mechanistic paradigms in mind.

Application of a new discreet form of Gauss’ theorem for measuring volume

Volume measurements are useful in many branches of science and medicine. They are usually accomplished by acquiring a sequence of cross sectional images through the object using an appropriate scanning modality, for example x-ray computed tomography (CT), magnetic resonance (MR) or ultrasound (US). In the cases of CT and MR, a dividing cubes algorithm can be used to describe the surface as a triangle mesh. However, such algorithms are not suitable for US data, especially when the image sequence is multiplanar (as it usually is). This problem may be overcome by manually tracing regions of interest (ROIs) on the registered multiplanar images and connecting the points into a triangular mesh. In this paper we describe and evaluate a new discreet form of Gauss’ theorem which enables the calculation of the volume of any enclosed surface described by a triangular mesh. The volume is calculated by summing the vector product of the centroid, area and normal of each surface triangle. The algorithm was tested on computer-generated objects, US-scanned balloons, livers and kidneys and CT-scanned clay rocks. The results, expressed as the mean percentage difference ± one standard deviation were 1.2 ± 2.3, 5.5 ± 4.7, 3.0 ± 3.2 and −1.2 ± 3.2% for balloons, livers, kidneys and rocks respectively. The results compare favourably with other volume estimation methods such as planimetry and tetrahedral decomposition.

Non-photorealistic rendering of virtual implant models for computer-assisted fluoroscopy-based surgical procedures

Surgical navigation systems visualize the positions and orientations of surgical instruments and implants as graphical overlays onto a medical image of the operated anatomy on a computer monitor. The orthopaedic surgical navigation systems could be categorized according to the image modalities that are used for the visualization of surgical action. In the so-called CT-based systems or 'surgeon-defined anatomy' based systems, where a 3D volume or surface representation of the operated anatomy could be constructed from the preoperatively acquired tomographic data or through intraoperatively digitized anatomy landmarks, a photorealistic rendering of the surgical action has been identified to greatly improve usability of these navigation systems. However, this may not hold true when the virtual representation of surgical instruments and implants is superimposed onto 2D projection images in a fluoroscopy-based navigation system due to the so-called image occlusion problem. Image occlusion occurs when the field of view of the fluoroscopic image is occupied by the virtual representation of surgical implants or instruments. In these situations, the surgeon may miss part of the image details, even if transparency and/or wire-frame rendering is used. In this paper, we propose to use non-photorealistic rendering to overcome this difficulty. Laboratory testing results on foamed plastic bones during various computer-assisted fluoroscopybased surgical procedures including total hip arthroplasty and long bone fracture reduction and osteosynthesis are shown.

Volume Haptics and Dendritic Spine Editing

Esta tesis se ha desarrollado en el contexto del proyecto Cajal Blue Brain, una iniciativa europea dedicada al estudio del cerebro. Uno de los objetivos de esta iniciativa es desarrollar nuevos métodos y nuevas tecnologías que simplifiquen el análisis de datos en el campo neurocientífico. El presente trabajo se ha centrado en diseñar herramientas que combinen información proveniente de distintos canales sensoriales con el fin de acelerar la interacción y análisis de imágenes neurocientíficas. En concreto se estudiará la posibilidad de combinar información visual con información háptica. Las espinas dendríticas son pequeñas protuberancias que recubren la superficie dendrítica de muchas neuronas del cerebro. A día de hoy, se cree que tienen un papel clave en la transmisión de señales neuronales. Motivo por el cual, el interés por parte de la comunidad científica por estas estructuras ha ido en aumento a medida que las técnicas de adquisición de imágenes mejoraban hasta alcanzar una calidad suficiente para analizar dichas estructuras. A menudo, los neurocientíficos utilizan técnicas de microscopía con luz para obtener los datos que les permitan analizar estructuras neuronales tales como neuronas, dendritas y espinas dendríticas. A pesar de que estas técnicas ofrezcan ciertas ventajas frente a su equivalente electrónico, las técnicas basadas en luz permiten una menor resolución. En particular, estructuras pequeñas como las espinas dendríticas pueden capturarse de forma incorrecta en las imágenes obtenidas, impidiendo su análisis. En este trabajo, se presenta una nueva técnica, que permite editar imágenes volumétricas, mediante un dispositivo háptico, con el fin de reconstruir de los cuellos de las espinas dendríticas. Con este objetivo, en un primer momento se desarrolló un algoritmo que proporciona retroalimentación háptica en datos volumétricos, completando la información que provine del canal visual. Dicho algoritmo de renderizado háptico permite a los usuarios tocar y percibir una isosuperficie en el volumen de datos. El algoritmo asegura un renderizado robusto y eficiente. Se utiliza un método basado en las técnicas de “marching tetrahedra” para la extracción local de una isosuperficie continua, lineal y definida por intervalos. La robustez deriva tanto de una etapa de detección de colisiones continua de la isosuperficie extraída, como del uso de técnicas eficientes de renderizado basadas en un proxy puntual. El método de “marching tetrahedra” propuesto garantiza que la topología de la isosuperficie extraída coincida con la topología de una isosuperficie equivalente determinada utilizando una interpolación trilineal. Además, con el objetivo de mejorar la coherencia entre la información háptica y la información visual, el algoritmo de renderizado háptico calcula un segundo proxy en la isosuperficie pintada en la pantalla. En este trabajo se demuestra experimentalmente las mejoras en, primero, la etapa de extracción de isosuperficie, segundo, la robustez a la hora de mantener el proxy en la isosuperficie deseada y finalmente la eficiencia del algoritmo. En segundo lugar, a partir del algoritmo de renderizado háptico propuesto, se desarrolló un procedimiento, en cuatro etapas, para la reconstrucción de espinas dendríticas. Este procedimiento, se puede integrar en los cauces de segmentación automática y semiautomática existentes como una etapa de pre-proceso previa. El procedimiento está diseñando para que tanto la navegación como el proceso de edición en sí mismo estén controlados utilizando un dispositivo háptico. Se han diseñado dos experimentos para evaluar esta técnica. El primero evalúa la aportación de la retroalimentación háptica y el segundo se centra en evaluar la idoneidad del uso de un háptico como dispositivo de entrada. En ambos casos, los resultados demuestran que nuestro procedimiento mejora la precisión de la reconstrucción. En este trabajo se describen también dos casos de uso de nuestro procedimiento en el ámbito de la neurociencia: el primero aplicado a neuronas situadas en la corteza cerebral humana y el segundo aplicado a espinas dendríticas situadas a lo largo de neuronas piramidales de la corteza del cerebro de una rata. Por último, presentamos el programa, Neuro Haptic Editor, desarrollado a lo largo de esta tesis junto con los diferentes algoritmos ya mencionados. ABSTRACT This thesis took place within the Cajal Blue Brain project, a European initiative dedicated to the study of the brain. One of the main goals of this project is the development of new methods and technologies simplifying data analysis in neuroscience. This thesis focused on the development of tools combining information originating from distinct sensory channels with the aim of accelerating both the interaction with neuroscience images and their analysis. In concrete terms, the objective is to study the possibility of combining visual information with haptic information. Dendritic spines are thin protrusions that cover the dendritic surface of numerous neurons in the brain and whose function seems to play a key role in neural circuits. The interest of the neuroscience community toward those structures kept increasing as and when acquisition methods improved, eventually to the point that the produced datasets enabled their analysis. Quite often, neuroscientists use light microscopy techniques to produce the dataset that will allow them to analyse neuronal structures such as neurons, dendrites and dendritic spines. While offering some advantages compared to their electronic counterpart, light microscopy techniques achieve lower resolutions. Particularly, small structures such as dendritic spines might suffer from a very low level of fluorescence in the final dataset, preventing further analysis. This thesis introduces a new technique enabling the edition of volumetric datasets in order to recreate dendritic spine necks using a haptic device. In order to fulfil this objective, we first presented an algorithm to provide haptic feedback directly from volumetric datasets, as an aid to regular visualization. The haptic rendering algorithm lets users perceive isosurfaces in volumetric datasets, and it relies on several design features that ensure a robust and efficient rendering. A marching tetrahedra approach enables the dynamic extraction of a piecewise linear continuous isosurface. Robustness is derived using a Continuous Collision Detection step coupled with acknowledged proxy-based rendering methods over the extracted isosurface. The introduced marching tetrahedra approach guarantees that the extracted isosurface will match the topology of an equivalent isosurface computed using trilinear interpolation. The proposed haptic rendering algorithm improves the coherence between haptic and visual cues computing a second proxy on the isosurface displayed on screen. Three experiments demonstrate the improvements on the isosurface extraction stage as well as the robustness and the efficiency of the complete algorithm. We then introduce our four-steps procedure for the complete reconstruction of dendritic spines. Based on our haptic rendering algorithm, this procedure is intended to work as an image processing stage before the automatic segmentation step giving the final representation of the dendritic spines. The procedure is designed to allow both the navigation and the volume image editing to be carried out using a haptic device. We evaluated our procedure through two experiments. The first experiment concerns the benefits of the force feedback and the second checks the suitability of the use of a haptic device as input. In both cases, the results shows that the procedure improves the editing accuracy. We also report two concrete cases where our procedure was employed in the neuroscience field, the first one concerning dendritic spines in the human cortex, the second one referring to an ongoing experiment studying dendritic spines along dendrites of mouse cortical pyramidal neurons. Finally, we present the software program, Neuro Haptic Editor, that was built along the development of the different algorithms implemented during this thesis, and used by neuroscientists to use our procedure.

A novel 3-D segmentation algorithm for anatomic liver and tumor volume calculations for liver cancer treatment planning

Three-Dimensional (3-D) imaging is vital in computer-assisted surgical planning including minimal invasive surgery, targeted drug delivery, and tumor resection. Selective Internal Radiation Therapy (SIRT) is a liver directed radiation therapy for the treatment of liver cancer. Accurate calculation of anatomical liver and tumor volumes are essential for the determination of the tumor to normal liver ratio and for the calculation of the dose of Y-90 microspheres that will result in high concentration of the radiation in the tumor region as compared to nearby healthy tissue. Present manual techniques for segmentation of the liver from Computed Tomography (CT) tend to be tedious and greatly dependent on the skill of the technician/doctor performing the task. ^ This dissertation presents the development and implementation of a fully integrated algorithm for 3-D liver and tumor segmentation from tri-phase CT that yield highly accurate estimations of the respective volumes of the liver and tumor(s). The algorithm as designed requires minimal human intervention without compromising the accuracy of the segmentation results. Embedded within this algorithm is an effective method for extracting blood vessels that feed the tumor(s) in order to plan effectively the appropriate treatment. ^ Segmentation of the liver led to an accuracy in excess of 95% in estimating liver volumes in 20 datasets in comparison to the manual gold standard volumes. In a similar comparison, tumor segmentation exhibited an accuracy of 86% in estimating tumor(s) volume(s). Qualitative results of the blood vessel segmentation algorithm demonstrated the effectiveness of the algorithm in extracting and rendering the vasculature structure of the liver. Results of the parallel computing process, using a single workstation, showed a 78% gain. Also, statistical analysis carried out to determine if the manual initialization has any impact on the accuracy showed user initialization independence in the results. ^ The dissertation thus provides a complete 3-D solution towards liver cancer treatment planning with the opportunity to extract, visualize and quantify the needed statistics for liver cancer treatment. Since SIRT requires highly accurate calculation of the liver and tumor volumes, this new method provides an effective and computationally efficient process required of such challenging clinical requirements.^