Segmentation of Calculi from Ultrasound Kidney Images by Region Indictor with Contour Segmentation Method

In this proposed Region Indicator with Contour Segmentation (RICS) method, five major steps are followed to select the exact calculi region from the renal calculi images. In the first and second stage, the region indices library and renal calculi region parameters are computed. After that, the image contrast is enhanced by the Histogram Equalization and the most interested pixel values of enhanced image are selected by the k-means clustering. The most interested pixel values are utilized to find the accurate calculi from the renal images. In the final stage, a number of regions are selected based on the contour process. Subsequently, pixel matching and sequence of thresholding process are performed to find the calculi. In addition, the usage of ANFIS in supervised learning has made the technique more efficient than the previous techniques. Here, the utilization of contour reduces the relative error in between the Expert radiologist and the segmented calculi, which are obtained from the proposed algorithm. Thus, the obtained error is minimized that leads to high efficiency. The implementation result shows the effectiveness of the proposed RICS segmentation method in segmenting the renal calculi in terms of sensitivity and specificity. And also, the proposed method improves the calculi area detection accuracy with reduced in computational time

Navigation system based in motion tracking sensor for percutaneous renal access

Tese de Doutoramento em Engenharia BiomédicaMinimally-invasive kidney interventions are daily performed to diagnose and treat several renal diseases. Percutaneous renal access (PRA) is an essential but challenging stage for most of these procedures, since its outcome is directly linked to the physician’s ability to precisely visualize and reach the anatomical target. Nowadays, PRA is always guided with medical imaging assistance, most frequently using X-ray based imaging (e.g. fluoroscopy). Thus, radiation on the surgical theater represents a major risk to the medical team, where its exclusion from PRA has a direct impact diminishing the dose exposure on both patients and physicians. To solve the referred problems this thesis aims to develop a new hardware/software framework to intuitively and safely guide the surgeon during PRA planning and puncturing. In terms of surgical planning, a set of methodologies were developed to increase the certainty of reaching a specific target inside the kidney. The most relevant abdominal structures for PRA were automatically clustered into different 3D volumes. For that, primitive volumes were merged as a local optimization problem using the minimum description length principle and image statistical properties. A multi-volume Ray Cast method was then used to highlight each segmented volume. Results show that it is possible to detect all abdominal structures surrounding the kidney, with the ability to correctly estimate a virtual trajectory. Concerning the percutaneous puncturing stage, either an electromagnetic or optical solution were developed and tested in multiple in vitro, in vivo and ex vivo trials. The optical tracking solution aids in establishing the desired puncture site and choosing the best virtual puncture trajectory. However, this system required a line of sight to different optical markers placed at the needle base, limiting the accuracy when tracking inside the human body. Results show that the needle tip can deflect from its initial straight line trajectory with an error higher than 3 mm. Moreover, a complex registration procedure and initial setup is needed. On the other hand, a real-time electromagnetic tracking was developed. Hereto, a catheter was inserted trans-urethrally towards the renal target. This catheter has a position and orientation electromagnetic sensor on its tip that function as a real-time target locator. Then, a needle integrating a similar sensor is used. From the data provided by both sensors, one computes a virtual puncture trajectory, which is displayed in a 3D visualization software. In vivo tests showed a median renal and ureteral puncture times of 19 and 51 seconds, respectively (range 14 to 45 and 45 to 67 seconds). Such results represent a puncture time improvement between 75% and 85% when comparing to state of the art methods. 3D sound and vibrotactile feedback were also developed to provide additional information about the needle orientation. By using these kind of feedback, it was verified that the surgeon tends to follow a virtual puncture trajectory with a reduced amount of deviations from the ideal trajectory, being able to anticipate any movement even without looking to a monitor. Best results show that 3D sound sources were correctly identified 79.2 ± 8.1% of times with an average angulation error of 10.4º degrees. Vibration sources were accurately identified 91.1 ± 3.6% of times with an average angulation error of 8.0º degrees. Additionally to the EMT framework, three circular ultrasound transducers were built with a needle working channel. One explored different manufacture fabrication setups in terms of the piezoelectric materials, transducer construction, single vs. multi array configurations, backing and matching material design. The A-scan signals retrieved from each transducer were filtered and processed to automatically detect reflected echoes and to alert the surgeon when undesirable anatomical structures are in between the puncture path. The transducers were mapped in a water tank and tested in a study involving 45 phantoms. Results showed that the beam cross-sectional area oscillates around the ceramics radius and it was possible to automatically detect echo signals in phantoms with length higher than 80 mm. Hereupon, it is expected that the introduction of the proposed system on the PRA procedure, will allow to guide the surgeon through the optimal path towards the precise kidney target, increasing surgeon’s confidence and reducing complications (e.g. organ perforation) during PRA. Moreover, the developed framework has the potential to make the PRA free of radiation for both patient and surgeon and to broad the use of PRA to less specialized surgeons.Intervenções renais minimamente invasivas são realizadas diariamente para o tratamento e diagnóstico de várias doenças renais. O acesso renal percutâneo (ARP) é uma etapa essencial e desafiante na maior parte destes procedimentos. O seu resultado encontra-se diretamente relacionado com a capacidade do cirurgião visualizar e atingir com precisão o alvo anatómico. Hoje em dia, o ARP é sempre guiado com recurso a sistemas imagiológicos, na maior parte das vezes baseados em raios-X (p.e. a fluoroscopia). A radiação destes sistemas nas salas cirúrgicas representa um grande risco para a equipa médica, aonde a sua remoção levará a um impacto direto na diminuição da dose exposta aos pacientes e cirurgiões. De modo a resolver os problemas existentes, esta tese tem como objetivo o desenvolvimento de uma framework de hardware/software que permita, de forma intuitiva e segura, guiar o cirurgião durante o planeamento e punção do ARP. Em termos de planeamento, foi desenvolvido um conjunto de metodologias de modo a aumentar a eficácia com que o alvo anatómico é alcançado. As estruturas abdominais mais relevantes para o procedimento de ARP, foram automaticamente agrupadas em volumes 3D, através de um problema de optimização global com base no princípio de “minimum description length” e propriedades estatísticas da imagem. Por fim, um procedimento de Ray Cast, com múltiplas funções de transferência, foi utilizado para enfatizar as estruturas segmentadas. Os resultados mostram que é possível detetar todas as estruturas abdominais envolventes ao rim, com a capacidade para estimar corretamente uma trajetória virtual. No que diz respeito à fase de punção percutânea, foram testadas duas soluções de deteção de movimento (ótica e eletromagnética) em múltiplos ensaios in vitro, in vivo e ex vivo. A solução baseada em sensores óticos ajudou no cálculo do melhor ponto de punção e na definição da melhor trajetória a seguir. Contudo, este sistema necessita de uma linha de visão com diferentes marcadores óticos acoplados à base da agulha, limitando a precisão com que a agulha é detetada no interior do corpo humano. Os resultados indicam que a agulha pode sofrer deflexões à medida que vai sendo inserida, com erros superiores a 3 mm. Por outro lado, foi desenvolvida e testada uma solução com base em sensores eletromagnéticos. Para tal, um cateter que integra um sensor de posição e orientação na sua ponta, foi colocado por via trans-uretral junto do alvo renal. De seguida, uma agulha, integrando um sensor semelhante, é utilizada para a punção percutânea. A partir da diferença espacial de ambos os sensores, é possível gerar uma trajetória de punção virtual. A mediana do tempo necessário para puncionar o rim e ureter, segundo esta trajetória, foi de 19 e 51 segundos, respetivamente (variações de 14 a 45 e 45 a 67 segundos). Estes resultados representam uma melhoria do tempo de punção entre 75% e 85%, quando comparados com o estado da arte dos métodos atuais. Além do feedback visual, som 3D e feedback vibratório foram explorados de modo a fornecer informações complementares da posição da agulha. Verificou-se que com este tipo de feedback, o cirurgião tende a seguir uma trajetória de punção com desvios mínimos, sendo igualmente capaz de antecipar qualquer movimento, mesmo sem olhar para o monitor. Fontes de som e vibração podem ser corretamente detetadas em 79,2 ± 8,1% e 91,1 ± 3,6%, com erros médios de angulação de 10.4º e 8.0 graus, respetivamente. Adicionalmente ao sistema de navegação, foram também produzidos três transdutores de ultrassom circulares com um canal de trabalho para a agulha. Para tal, foram exploradas diferentes configurações de fabricação em termos de materiais piezoelétricos, transdutores multi-array ou singulares e espessura/material de layers de suporte. Os sinais originados em cada transdutor foram filtrados e processados de modo a detetar de forma automática os ecos refletidos, e assim, alertar o cirurgião quando existem variações anatómicas ao longo do caminho de punção. Os transdutores foram mapeados num tanque de água e testados em 45 phantoms. Os resultados mostraram que o feixe de área em corte transversal oscila em torno do raio de cerâmica, e que os ecos refletidos são detetados em phantoms com comprimentos superiores a 80 mm. Desta forma, é expectável que a introdução deste novo sistema a nível do ARP permitirá conduzir o cirurgião ao longo do caminho de punção ideal, aumentado a confiança do cirurgião e reduzindo possíveis complicações (p.e. a perfuração dos órgãos). Além disso, de realçar que este sistema apresenta o potencial de tornar o ARP livre de radiação e alarga-lo a cirurgiões menos especializados.The present work was only possible thanks to the support by the Portuguese Science and Technology Foundation through the PhD grant with reference SFRH/BD/74276/2010 funded by FCT/MEC (PIDDAC) and by Fundo Europeu de Desenvolvimento Regional (FEDER), Programa COMPETE - Programa Operacional Factores de Competitividade (POFC) do QREN

Image Processing and Analysis for Preclinical and Clinical Applications

Radiomics is one of the most successful branches of research in the field of image processing and analysis, as it provides valuable quantitative information for the personalized medicine. It has the potential to discover features of the disease that cannot be appreciated with the naked eye in both preclinical and clinical studies. In general, all quantitative approaches based on biomedical images, such as positron emission tomography (PET), computed tomography (CT) and magnetic resonance imaging (MRI), have a positive clinical impact in the detection of biological processes and diseases as well as in predicting response to treatment. This Special Issue, “Image Processing and Analysis for Preclinical and Clinical Applications”, addresses some gaps in this field to improve the quality of research in the clinical and preclinical environment. It consists of fourteen peer-reviewed papers covering a range of topics and applications related to biomedical image processing and analysis

Physiological system modelling and clinical simulation for diagnosis

Chapter 0 Contains the thesis introduction thesis and concepts of NDIs, derivations and applications. It also summarizes the PNDIs that are derived in the subsequent chapters. Chapter 1 Introduces the concept of using Physiological Non-Dimensional Indexes (PNDI) for distinguishing or classifying patients who were diabetic from non-diabetic and those who are the risk of becoming diabetic. In the authors work, he has also demonstrated that those who were diabetic were actually at-risk and those who were normal were in fact at the rim of becoming diabetic. All the works were verified against with clinical data by parametric identification techniques. Chapter 2 Using the findings of the above chapter, the author conceptualized, and design and simulated a dynamic activity-based insulin infusion system. He has used the clinical data of diabetic patients in the above chapter for demonstrating the operations of the system. He has even demonstrated the stability of the system by having continual simulations till 4-hour. Chapter 3 In this chapter, the author has derived a series of system equations for identification of pulmonary diseases based in the inhale and exhale gas mixtures concentrations and volume space. Chapter 4 In this chapter, the author has derived a series of system equations for identification of diseased lungs based of the lungs’ pressurevolume graphs. He has even demonstrated the techniques of obtaining the Cardiac Output (CO) non-invasively. Chapter 5 The author has demonstrated how to obtain the relative urine outflow non-invasively for normal kidneys. Chapter 6 The author has described the significance and derivation background of PNDI