Liver Segmentation and its Application to Hepatic Interventions

The thesis addresses the development of an intuitive and accurate liver segmentation approach, its integration into software prototypes for the planning of liver interventions, and research on liver regeneration. The developed liver segmentation approach is based on a combination of the live wire paradigm and shape-based interpolation. Extended with two correction modes and integrated into a user-friendly workflow, the method has been applied to more than 5000 data sets. The combination of the liver segmentation with image analysis of hepatic vessels and tumors allows for the computation of anatomical and functional remnant liver volumes. In several projects with clinical partners world-wide, the benefit of the computer-assisted planning was shown. New insights about the postoperative liver function and regeneration could be gained, and most recent investigations into the analysis of MRI data provide the option to further improve hepatic intervention planning

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

Preclinical MRI of the Kidney

This Open Access volume provides readers with an open access protocol collection and wide-ranging recommendations for preclinical renal MRI used in translational research. The chapters in this book are interdisciplinary in nature and bridge the gaps between physics, physiology, and medicine. They are designed to enhance training in renal MRI sciences and improve the reproducibility of renal imaging research. Chapters provide guidance for exploring, using and developing small animal renal MRI in your laboratory as a unique tool for advanced in vivo phenotyping, diagnostic imaging, and research into potential new therapies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Preclinical MRI of the Kidney: Methods and Protocols is a valuable resource and will be of importance to anyone interested in the preclinical aspect of renal and cardiorenal diseases in the fields of physiology, nephrology, radiology, and cardiology. This publication is based upon work from COST Action PARENCHIMA, supported by European Cooperation in Science and Technology (COST). COST (www.cost.eu) is a funding agency for research and innovation networks. COST Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. PARENCHIMA (renalmri.org) is a community-driven Action in the COST program of the European Union, which unites more than 200 experts in renal MRI from 30 countries with the aim to improve the reproducibility and standardization of renal MRI biomarkers