Fast fully automatic myocardial segmentation in 4D cine cardiac magnetic resonance datasets

Dissertação de mestrado integrado em Engenharia BiomédicaCardiovascular diseases (CVDs) are the leading cause of death in the world, representing 30% of all global deaths. Among others, assessment of the left ventricular (LV) morphology and global function using non-invasive cardiac imaging is an interesting technique for diagnosis and treatment follow-up of patients with CVDs. Nowadays, cardiac magnetic resonance (CMR) imaging is the gold-standard technique for the quantification of LV volumes, mass and ejection fraction, requiring the delineation of endocardial and epicardial contours of the left ventricle from cine MR images. In clinical practice, the physicians perform this segmentation manually, being a tedious, time consuming and unpractical task. Even though several (semi-)automated methods have been presented for LV CMR segmentation, fast, automatic and optimal boundaries assessment is still lacking, usually requiring the physician to manually correct the contours. In the present work, we propose a novel fast fully automatic 3D+time LV segmentation framework for CMR datasets. The proposed framework presents three conceptual blocks: 1) an automatic 2D mid-ventricular initialization and segmentation; 2) an automatic stack initialization followed by a 3D segmentation at the end-diastolic phase; and 3) a tracking procedure to delineate both endo and epicardial contours throughout the cardiac cycle. In each block, specific CMR-targeted algorithms are proposed for the different steps required. Hereto, we propose automatic and feasible initialization procedures. Moreover, we adapt the recent B-spline Explicit Active Surfaces (BEAS) framework to the properties of CMR image segmentation by integrating dedicated energy terms and making use of a cylindrical coordinate system that better fits the topology of CMR data. At last, two tracking methods are presented and compared. The proposed framework has been validated on 45 4D CMR datasets from a publicly available database and on a large database from an ongoing multi-center clinical trial with 318 4D datasets. In the technical validation, the framework showed competitive results against the state-of-the-art methods, presenting leading results in both accuracy and average computational time in the common database used for comparative purposes. Moreover, the results in the large scale clinical validation confirmed the high feasibility and robustness of the proposed framework for accurate LV morphology and global function assessment. In combination with the low computational burden of the method, the present methodology seems promising to be used in daily clinical practice.As doenças cardiovasculares (DCVs) são a principal causa de morte no mundo, representando 30% destas a nível global. Na prática clínica, uma técnica empregue no diagnóstico de pacientes com DCVs é a avaliação da morfologia e da função global do ventrículo esquerdo (VE), através de técnicas de imagiologia não-invasivas. Atualmente, a ressonância magnética cardíaca (RMC) é a modalidade de referência na quantificação dos volumes, massa e fração de ejeção do VE, exigindo a delimitação dos contornos do endocárdio e epicárdio a partir de imagens dinâmicas de RMC. Na prática clínica diária, o método preferencial é a segmentação manual. No entanto, esta é uma tarefa demorada, sujeita a erro humano e pouco prática. Apesar de até à data diversos métodos (semi)-automáticos terem sido apresentados para a segmentação do VE em imagens de RMC, ainda não existe um método capaz de avaliar idealmente os contornos de uma forma automática, rápida e precisa, levando a que geralmente o médico necessite de corrigir manualmente os contornos. No presente trabalho é proposta uma nova framework para a segmentação automática do VE em imagens 3D+tempo de RMC. O algoritmo apresenta três blocos principais: 1) uma inicialização e segmentação automática 2D num corte medial do ventrículo; 2) uma inicialização e segmentação tridimensional no volume correspondente ao final da diástole; e 3) um algoritmo de tracking para obter os contornos ao longo de todo o ciclo cardíaco. Neste sentido, são propostos procedimentos de inicialização automática com elevada robustez. Mais ainda, é proposta uma adaptação da recente framework “B-spline Explicit Active Surfaces” (BEAS) com a integração de uma energia específica para as imagens de RMC e utilizando uma formulação cilíndrica para tirar partido da topologia destas imagens. Por último, são apresentados e comparados dois algoritmos de tracking para a obtenção dos contornos ao longo do tempo. A framework proposta foi validada em 45 datasets de RMC provenientes de uma base de dados disponível ao público, bem como numa extensa base de dados com 318 datasets para uma validação clínica. Na avaliação técnica, a framework proposta obteve resultados competitivos quando comparada com outros métodos do estado da arte, tendo alcançado resultados de precisão e tempo computacional superiores a estes. Na validação clínica em larga escala, a framework provou apresentar elevada viabilidade e robustez na avaliação da morfologia e função global do VE. Em combinação com o baixo custo computacional do algoritmo, a presente metodologia apresenta uma perspetiva promissora para a sua aplicação na prática clínica diária

Fast left ventricle tracking in CMR images using localized anatomical affine optical flow

"Progress in Biomedical Optics and Imaging, vol. 16, nr. 41"In daily cardiology practice, assessment of left ventricular (LV) global function using non-invasive imaging remains central for the diagnosis and follow-up of patients with cardiovascular diseases. Despite the different methodologies currently accessible for LV segmentation in cardiac magnetic resonance (CMR) images, a fast and complete LV delineation is still limitedly available for routine use. In this study, a localized anatomically constrained affine optical flow method is proposed for fast and automatic LV tracking throughout the full cardiac cycle in short-axis CMR images. Starting from an automatically delineated LV in the end-diastolic frame, the endocardial and epicardial boundaries are propagated by estimating the motion between adjacent cardiac phases using optical flow. In order to reduce the computational burden, the motion is only estimated in an anatomical region of interest around the tracked boundaries and subsequently integrated into a local affine motion model. Such localized estimation enables to capture complex motion patterns, while still being spatially consistent. The method was validated on 45 CMR datasets taken from the 2009 MICCAI LV segmentation challenge. The proposed approach proved to be robust and efficient, with an average distance error of 2.1 mm and a correlation with reference ejection fraction of 0.98 (1.9 ± 4.5%). Moreover, it showed to be fast, taking 5 seconds for the tracking of a full 4D dataset (30 ms per image). Overall, a novel fast, robust and accurate LV tracking methodology was proposed, enabling accurate assessment of relevant global function cardiac indices, such as volumes and ejection fraction.The authors acknowledge funding support from FCT - Fundação para a Ciência e Tecnologia, Portugal, in the scope of the PhD grant SFRH/BD/93443/2013 and the project EXPL/BBB-BMD/2473/2013. D. Barbosa would also like to acknowledge the kind support of the Fundação Luso-Americana para o Desenvolvimento (FLAD), which has funded the travel costs for participation at SPIE Medical Imaging 2015.info:eu-repo/semantics/publishedVersio

Automatic 3D aortic annulus sizing by computed tomography in the planning of transcatheter aortic valve implantation

Background: Accurate imaging assessment of aortic annulus (AoA) dimension is paramount to decide on the correct transcatheter heart valve (THV) size for patients undergoing transcatheter aortic valve implantation (TAVI). We evaluated the feasibility and accuracy of a novel automatic framework for multi detector row computed tomography (MDCT)-based TAVI planning. Methods: Among 122 consecutive patients undergoing TAVI and retrospectively reviewed for this study, 104 patients with preoperative MDCT of sufficient quality were enrolled and analyzed with the proposed software. Fully automatic (FA) and semi-automatic (SA) AoA measurements were compared to manual measurements, with both automated and manual-based interobserver variability (IOV) being assessed. Finally, the effect of these measures on hypothetically selected THV size was evaluated against the implanted size, as well as with respect to manually-derived sizes. Results: FA analysis was feasible in 92.3% of the cases, increasing to 100% if using the SA approach. Automatically-extracted measurements showed excellent agreement with manually-derived ones, with small biases and narrow limits of agreement, and comparable to the interobserver agreement. The SA approach presented a statistically lower IOV than manual analysis, showing the potential to reduce interobserver sizing disagreements. Moreover, the automated approaches displayed close agreement with the implanted sizes, similar to the ones obtained by the experts. Conclusion: The proposed automatic framework provides an accurate and robust tool for AoA measurements and THV sizing in patients undergoing TAVI.FCT - Fundação para a Ciência e a Tecnologia, Portugal, and the European Social Found, European Union, through the Programa Operacional Capital Humano (POCH) in the scope of the PhD grants SFRH/BD/93443/2013 (S. Queirós) and SFRH/BD/95438/2013 (P. Morais), and the project ‘PersonalizedNOS (01-0145-FEDER-000013)’ co-funded by Programa Operacional Regional do Norte (QREN), through Fundo Europeu de Desenvolvimento Regional (FEDER)info:eu-repo/semantics/publishedVersio

An electromagnetic tracker system for the design of a dental superstructure

Nowadays, different techniques are available for manufacturing full-arch implant-supported prosthesis, many of them based on an impression procedure. Nevertheless, the long-term success of the prosthesis is highly influenced by the accuracy during such process, being affected by factors such as the impression material, implant position, angulation and depth. This paper investigates the feasibility of a 3D electromagnetic motion tracking system as an acquisition method for modeling such prosthesis. To this extent, we propose an implant acquisition method at the patient mouth, using a specific prototyped tool coupled with a tracker sensor, and a set of calibration procedures (for distortion correction and tool calibration), that ultimately obtains combined measurements of the implant's position and angulation, and eliminating the use of any impression material. However, in the particular case of the evaluated tracking system, the order of magnitude of the obtained errors invalidates its use for this specific application.This work has been supported by FCT – Fundação para a Ciência e Tecnologia in the scope of the Ph.D. grant SFRH/BD/68270/2010 and the project EXPL/BBB-BMD/2146/2013

Electromagnetic tracker feasibility in the design of a dental superstructure for edentulous patients

The success of the osseointegration concept and the Branemark protocol is highly associated to the accuracy in the production of an implant-supported prosthesis. One of most critical steps for long-term success of these prosthesis is the accuracy obtained during the impression procedure, which is affected by factors such as the impression material, implant position, angulation and depth. This paper investigates the feasibility of 3D electromagnetic motion tracking systems as an acquisition method for modeling full-arch implant-supported prosthesis. To this extent, we propose an implant acquisition method at the patient mouth and a calibration procedure, based on a 3D electromagnetic tracker that obtains combined measurements of implant's position and angulation, eliminating the use of any impression material. Three calibration algorithms (namely linear interpolation, higher-order polynomial and Hardy multiquadric) were tested to compensate for the electromagnetic tracker distortions introduced by the presence of nearby metals. Moreover, implants from different suppliers were also tested to study its impact on tracking accuracy. The calibration methodology and the algorithms employed proved to implement a suitable strategy for the evaluation of novel dental impression techniques. However, in the particular case of the evaluated electromagnetic tracking system, the order of magnitude of the obtained errors invalidates its use for the full-arch modeling of implant-supported prosthesis.This work has been supported by FCT – Fundação para a Ciência e Tecnologia in the scope of the Ph.D. grant SFRH/BD/68270/2010 and the project EXPL/BBB-BMD/2146/2013

Segmentation of kidney and renal collecting system on 3D computed tomography images

Surgical training for minimal invasive kidney interventions (MIKI) has huge importance within the urology field. Within this topic, simulate MIKI in a patient-specific virtual environment can be used for pre-operative planning using the real patient's anatomy, possibly resulting in a reduction of intra-operative medical complications. However, the validated VR simulators perform the training in a group of standard models and do not allow patient-specific training. For a patient-specific training, the standard simulator would need to be adapted using personalized models, which can be extracted from pre-operative images using segmentation strategies. To date, several methods have already been proposed to accurately segment the kidney in computed tomography (CT) images. However, most of these works focused on kidney segmentation only, neglecting the extraction of its internal compartments. In this work, we propose to adapt a coupled formulation of the B-Spline Explicit Active Surfaces (BEAS) framework to simultaneously segment the kidney and the renal collecting system (CS) from CT images. Moreover, from the difference of both kidney and CS segmentations, one is able to extract the renal parenchyma also. The segmentation process is guided by a new energy functional that combines both gradient and region-based energies. The method was evaluated in 10 kidneys from 5 CT datasets, with different image properties. Overall, the results demonstrate the accuracy of the proposed strategy, with a Dice overlap of 92.5%, 86.9% and 63.5%, and a point-to-surface error around 1.6 mm, 1.9 mm and 4 mm for the kidney, renal parenchyma and CS, respectively.NORTE-01-0145-FEDER0000I3, and NORTE-01-0145-FEDER-024300, supported by Northern Portugal Regional Operational Programme (Norte2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER), and also been funded by FEDER funds, through Competitiveness Factors Operational Programme (COMPETE), and by national funds, through the FCT-Fundacao para a Ciência e Tecnologia, under the scope of the project POCI-01-0145-FEDER-007038. The authors acknowledge FCT-Fundação para a Ciância e a Tecnologia, Portugal, and the European Social Found, European Union, for funding support through the Programa Operacional Capital Humano (POCH).info:eu-repo/semantics/publishedVersio

Fully Automatic 3D-TEE Segmentation for the Planning of Transcatheter Aortic Valve Implantation

A novel fully automatic framework for aortic valve (AV) trunk segmentation in three-dimensional (3-D) transesophageal echocardiography (TEE) datasets is proposed. The methodology combines a previously presented semiautomatic segmentation strategy by using shape-based B-spline Explicit Active Surfaces with two novel algorithms to automate the quantification of relevant AV measures. The first combines a fast rotation-invariant 3-D generalized Hough transform with a vessel-like dark tube detector to initialize the segmentation. After segmenting the AV wall, the second algorithm focuses on aligning this surface with the reference ones in order to estimate the short-axis (SAx) planes (at the left ventricular outflow tract, annulus, sinuses of Valsalva, and sinotubular junction) in which to perform the measurements. The framework has been tested in 20 3-D-TEE datasets with both stenotic and nonstenotic AVs. The initialization algorithm presented a median error of around 3 mm for the AV axis endpoints, with an overall feasibility of 90%. In its turn, the SAx detection algorithm showed to be highly reproducible, with indistinguishable results compared with the variability found between the experts' defined planes. Automatically extracted measures at the four levels showed a good agreement with the experts' ones, with limits of agreement similar to the interobserver variability. Moreover, a validation set of 20 additional stenotic AV datasets corroborated the method's applicability and accuracy. The proposed approach mitigates the variability associated with the manual quantification while significantly reducing the required analysis time (12 s versus 5 to 10 min), which shows its appeal for automatic dimensioning of the AV morphology in 3-D-TEE for the planning of transcatheter AV implantation.This work was supported by the project "ON.2 SR&TD Integrated Program (Norte-07-0124-FEDER-000017)" cofunded by the Programa Operacional Regional do Norte (ON.2- O Novo Norte), Quadro de Referencia Estrategico Nacional, through Fundo Europeu de Desenvolvimento Regional. The work of S. Queiros and P. Morais was supported by the FCT-Fundacao para a Ciencia e a Tecnologia and the European Social Found through the Programa Operacional Capital Humano in the scope of the Ph.D. Grants SFRH/BD/93443/2013 and SFRH/BD/95438/2013, respectively. J. L. Vilaca and J. D'hooge are joint last authors. Asterisk indicates corresponding author.info:eu-repo/semantics/publishedVersio

Top-down human pose estimation with depth images and domain adaptation

In this paper, a method for estimation of human pose is proposed, making use of ToF (Time of Flight) cameras. For this, a YOLO based object detection method was used, to develop a top-down method. In the first stage, a network was developed to detect people in the image. In the second stage, a network was developed to estimate the joints of each person, using the image result from the first stage. We show that a deep learning network trained from scratch with ToF images yields better results than taking a deep neural network pretrained on RGB data and retraining it with ToF data. We also show that a top-down detector, with a person detector and a joint detector works better than detecting the body joints over the entire image.This work is supported by: European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project no 002797; Funding Reference: POCI-01-0247-FEDER-002797]

Personalized dynamic phantom of the right and left ventricles based on patient-specific anatomy for echocardiography studies — Preliminary results

Dynamic phantoms of the heart are becoming a reality, with their use spread across both medical and research fields. Their purpose is to mimic the cardiac anatomy, as well as its motion. This work aims to create a dynamic, ultrasound-compatible, realistic and flexible phantom of the left and right ventricles, with application in the diagnosis, planning, treatment and training in the cardiovascular field for studies using echocardiography. Here, we focus on its design and production with polyvinyl alcohol cryogel (PVA-C), to be assembled with a pump and an electromechanical (E/M) system in a water tank. Based on a patient-specific anatomical model and produced using a 3D printing technique and molding, the PVA-C phantom mimics the ventricles' natural anatomy and material properties, while the pump and E/M systems mimic the natural movements and pressures. The PVA-C phantom was assessed by imaging and measuring it using a four-dimensional ultrasound machine. The PVA-C phantom demonstrated to be a versatile option to produce patient-specific biventricular models, preserving their shape after manufacturing and presenting good echogenic properties. Both chambers were clearly seen in the ultrasound images, together with the interventricular septum and the myocardial wall. Automated left ventricle measures revealed a decrease of its volume with regard to the designed model (98 ml to 74 ml). Overall, the preliminary results are satisfactory and encourage its use for the abovementioned purposesFEDER funds through the Competitiveness Factors Operational Programme (COMPETE), and by National funds through the Foundation for Science and Technology (FCT) under the project POCI -01-0145-FEDER-007038 and EXPL/BBB-BMD/2473/2013, and by the projects NORTE-01-0145-FEDER-000013 and NORTE-01-0145-FEDER-024300, supported by the NORTE 2020, under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). J. Gomes-Fonseca, P. Morais, S. Queirós, and F. Veloso were funded by FCT under the Ph.D. grants PD/BDE/113597/2015, SFRH/BD/95438/2013, SFRH/BD/93443/2013, and SFRH/BD/131545/2017info:eu-repo/semantics/publishedVersio

Targeting lactate transport suppresses in vivo breast tumour growth.

BACKGROUND Most cancers, including breast cancer, have high rates of glucose consumption, associated with lactate production, a process referred as "Warburg effect". Acidification of the tumour microenvironment by lactate extrusion, performed by lactate transporters (MCTs), is associated with higher cell proliferation, migration, invasion, angiogenesis and increased cell survival. Previously, we have described MCT1 up-regulation in breast carcinoma samples and demonstrated the importance of in vitro MCT inhibition. In this study, we performed siRNA knockdown of MCT1 and MCT4 in basal-like breast cancer cells in both normoxia and hypoxia conditions to validate the potential of lactate transport inhibition in breast cancer treatment. RESULTS The effect of MCT knockdown was evaluated on lactate efflux, proliferation, cell biomass, migration and invasion and induction of tumour xenografts in nude mice. MCT knockdown led to a decrease in in vitro tumour cell aggressiveness, with decreased lactate transport, cell proliferation, migration and invasion and, importantly, to an inhibition of in vivo tumour formation and growth. CONCLUSIONS This work supports MCTs as promising targets in cancer therapy, demonstrates the contribution of MCTs to cancer cell aggressiveness and, more importantly, shows, for the first time, the disruption of in vivo breast tumour growth by targeting lactate transport.This work was supported by Fundação para a Ciência e a Tecnologia (FCT) (grant number PTDC/ SAU-FCF/104347/2008), under the scope of “Programa Operacional Temático Factores de Competitividade” (COMPETE) of “Quadro Comunitário de Apoio III” and co-financed by the Fundo Europeu De Desenvolvimento Regional (FEDER). FM-S, VM-G and AHJM received doctoral fellowships from FCT (refs. SFRH/BD/87139/2012, SFRH/BD/ 51997/2012 and SFRH/ BD/68270/2010, respectively). SG received a postdoctoral fellowship from UMINHO/BPD/18/2014 and CP from FCT (ref. SFRH/BPD/69479/2010)