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Nguyen TD, Kadri OE, Voronov RS. An Introductory Overview of Image-Based Computational Modeling in Personalized Cardiovascular Medicine. Front Bioeng Biotechnol 2020; 8:529365. [PMID: 33102452 PMCID: PMC7546862 DOI: 10.3389/fbioe.2020.529365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023] Open
Abstract
Cardiovascular diseases account for the number one cause of deaths in the world. Part of the reason for such grim statistics is our limited understanding of the underlying mechanisms causing these devastating pathologies, which is made difficult by the invasiveness of the procedures associated with their diagnosis (e.g., inserting catheters into the coronal artery to measure blood flow to the heart). Likewise, it is also difficult to design and test assistive devices without implanting them in vivo. However, with the recent advancements made in biomedical scanning technologies and computer simulations, image-based modeling (IBM) has arisen as the next logical step in the evolution of non-invasive patient-specific cardiovascular medicine. Yet, due to its novelty, it is still relatively unknown outside of the niche field. Therefore, the goal of this manuscript is to review the current state-of-the-art and the limitations of the methods used in this area of research, as well as their applications to personalized cardiovascular investigations and treatments. Specifically, the modeling of three different physics – electrophysiology, biomechanics and hemodynamics – used in the cardiovascular IBM is discussed in the context of the physiology that each one of them describes and the mechanisms of the underlying cardiac diseases that they can provide insight into. Only the “bare-bones” of the modeling approaches are discussed in order to make this introductory material more accessible to an outside observer. Additionally, the imaging methods, the aspects of the unique cardiac anatomy derived from them, and their relation to the modeling algorithms are reviewed. Finally, conclusions are drawn about the future evolution of these methods and their potential toward revolutionizing the non-invasive diagnosis, virtual design of treatments/assistive devices, and increasing our understanding of these lethal cardiovascular diseases.
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Affiliation(s)
- Thanh Danh Nguyen
- Otto H. York Department of Chemical and Materials Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States
| | - Olufemi E Kadri
- Otto H. York Department of Chemical and Materials Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States.,UC-P&G Simulation Center, University of Cincinnati, Cincinnati, OH, United States
| | - Roman S Voronov
- Otto H. York Department of Chemical and Materials Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States.,Department of Biomedical Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States
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Zabihollahy F, Rajan S, Ukwatta E. Machine Learning-Based Segmentation of Left Ventricular Myocardial Fibrosis from Magnetic Resonance Imaging. Curr Cardiol Rep 2020; 22:65. [PMID: 32562100 DOI: 10.1007/s11886-020-01321-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE OF REVIEW Myocardial fibrosis (MF) arises due to myocardial infarction and numerous cardiac diseases. MF may lead to several heart disorders, such as heart failure, arrhythmias, and ischemia. Cardiac magnetic resonance (CMR) imaging techniques, such as late gadolinium enhancement (LGE) CMR, enable non-invasive assessment of MF in the left ventricle (LV). Manual assessment of MF on CMR is a tedious and time-consuming task that is subject to high observer variability. Automated segmentation and quantification of MF is important for risk stratification and treatment planning in patients with heart disorders. This article aims to review the machine learning (ML)-based methodologies developed for MF quantification in the LV using CMR images. RECENT FINDINGS With the availability of relatively large labeled datasets supervised learning methods based on both conventional ML and state-of-the-art deep learning (DL) methods have been successfully applied for automated segmentation of MF. The incorporation of ML algorithms into imaging techniques such as 3D LGE CMR permits fast characterization of MF on CMR imaging and may enhance the diagnosis and prognosis of patients with heart disorders. Concurrently, the studies using cine CMR images have revealed that accurate segmentation of MF on non-contrast CMR imaging might be possible. The application of ML/DL tools in CMR image interpretation is likely to result in accurate and efficient quantification of MF.
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Affiliation(s)
- Fatemeh Zabihollahy
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada.
| | - S Rajan
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - E Ukwatta
- School of Engineering, University of Guelph, Guelph, ON, Canada
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Zabihollahy F, White JA, Ukwatta E. Convolutional neural network-based approach for segmentation of left ventricle myocardial scar from 3D late gadolinium enhancement MR images. Med Phys 2019; 46:1740-1751. [PMID: 30734937 DOI: 10.1002/mp.13436] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 01/10/2019] [Accepted: 01/31/2019] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Accurate three-dimensional (3D) segmentation of myocardial replacement fibrosis (i.e., scar) is emerging as a potentially valuable tool for risk stratification and procedural planning in patients with ischemic cardiomyopathy. The main purpose of this study was to develop a semiautomated method using a 3D convolutional neural network (CNN)-based for the segmentation of left ventricle (LV) myocardial scar from 3D late gadolinium enhancement magnetic resonance (LGE-MR) images. METHODS Our proposed CNN is built upon several convolutional and pooling layers aimed at choosing appropriate features from LGE-MR images to distinguish between myocardial scar and healthy tissues of the left ventricle. In contrast to previous methods that consider image intensity as the sole feature, CNN-based algorithms have the potential to improve the accuracy of scar segmentation through the creation of unconventional features that separate scar from normal myocardium in the feature space. The first step of our pipeline was to manually delineate the left ventricular myocardium, which was used as the region of interest for scar segmentation. Our developed algorithm was trained using 265,220 volume patches extracted from ten 3D LGE-MR images, then was validated on 450,454 patches from a testing dataset of 24 3D LGE-MR images, all obtained from patients with chronic myocardial infarction. We evaluated our method in the context of several alternative methods by comparing algorithm-generated segmentations to manual delineations performed by experts. RESULTS Our CNN-based method reported an average Dice similarity coefficient (DSC) and Jaccard Index (JI) of 93.63% ± 2.6% and 88.13% ± 4.70%. In comparison to several previous methods, including K-nearest neighbor (KNN), hierarchical max flow (HMF), full width at half maximum (FWHM), and signal threshold to reference mean (STRM), the developed algorithm reported significantly higher accuracy for DSC with a P-value less than 0.0001. CONCLUSIONS Our experimental results demonstrated that our CNN-based proposed method yielded the highest accuracy of all contemporary LV myocardial scar segmentation methodologies, inclusive of the most widely used signal intensity-based methods, such as FWHM and STRM. To our knowledge, this is the first description of LV myocardial scar tissue segmentation from 3D LGE-MR images using a CNN-based method.
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Affiliation(s)
- Fatemeh Zabihollahy
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - James A White
- Stephenson Cardiac Imaging Centre, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, USA
| | - Eranga Ukwatta
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
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Masoomi MA, Al-Shammeri I, Kalafallah K, Elrahman HM, Ragab O, Ahmed E, Al-Shammeri J, Arafat S. Wiener filter improves diagnostic accuracy of CAD SPECT images-comparison to angiography and CT angiography. Medicine (Baltimore) 2019; 98:e14207. [PMID: 30681596 PMCID: PMC6358408 DOI: 10.1097/md.0000000000014207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Many discrepancy in selection of proper filter and its parameters for individual cases exists. The authors investigate the impact of the most common filters on patient NM images with coronary artery disease (CAD), and compare the results with the computerized tomography (CT)-Angio and angiography for accuracy.The investigation initiated by performing various single photon emission computerized tomography (SPECT)/CT scan of the national electrical manufacturers association chest phantoms having hot and cold inserts. Data acquired on GE 670 PRO SPECT/CT; 360Ø, 64 frames, 60 seconds, low energy high resolution (LEHR) 128, low energy general purpose (LEGP) with CT attenuation (120 kV and 170 mA). The images reconstructed with filtered back projection and ITERATIVE ordered-subset expectation maximization utilizing filters; Hann, Butterworth, Metz, Hamming, and Wiener. The Image contrast was calculated to assess absolute nearness of the inserts. Based on the preliminary results, then scans of 92 patients with CAD; 64 males and 28 females, age 41 to 77 years old, who had been reported earlier reprocessed with the nominated filter and were reported by 2 NM expert. The results compared to the earlier reports and to the CT-Angio and angiography.The optimization suggested 3 filters; Wiener (Wi), Metz and Butterworth (But) provide the highest contrast (99- 66.4%) and (81- 32%) for the cold and hot inserts respectively, with the (Wi) filter to be the better option. The reprocessed patients scan with the (Wi) presented an elevated diagnostic accuracy, correlated well with the CT-Angio and angiography results (P < .001 and r = 0.79 for [Wi] and P = .004 and r = 0.39 for [But]). The percentage of the false negative for moderate to severe CAD cases reported using Wi filter reduced from 27% to 7% and similarly for mild CAD cases from 7% to 1%.It appears the Wiener filter could produce results with the highest contrast for phantom imaging of various cold and hot spheres and for the patient data which is more consistent with angiography results, with much-elevated accuracy in intermediate cases (r = 0.79 for Wiener and r = 0.39 for Butterworth vs angiography). However, the optimum parameters obtained for the filters have no relation with the resolution of the imaging system, but the details of the objects could be improved.
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Affiliation(s)
- Michael A. Masoomi
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
| | - Iman Al-Shammeri
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
| | - Khaled Kalafallah
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
- Department of Nuclear Medicine, Kuwait Cancer Control Centre, Sabah Medical District, Shuwaikh
| | - Hany M.A. Elrahman
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
| | - Osama Ragab
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
| | - Ebba Ahmed
- Department of Nuclear Medicine and Molecular Imaging, Adan HospitalHadiya, KW
| | - Jehan Al-Shammeri
- Department of Nuclear Medicine, Faculty of Medicine, Heath Science Centre, Kuwait University
| | - Sharif Arafat
- Department of Cardiology, Dabbous Cardiac Centre, Adan Hospital, Hadiya, Kuwait
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Ukwatta E, Nikolov P, Zabihollahy F, Trayanova NA, Wright GA. Virtual electrophysiological study as a tool for evaluating efficacy of MRI techniques in predicting adverse arrhythmic events in ischemic patients. Phys Med Biol 2018; 63:225008. [PMID: 30412472 DOI: 10.1088/1361-6560/aae8b2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Myocardial infarct (MI) related indices determined by late gadolinium enhancement (LGE) MRI have been widely investigated in determining patients suitable for implantable cardiovascular-defibrillator (ICD) therapy to complement left ventricular ejection fraction (LV EF). In comparison to LGE-MRI using inversion-recovery fast-gradient-echo (IR-FGRE), T1 mapping techniques, such as multi contrast late enhancement (MCLE), have been shown to provide more quantitative and reproducible estimates of infarct regions. The objective of this study is to use individualized heart computer models in determining the efficacy of IR-FGRE and MCLE techniques in predicting the occurrence of post-MI ventricular tachycardia (VT). Twenty-seven patients with MI underwent LGE-MRI using IR-FGRE and MCLE prior to ICD implantation and were followed up for 6-46 months. Individualized image-based computational models were built separately for each imaging technique; simulations of propensity to VT were conducted with each model. The imaging methods were evaluated by comparing simulated inducibility of VT to clinical outcome (appropriate ICD therapy) in patients. Twelve patients had at least one appropriate ICD therapy for VT at follow-up. For both MCLE and IR-FGRE, the outcomes of the simulations of VT were significantly associated with the events of appropriate ICD therapy. This indicates that, as compared to conventional measurements such as LV EF, the simulations of VT corresponding to both MCLE and IR-FGRE were more sensitive in predicting appropriate ICD therapy in post-MI patients.
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Affiliation(s)
- Eranga Ukwatta
- School of Engineering, University of Guelph, Guelph, ON, Canada. Author to whom any correspondence should be addressed
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Ukwatta E, Arevalo H, Li K, Yuan J, Qiu W, Malamas P, Wu KC, Trayanova NA, Vadakkumpadan F. Myocardial Infarct Segmentation From Magnetic Resonance Images for Personalized Modeling of Cardiac Electrophysiology. IEEE TRANSACTIONS ON MEDICAL IMAGING 2016; 35:1408-1419. [PMID: 26731693 PMCID: PMC4891256 DOI: 10.1109/tmi.2015.2512711] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Accurate representation of myocardial infarct geometry is crucial to patient-specific computational modeling of the heart in ischemic cardiomyopathy. We have developed a methodology for segmentation of left ventricular (LV) infarct from clinically acquired, two-dimensional (2D), late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) images, for personalized modeling of ventricular electrophysiology. The infarct segmentation was expressed as a continuous min-cut optimization problem, which was solved using its dual formulation, the continuous max-flow (CMF). The optimization objective comprised of a smoothness term, and a data term that quantified the similarity between image intensity histograms of segmented regions and those of a set of training images. A manual segmentation of the LV myocardium was used to initialize and constrain the developed method. The three-dimensional geometry of infarct was reconstructed from its segmentation using an implicit, shape-based interpolation method. The proposed methodology was extensively evaluated using metrics based on geometry, and outcomes of individualized electrophysiological simulations of cardiac dys(function). Several existing LV infarct segmentation approaches were implemented, and compared with the proposed method. Our results demonstrated that the CMF method was more accurate than the existing approaches in reproducing expert manual LV infarct segmentations, and in electrophysiological simulations. The infarct segmentation method we have developed and comprehensively evaluated in this study constitutes an important step in advancing clinical applications of personalized simulations of cardiac electrophysiology.
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Affiliation(s)
- Eranga Ukwatta
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Correspondent author:
| | - Hermenegild Arevalo
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kristina Li
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jing Yuan
- Robarts Research Institute, Western University, London, ON, Canada
| | - Wu Qiu
- Robarts Research Institute, Western University, London, ON, Canada
| | - Peter Malamas
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Katherine C. Wu
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Natalia A. Trayanova
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Fijoy Vadakkumpadan
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
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Ukwatta E, Arevalo H, Rajchl M, White J, Pashakhanloo F, Prakosa A, Herzka DA, McVeigh E, Lardo AC, Trayanova NA, Vadakkumpadan F. Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology. Med Phys 2016; 42:4579-90. [PMID: 26233186 DOI: 10.1118/1.4926428] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. METHODS The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. RESULTS The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. CONCLUSIONS The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.
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Affiliation(s)
- Eranga Ukwatta
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205 and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Hermenegild Arevalo
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205 and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Martin Rajchl
- Department of Computing, Imperial College London, London SW7 2AZ, United Kingdom
| | - James White
- Stephenson Cardiovascular MR Centre, University of Calgary, Calgary, Alberta T2N 2T9, Canada
| | - Farhad Pashakhanloo
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205 and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Adityo Prakosa
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205 and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Daniel A Herzka
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Elliot McVeigh
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
| | - Albert C Lardo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205 and Division of Cardiology, Johns Hopkins Institute of Medicine, Baltimore, Maryland 21224
| | - Natalia A Trayanova
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205; and Department of Biomedical Engineering, Johns Hopkins Institute of Medicine, Baltimore, Maryland 21205
| | - Fijoy Vadakkumpadan
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21205 and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205
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Qin X, Fei B. DTI template-based estimation of cardiac fiber orientations from 3D ultrasound. Med Phys 2016; 42:2915-24. [PMID: 26127045 DOI: 10.1118/1.4921121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
PURPOSE Cardiac muscle fibers directly affect the mechanical, physiological, and pathological properties of the heart. Patient-specific quantification of cardiac fiber orientations is an important but difficult problem in cardiac imaging research. In this study, the authors proposed a cardiac fiber orientation estimation method based on three-dimensional (3D) ultrasound images and a cardiac fiber template that was obtained from magnetic resonance diffusion tensor imaging (DTI). METHODS A DTI template-based framework was developed to estimate cardiac fiber orientations from 3D ultrasound images using an animal model. It estimated the cardiac fiber orientations of the target heart by deforming the fiber orientations of the template heart, based on the deformation field of the registration between the ultrasound geometry of the target heart and the MRI geometry of the template heart. In the experiments, the animal hearts were imaged by high-frequency ultrasound, T1-weighted MRI, and high-resolution DTI. RESULTS The proposed method was evaluated by four different parameters: Dice similarity coefficient (DSC), target errors, acute angle error (AAE), and inclination angle error (IAE). Its ability of estimating cardiac fiber orientations was first validated by a public database. Then, the performance of the proposed method on 3D ultrasound data was evaluated by an acquired database. Their average values were 95.4% ± 2.0% for the DSC of geometric registrations, 21.0° ± 0.76° for AAE, and 19.4° ± 1.2° for IAE of fiber orientation estimations. Furthermore, the feasibility of this framework was also performed on 3D ultrasound images of a beating heart. CONCLUSIONS The proposed framework demonstrated the feasibility of using 3D ultrasound imaging to estimate cardiac fiber orientation of in vivo beating hearts and its further improvements could contribute to understanding the dynamic mechanism of the beating heart and has the potential to help diagnosis and therapy of heart disease.
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Affiliation(s)
- Xulei Qin
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia 30329
| | - Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia 30329; Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30329; Winship Cancer Institute of Emory University, Atlanta, Georgia 30329; and Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia 30329
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Trayanova NA, Chang KC. How computer simulations of the human heart can improve anti-arrhythmia therapy. J Physiol 2016; 594:2483-502. [PMID: 26621489 DOI: 10.1113/jp270532] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/25/2015] [Indexed: 01/26/2023] Open
Abstract
Over the last decade, the state-of-the-art in cardiac computational modelling has progressed rapidly. The electrophysiological function of the heart can now be simulated with a high degree of detail and accuracy, opening the doors for simulation-guided approaches to anti-arrhythmic drug development and patient-specific therapeutic interventions. In this review, we outline the basic methodology for cardiac modelling, which has been developed and validated over decades of research. In addition, we present several recent examples of how computational models of the human heart have been used to address current clinical problems in cardiac electrophysiology. We will explore the use of simulations to improve anti-arrhythmic pacing and defibrillation interventions; to predict optimal sites for clinical ablation procedures; and to aid in the understanding and selection of arrhythmia risk markers. Together, these studies illustrate how the tremendous advances in cardiac modelling are poised to revolutionize medical treatment and prevention of arrhythmia.
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Affiliation(s)
- Natalia A Trayanova
- Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kelly C Chang
- Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
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Balakrishnan M, Chakravarthy VS, Guhathakurta S. Simulation of Cardiac Arrhythmias Using a 2D Heterogeneous Whole Heart Model. Front Physiol 2015; 6:374. [PMID: 26733873 PMCID: PMC4685512 DOI: 10.3389/fphys.2015.00374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023] Open
Abstract
Simulation studies of cardiac arrhythmias at the whole heart level with electrocardiogram (ECG) gives an understanding of how the underlying cell and tissue level changes manifest as rhythm disturbances in the ECG. We present a 2D whole heart model (WHM2D) which can accommodate variations at the cellular level and can generate the ECG waveform. It is shown that, by varying cellular-level parameters like the gap junction conductance (GJC), excitability, action potential duration (APD) and frequency of oscillations of the auto-rhythmic cell in WHM2D a large variety of cardiac arrhythmias can be generated including sinus tachycardia, sinus bradycardia, sinus arrhythmia, sinus pause, junctional rhythm, Wolf Parkinson White syndrome and all types of AV conduction blocks. WHM2D includes key components of the electrical conduction system of the heart like the SA (Sino atrial) node cells, fast conducting intranodal pathways, slow conducting atriovenctricular (AV) node, bundle of His cells, Purkinje network, atrial, and ventricular myocardial cells. SA nodal cells, AV nodal cells, bundle of His cells, and Purkinje cells are represented by the Fitzhugh-Nagumo (FN) model which is a reduced model of the Hodgkin-Huxley neuron model. The atrial and ventricular myocardial cells are modeled by the Aliev-Panfilov (AP) two-variable model proposed for cardiac excitation. WHM2D can prove to be a valuable clinical tool for understanding cardiac arrhythmias.
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Affiliation(s)
- Minimol Balakrishnan
- Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | | | - Soma Guhathakurta
- Department of Engineering Design, Indian Institute of Technology MadrasChennai, India
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Burton RAB, Lee P, Casero R, Garny A, Siedlecka U, Schneider JE, Kohl P, Grau V. Three-dimensional histology: tools and application to quantitative assessment of cell-type distribution in rabbit heart. Europace 2015; 16 Suppl 4:iv86-iv95. [PMID: 25362175 PMCID: PMC4217519 DOI: 10.1093/europace/euu234] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aims Cardiac histo-anatomical organization is a major determinant of function. Changes in tissue structure are a relevant factor in normal and disease development, and form targets of therapeutic interventions. The purpose of this study was to test tools aimed to allow quantitative assessment of cell-type distribution from large histology and magnetic resonance imaging- (MRI) based datasets. Methods and results Rabbit heart fixation during cardioplegic arrest and MRI were followed by serial sectioning of the whole heart and light-microscopic imaging of trichrome-stained tissue. Segmentation techniques developed specifically for this project were applied to segment myocardial tissue in the MRI and histology datasets. In addition, histology slices were segmented into myocytes, connective tissue, and undefined. A bounding surface, containing the whole heart, was established for both MRI and histology. Volumes contained in the bounding surface (called ‘anatomical volume’), as well as that identified as containing any of the above tissue categories (called ‘morphological volume’), were calculated. The anatomical volume was 7.8 cm3 in MRI, and this reduced to 4.9 cm3 after histological processing, representing an ‘anatomical’ shrinkage by 37.2%. The morphological volume decreased by 48% between MRI and histology, highlighting the presence of additional tissue-level shrinkage (e.g. an increase in interstitial cleft space). The ratio of pixels classified as containing myocytes to pixels identified as non-myocytes was roughly 6:1 (61.6 vs. 9.8%; the remaining fraction of 28.6% was ‘undefined’). Conclusion Qualitative and quantitative differentiation between myocytes and connective tissue, using state-of-the-art high-resolution serial histology techniques, allows identification of cell-type distribution in whole-heart datasets. Comparison with MRI illustrates a pronounced reduction in anatomical and morphological volumes during histology processing.
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Affiliation(s)
- Rebecca A B Burton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Peter Lee
- Department of Physics, University of Oxford, Oxford OX1 3RH, UK
| | - Ramón Casero
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
| | - Alan Garny
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Urszula Siedlecka
- The Heart Science Centre, National Heart and Lung Institute, Imperial College London, Harefield UB9 6JH, UK
| | - Jürgen E Schneider
- British Heart Foundation Experimental MR Unit, Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Kohl
- The Heart Science Centre, National Heart and Lung Institute, Imperial College London, Harefield UB9 6JH, UK
| | - Vicente Grau
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
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Ukwatta E, Rajchl M, White J, Pashakhanloo F, Herzka DA, McVeigh E, Lardo AC, Trayanova N, Vadakkumpadan F. Image-based Reconstruction of 3D Myocardial Infarct Geometry for Patient Specific Applications. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9413. [PMID: 26633913 DOI: 10.1117/12.2082113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Accurate reconstruction of the three-dimensional (3D) geometry of a myocardial infarct from two-dimensional (2D) multi-slice image sequences has important applications in the clinical evaluation and treatment of patients with ischemic cardiomyopathy. However, this reconstruction is challenging because the resolution of common clinical scans used to acquire infarct structure, such as short-axis, late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) images, is low, especially in the out-of-plane direction. In this study, we propose a novel technique to reconstruct the 3D infarct geometry from low resolution clinical images. Our methodology is based on a function called logarithm of odds (LogOdds), which allows the broader class of linear combinations in the LogOdds vector space as opposed to being limited to only a convex combination in the binary label space. To assess the efficacy of the method, we used high-resolution LGE-CMR images of 36 human hearts in vivo, and 3 canine hearts ex vivo. The infarct was manually segmented in each slice of the acquired images, and the manually segmented data were downsampled to clinical resolution. The developed method was then applied to the downsampled image slices, and the resulting reconstructions were compared with the manually segmented data. Several existing reconstruction techniques were also implemented, and compared with the proposed method. The results show that the LogOdds method significantly outperforms all the other tested methods in terms of region overlap.
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Affiliation(s)
- Eranga Ukwatta
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Martin Rajchl
- Department of Computing, Imperial College London, London, United Kingdom
| | - James White
- Stephenson Cardiovascular MR Centre, University of Calgary, Calgary, AB, Canada
| | - Farhad Pashakhanloo
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Daniel A Herzka
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Elliot McVeigh
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Albert C Lardo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States ; School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Natalia Trayanova
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States ; School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Fijoy Vadakkumpadan
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
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Pathmanathan P, Shotwell MS, Gavaghan DJ, Cordeiro JM, Gray RA. Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:4-18. [PMID: 25661325 DOI: 10.1016/j.pbiomolbio.2015.01.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 01/13/2015] [Accepted: 01/27/2015] [Indexed: 11/29/2022]
Abstract
Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate consequences of variability; and (iv) improve the ability to validate a model. To our knowledge this article is the first to quantify population variability in membrane dynamics in this manner, and the first to perform formal UQ for a component of a cardiac model. The approach is likely to find much wider applicability across systems biology as current application domains reach greater levels of maturity.
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Affiliation(s)
- Pras Pathmanathan
- U.S. Food and Drug Administration, 10903 New Hampshire Avenue (WO 62), Silver Spring, MD 20993, USA.
| | - Matthew S Shotwell
- Department of Biostatistics, Vanderbilt University Medical Center, 2525 West End, Ste. 11000, Nashville, TN 37203, USA.
| | - David J Gavaghan
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK.
| | | | - Richard A Gray
- U.S. Food and Drug Administration, 10903 New Hampshire Avenue (WO 62), Silver Spring, MD 20993, USA.
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Du P, Paskaranandavadivel N, O'Grady G, Tang SJ, Cheng LK. A theoretical study of the initiation, maintenance and termination of gastric slow wave re-entry. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2014; 32:405-23. [PMID: 25552487 DOI: 10.1093/imammb/dqu023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/02/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED Gastric slow wave dysrhythmias are associated with motility disorders. Periods of tachygastria associated with slow wave re-entry were recently recognized as one important dysrhythmia mechanism, but factors promoting and sustaining gastric re-entry are currently unknown. This study reports two experimental forms of gastric re-entry and presents a series of multi-scale models that define criteria for slow wave re-entry initiation, maintenance and termination. High-resolution electrical mapping was conducted in porcine and canine models and two spatiotemporal patterns of re-entrant activities were captured: single-loop rotor and double-loop figure-of-eight. Two separate multi-scale mathematical models were developed to reproduce the velocity and entrainment frequency of these experimental recordings. A single-pulse stimulus was used to invoke a rotor re-entry in the porcine model and a figure-of-eight re-entry in the canine model. In both cases, the simulated re-entrant activities were found to be perpetuated by tachygastria that was accompanied by a reduction in the propagation velocity in the re-entrant pathways. The simulated re-entrant activities were terminated by a single-pulse stimulus targeted at the tip of re-entrant wave, after which normal antegrade propagation was restored by the underlying intrinsic frequency gradient. MAIN FINDINGS (i) the stability of re-entry is regulated by stimulus timing, intrinsic frequency gradient and conductivity; (ii) tachygastria due to re-entry increases the frequency gradient while showing decreased propagation velocity; (iii) re-entry may be effectively terminated by a targeted stimulus at the core, allowing the intrinsic slow wave conduction system to re-establish itself.
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Affiliation(s)
- Peng Du
- Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Greg O'Grady
- Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Shou-Jiang Tang
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Leo K Cheng
- Auckland Bioengineering Institute, University of Auckland, New Zealand and Department of Surgery, Vanderbilt University, Nashville, TN, USA
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Trayanova NA, Boyle PM, Arevalo HJ, Zahid S. Exploring susceptibility to atrial and ventricular arrhythmias resulting from remodeling of the passive electrical properties in the heart: a simulation approach. Front Physiol 2014; 5:435. [PMID: 25429272 PMCID: PMC4228852 DOI: 10.3389/fphys.2014.00435] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 12/19/2022] Open
Abstract
Under diseased conditions, remodeling of the cardiac tissue properties (“passive properties”) takes place; these are aspects of electrophysiological behavior that are not associated with active ion transport across cell membranes. Remodeling of the passive electrophysiological properties most often results from structural remodeling, such as gap junction down-regulation and lateralization, fibrotic growth infiltrating the myocardium, or the development of an infarct scar. Such structural remodeling renders atrial or ventricular tissue as a major substrate for arrhythmias. The current review focuses on these aspects of cardiac arrhythmogenesis. Due to the inherent complexity of cardiac arrhythmias, computer simulations have provided means to elucidate interactions pertinent to this spatial scale. Here we review the current state-of-the-art in modeling atrial and ventricular arrhythmogenesis as arising from the disease-induced changes in the passive tissue properties, as well as the contributions these modeling studies have made to our understanding of the mechanisms of arrhythmias in the heart. Because of the rapid advance of structural imaging methodologies in cardiac electrophysiology, we chose to present studies that have used such imaging methodologies to construct geometrically realistic models of cardiac tissue, or the organ itself, where the regional remodeling properties of the myocardium can be represented in a realistic way. We emphasize how the acquired knowledge can be used to pave the way for clinical applications of cardiac organ modeling under the conditions of structural remodeling.
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Affiliation(s)
- Natalia A Trayanova
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Patrick M Boyle
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Hermenegild J Arevalo
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Sohail Zahid
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University Baltimore, MD, USA
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Gaver DP. Invited editorial on "Surface tension in situ in flooded alveolus unaltered by albumin". J Appl Physiol (1985) 2014; 117:423-4. [PMID: 25038107 DOI: 10.1152/japplphysiol.00631.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Donald P Gaver
- Department of Biomedical Engineering, Tulane University, New Orleans, Louisiana
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Abstract
Nuclear cardiac imaging is a noninvasive, sensitive method providing information on cardiac structure and physiology. Single photon emission tomography (SPECT) evaluates myocardial perfusion, viability, and function and is widely used in clinical routine. The quality of the tomographic image is a key for accurate diagnosis. Image filtering, a mathematical processing, compensates for loss of detail in an image while reducing image noise, and it can improve the image resolution and limit the degradation of the image. SPECT images are then reconstructed, either by filter back projection (FBP) analytical technique or iteratively, by algebraic methods. The aim of this study is to review filters in cardiac 2D, 3D, and 4D SPECT applications and how these affect the image quality mirroring the diagnostic accuracy of SPECT images. Several filters, including the Hanning, Butterworth, and Parzen filters, were evaluated in combination with the two reconstruction methods as well as with a specified MatLab program. Results showed that for both 3D and 4D cardiac SPECT the Butterworth filter, for different critical frequencies and orders, produced the best results. Between the two reconstruction methods, the iterative one might be more appropriate for cardiac SPECT, since it improves lesion detectability due to the significant improvement of image contrast.
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Pathmanathan P, Gray RA. Ensuring reliability of safety-critical clinical applications of computational cardiac models. Front Physiol 2013; 4:358. [PMID: 24376423 PMCID: PMC3858646 DOI: 10.3389/fphys.2013.00358] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/21/2013] [Indexed: 12/21/2022] Open
Abstract
Computational models of cardiac electrophysiology have been used for over half a century to investigate physiological mechanisms and generate hypotheses for experimental testing, and are now starting to play a role in clinical applications. There is currently a great deal of interest in using models as diagnostic or therapeutic aids, for example using patient-specific whole-heart simulations to optimize cardiac resynchronization therapy, ablation therapy, and defibrillation. However, if models are to be used in safety-critical clinical decision making, the reliability of their predictions needs to be thoroughly investigated. In engineering and the physical sciences, the field of “verification, validation and uncertainty quantification” (VVUQ) [also known as “verification and validation” (V&V)] has been developed for rigorously evaluating the credibility of computational model predictions. In this article we first discuss why it is vital that cardiac models be developed and evaluated within a VVUQ framework, and then consider cardiac models in the context of each of the stages in VVUQ. We identify some of the major difficulties which may need to be overcome for cardiac models to be used in safely-critical clinical applications.
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Affiliation(s)
- Pras Pathmanathan
- Center for Devices and Radiological Health, U.S. Food and Drug Administration Silver Spring, MD, USA ; Department of Computer Science, University of Oxford Oxford, UK
| | - Richard A Gray
- Center for Devices and Radiological Health, U.S. Food and Drug Administration Silver Spring, MD, USA
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