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Cited by 112Cardiac electrophysiology and arrhythmiasCardiac Arrhythmias and TreatmentsCardiac pacing and defibrillation studies

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A publicly available virtual cohort of four-chamber heart meshes for cardiac electro-mechanics simulations

Open access
Strocchi, Marina, Augustin, Christoph M., Gsell, Matthias A. F., Karabelas, Elias, Neic, Aurel, Gillette, Karli, Razeghi, Orod, Prassl, Anton J., Vigmond, Edward J., Behar, Jonathan M., Gould, Justin, Sidhu, Baldeep, Rinaldi, Christopher A., Bishop, Martin J., Plank, Gernot, Niederer, Steven A.·2020·PLoS ONE
DOI 10.1371/journal.pone.0235145PMC PMC7319311
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Abstract

Computational models of the heart are increasingly being used in the development of devices, patient diagnosis and therapy guidance. While software techniques have been developed for simulating single hearts, there remain significant challenges in simulating cohorts of virtual hearts from multiple patients. To facilitate the development of new simulation and model analysis techniques by groups without direct access to medical data, image analysis techniques and meshing tools, we have created the first publicly available virtual cohort of twenty-four four-chamber hearts. Our cohort was built from heart failure patients, age 67±14 years. We segmented four-chamber heart geometries from end-diastolic (ED) CT images and generated linear tetrahedral meshes with an average edge length of 1.1±0.2mm. Ventricular fibres were added in the ventricles with a rule-based method with an orientation of -60° and 80° at the epicardium and endocardium, respectively. We additionally refined the meshes to an average edge length of 0.39±0.10mm to show that all given meshes can be resampled to achieve an arbitrary desired resolution. We ran simulations for ventricular electrical activation and free mechanical contraction on all 1.1mm-resolution meshes to ensure that our meshes are suitable for electro-mechanical simulations. Simulations for electrical activation resulted in a total activation time of 149±16ms. Free mechanical contractions gave an average left ventricular (LV) and right ventricular (RV) ejection fraction (EF) of 35±1% and 30±2%, respectively, and a LV and RV stroke volume (SV) of 95±28mL and 65±11mL, respectively. By making the cohort publicly available, we hope to facilitate large cohort computational studies and to promote the development of cardiac computational electro-mechanics for clinical applications.

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Fig 1 Pipeline. CT images were acquired in 10 or 20 frames over a whole cardiac cycle. The end-diastolic (ED) geometry was then selected and automatically segmented [31]. The resulting segmentation was post-processed to generate labels representing the RV, LA and RA myocardium, the wall thickness for the aorta and the pulmonary artery, valve planes and rings at the cropped veins. The surface of the segmentation was then smoothed [37] and all the labels but the blood pools and the LV papillary muscles were extracted to generate a tetrahedral mesh. We extracted the endocardial and epicardial surfaces of the atria and ventricles and we assigned fibre orientation to the ventricles with a rule-based method [38]. Finally, we simulated electrical activation and mechanical contraction of the ventricles to test the usability of the meshes.
Fig 1 Pipeline. CT images were acquired in 10 or 20 frames over a whole cardiac cycle. The end-diastolic (ED) geometry was then selected and automatically segmented [31]. The resulting segmentation was post-processed to generate labels representing the RV, LA and RA myocardium, the wall thickness for the aorta and the pulmonary artery, valve planes and rings at the cropped veins. The surface of the segmentation was then smoothed [37] and all the labels but the blood pools and the LV papillary muscles were extracted to generate a tetrahedral mesh. We extracted the endocardial and epicardial surfaces of the atria and ventricles and we assigned fibre orientation to the ventricles with a rule-based method [38]. Finally, we simulated electrical activation and mechanical contraction of the ventricles to test the usability of the meshes.CC BY · PubMed Central
Fig 2 Twenty-four four-chamber heart meshes. The images show an anterior view of the twenty-four meshes generated with the pipeline described in the text.
Fig 2 Twenty-four four-chamber heart meshes. The images show an anterior view of the twenty-four meshes generated with the pipeline described in the text.CC BY · PubMed Central
Fig 3 Labels description. The images on the left and in the center show an anterior and a posterior view of one of the four-chamber meshes. The image on the right shows an anterior view of a clip of the geometry. On the right, the twenty-four labels of the mesh are listed. The first row shows the myocardium of the LV, RV, LA, RA and the wall of the cropped aorta and pulmonary artery (PA). The second row shows the rings at the cropped veins and at the LAA. The third row shows the valve planes added at all inlets and outlets of the LV, RV, LA and RA.
Fig 3 Labels description. The images on the left and in the center show an anterior and a posterior view of one of the four-chamber meshes. The image on the right shows an anterior view of a clip of the geometry. On the right, the twenty-four labels of the mesh are listed. The first row shows the myocardium of the LV, RV, LA, RA and the wall of the cropped aorta and pulmonary artery (PA). The second row shows the rings at the cropped veins and at the LAA. The third row shows the valve planes added at all inlets and outlets of the LV, RV, LA and RA.CC BY · PubMed Central
Fig 4 Universal ventricular coordinates. From left to right: apico-basal coordinate, ranging between 0 at the apex and 1 at the base (anterior view); transmural coordinate, varying from 0 at the endocardium of the LV and of the RV free wall to 1 at the epicardium (top view); rotational coordinate, ranging between −π at the LV free wall, to 0 at the septum and π back to the LV free wall; intra-ventricular coordinate, defined at -1 at the LV and +1 at the RV.
Fig 4 Universal ventricular coordinates. From left to right: apico-basal coordinate, ranging between 0 at the apex and 1 at the base (anterior view); transmural coordinate, varying from 0 at the endocardium of the LV and of the RV free wall to 1 at the epicardium (top view); rotational coordinate, ranging between −π at the LV free wall, to 0 at the septum and π back to the LV free wall; intra-ventricular coordinate, defined at -1 at the LV and +1 at the RV.CC BY · PubMed Central
Fig 5 Electro-mechanical coupling. A The activation times computed by the eikonal model (shown on mesh 01 in the green box) trigger an upstroke in transmembrane potential Vm at each node of the mesh (orange curve in the orange box). When the transmembrane potential overcomes -60mV (black dashed line), the rise in active tension is triggered (blue curve in the blue box). B We show the changes in transmembrane potential (top row) and the active tension (bottom row) over time on mesh 01.
Fig 5 Electro-mechanical coupling. A The activation times computed by the eikonal model (shown on mesh 01 in the green box) trigger an upstroke in transmembrane potential Vm at each node of the mesh (orange curve in the orange box). When the transmembrane potential overcomes -60mV (black dashed line), the rise in active tension is triggered (blue curve in the blue box). B We show the changes in transmembrane potential (top row) and the active tension (bottom row) over time on mesh 01.CC BY · PubMed Central
Fig 6 Anatomical differences. A LV, RV, LA and RA volumes. B Area of the mitral, tricuspid, aortic and pulmonary valve planes. C LV and RV long-axis lengths. D LV diameter. All quantities are shown for the twenty-four meshes.
Fig 6 Anatomical differences. A LV, RV, LA and RA volumes. B Area of the mitral, tricuspid, aortic and pulmonary valve planes. C LV and RV long-axis lengths. D LV diameter. All quantities are shown for the twenty-four meshes.CC BY · PubMed Central
Fig 7 Simulated activation times. The images show an anterior view of all meshes with the ventricles coloured according to the local activation time computed by the eikonal model. The grey regions were excluded by the eikonal solve and were therefore passive. The black structures represent the CRT leads segmented from the CT images. The RV lead was used as the initial activation point.
Fig 7 Simulated activation times. The images show an anterior view of all meshes with the ventricles coloured according to the local activation time computed by the eikonal model. The grey regions were excluded by the eikonal solve and were therefore passive. The black structures represent the CRT leads segmented from the CT images. The RV lead was used as the initial activation point.CC BY · PubMed Central
Fig 8 Simulated free active contraction. The images show the results for the free contraction simulations run on all meshes. For each mesh, we show the configuration at the end of LV systole (coloured according to the magnitude of the displacement vector ||u|| in mm) and the initial configuration (grey geometry).
Fig 8 Simulated free active contraction. The images show the results for the free contraction simulations run on all meshes. For each mesh, we show the configuration at the end of LV systole (coloured according to the magnitude of the displacement vector ||u|| in mm) and the initial configuration (grey geometry).CC BY · PubMed Central

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Metadata

Authors
Strocchi, M., Augustin, C. M., Gsell, M. A. F., Karabelas, E., Neic, A., Gillette, K., Razeghi, O., Prassl, A. J., Vigmond, E. J., Behar, J. M., Gould, J., Sidhu, B., Rinaldi, C. A., Bishop, M. J., Plank, G., & Niederer, S. A.
Affiliations
  • King's College London (GB)
  • Medical University of Graz (AT)
  • Université de Bordeaux (FR)
Corresponding author
Strocchi, Marina
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2020-06-26
Volume
15
Issue
6
Pages
e0235145
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0235145
PMC
PMC7319311
OpenAlex
W3037817333
Cited by
112
References
111
Citations by year
2026: 13 · 2025: 17 · 2024: 18 · 2023: 24 · 2022: 21 · 2021: 15 · 2020: 3
FWCI
9.75
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Portal (King's College London) (publishedVersion, other-oa)
  • HAL (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Oskar-Bordeaux (Universite de Bordeaux) (submittedVersion)
  • Unipub UB Graz (Universität Graz) (submittedVersion, cc-by)
Funders
  • Engineering and Physical Sciences Research Council (EP/M012492/1, NS/A000049/1, EP/L015226/1 and EP/P01268X/1)
  • British Heart Foundation (PG/15/91/31812 and PG/13/37/30280)
  • Kings Health Partners London National Institute for Health Research (NIHR) Biomedical Research Centre
  • H2020 Marie Skłodowska-Curie Actions (750835)
  • Austrian Science Fund (PI2760-B30)
Topics
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiac electrophysiology and arrhythmias
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiac Arrhythmias and Treatments
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiac pacing and defibrillation studies
Keywords
cardiac electromechanics, heart failure, tetrahedral meshes, ejection fraction, stroke volume
MeSH terms
Adult, Aged, Aged, 80 and over, Computer Simulation, Female, Heart Failure, Heart Ventricles, Humans, Male, Middle Aged, Surgical Mesh, Cohort Studies, Ventricular Function, Left, Ventricular Function, Right

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