Dataset Open Access

A Publicly Available Virtual Cohort of Four-chamber Heart Meshes for Cardiac Electro-mechanics Simulations

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 S.; Sidhu, Baldeep; Rinaldi, Christopher A.; Bishop, Martin J.; Plank, Gernot; Niederer, Steven A.


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  <identifier identifierType="DOI">10.5281/zenodo.3890034</identifier>
  <creators>
    <creator>
      <creatorName>Strocchi, Marina</creatorName>
      <givenName>Marina</givenName>
      <familyName>Strocchi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1312-251X</nameIdentifier>
      <affiliation>King's College London</affiliation>
    </creator>
    <creator>
      <creatorName>Augustin, Christoph M.</creatorName>
      <givenName>Christoph M.</givenName>
      <familyName>Augustin</familyName>
      <affiliation>Medical University of Graz</affiliation>
    </creator>
    <creator>
      <creatorName>Gsell, Matthias A. F.</creatorName>
      <givenName>Matthias A. F.</givenName>
      <familyName>Gsell</familyName>
      <affiliation>Medical University of Graz</affiliation>
    </creator>
    <creator>
      <creatorName>Karabelas, Elias</creatorName>
      <givenName>Elias</givenName>
      <familyName>Karabelas</familyName>
      <affiliation>King's College London</affiliation>
    </creator>
    <creator>
      <creatorName>Neic, Aurel</creatorName>
      <givenName>Aurel</givenName>
      <familyName>Neic</familyName>
      <affiliation>NumeriCor GmbH</affiliation>
    </creator>
    <creator>
      <creatorName>Gillette, Karli</creatorName>
      <givenName>Karli</givenName>
      <familyName>Gillette</familyName>
      <affiliation>Medical University of Graz</affiliation>
    </creator>
    <creator>
      <creatorName>Razeghi, Orod</creatorName>
      <givenName>Orod</givenName>
      <familyName>Razeghi</familyName>
      <affiliation>King's College London</affiliation>
    </creator>
    <creator>
      <creatorName>Prassl, Anton J.</creatorName>
      <givenName>Anton J.</givenName>
      <familyName>Prassl</familyName>
      <affiliation>Medical University of Graz</affiliation>
    </creator>
    <creator>
      <creatorName>Vigmond, Edward J.</creatorName>
      <givenName>Edward J.</givenName>
      <familyName>Vigmond</familyName>
      <affiliation>LIRYC, University of Bordeaux</affiliation>
    </creator>
    <creator>
      <creatorName>Behar, Jonathan M.</creatorName>
      <givenName>Jonathan M.</givenName>
      <familyName>Behar</familyName>
      <affiliation>King's College London, Guys and St Thomas' NHS Foundation Trust</affiliation>
    </creator>
    <creator>
      <creatorName>Gould, Justin S.</creatorName>
      <givenName>Justin S.</givenName>
      <familyName>Gould</familyName>
      <affiliation>King's College London, Guys and St Thomas' NHS Foundation Trust</affiliation>
    </creator>
    <creator>
      <creatorName>Sidhu, Baldeep</creatorName>
      <givenName>Baldeep</givenName>
      <familyName>Sidhu</familyName>
      <affiliation>King's College London, Guys and St Thomas' NHS Foundation Trust</affiliation>
    </creator>
    <creator>
      <creatorName>Rinaldi, Christopher A.</creatorName>
      <givenName>Christopher A.</givenName>
      <familyName>Rinaldi</familyName>
      <affiliation>King's College London, Guys and St Thomas' NHS Foundation Trust</affiliation>
    </creator>
    <creator>
      <creatorName>Bishop, Martin J.</creatorName>
      <givenName>Martin J.</givenName>
      <familyName>Bishop</familyName>
      <affiliation>King's College London</affiliation>
    </creator>
    <creator>
      <creatorName>Plank, Gernot</creatorName>
      <givenName>Gernot</givenName>
      <familyName>Plank</familyName>
      <affiliation>Medical University of Graz</affiliation>
    </creator>
    <creator>
      <creatorName>Niederer, Steven A.</creatorName>
      <givenName>Steven A.</givenName>
      <familyName>Niederer</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4612-6982</nameIdentifier>
      <affiliation>King's College London</affiliation>
    </creator>
  </creators>
  <titles>
    <title>A Publicly Available Virtual Cohort of Four-chamber Heart Meshes for Cardiac Electro-mechanics Simulations</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Four-chamber Heart, Heart Model, Electrophysiology, Mechanics, Finite Elements</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-06-11</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3890034</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3890033</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Motivation:&amp;nbsp;&lt;/strong&gt; 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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Dataset Description: &lt;/strong&gt;We present the first database of four-chamber heart models suitable for electro-mechanical simulations. Our database consists of twenty-four four-chamber heart models generated from end-diastolic CT acquired from heart failure patients recruited for cardiac resynchronization therapy upgrade. We also provide a higher resolution version for each of the twenty-four meshes.&lt;/p&gt;

&lt;p&gt;We segmented end-diastolic CT. The segmentation was then upsampled and smoothed. The final multi-label segmentation was used to generate a tetrahedral mesh. The resulting meshes had an average edge length of 1.1mm. The elements of all the twenty-four meshes are labelled as follows: 1) Left ventricle myocardium 2) Right ventricle myocardium 3) Left atrium myocardium 4) Right atrium myocardium 5) Aorta wall 6) Pulmonary artery wall 7) Left atrium appendage ring 8) Left superior pulmonary vein ring 9) Left inferior pulmonary vein ring 10) Right inferior pulmonary vein ring 11) Right superior pulmonary vein ring 12) Superior vena cava ring 13) Inferior vena cava ring 14) Mitral valve plane 15) Tricuspid valve plane 16) Aortic valve plane 17) Pulmonary valve plane 18) Left atrial appendage valve plane 19) Left superior pulmonary vein valve plane 20) Left inferior pulmonary vein valve plane 21) Right inferior pulmonary vein valve plane 22) Right superior pulmonary vein valve plane 23) Superior vena cava valve plane 24) Inferior vena cava valve plane.&lt;/p&gt;

&lt;p&gt;Ventricular fibres were generated using a rule-based method, with a fibre orientation varying transmurally from endocardium to epicardium from 80˚ to -60˚, respectively.&amp;nbsp; We defined a system of universal ventricular coordinates on the meshes, see Figure 1B: an apico-basal coordinate varying continuously from 0 at the apex to 1 at the base; a transmural coordinate varying continuously from 0 at the endocardium to 1 at the epicardium; a rotational coordinate varying continuously from &amp;ndash; &amp;pi; at the left ventricular free wall, 0 at the septum and then back to + &amp;pi; at the left ventricular free wall; intra-ventricular coordinate defined at -1 at the left ventricle and +1 at the right ventricle. This coordinate system was assigned to the ventricles in the four-chamber meshes and all the other labels were assigned with -100.&amp;nbsp;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;We also refined each mesh from 1.1mm resolution down to 0.39mm resolution. Each refined mesh has tags defined on its elements (same numbering as described above) and ventricular fibres.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Database format: &lt;/strong&gt;We provide a zipped folder for each mesh. Each folder contains the coarse and the finer versions of the same mesh. All twenty-four 1mm-meshes are supplied in case format, readable with paraview. All binary files containing the meshes data (ens and geo formats) are provided within the zipped folder. Points coordinates are given in mm. Element tags are assigned to the elements of the mesh as well as fibres and sheet directions. Fibres and sheet directions are assigned to the ventricles according to a rule-based method, while non-ventricular elements are assigned with default vectors [1; 0; 0] and [0; 1; 0]. UVCs are assigned to the nodes of the meshes. We also provide the location of the cardiac resynchronisation therapy right-ventricular electrode used to initiate ventricular excitation. This is given as a label on the nodes called electrode endo rv, which is 1 at the stimulated nodes. Finer meshes are provided in vtk format, also readable in paraview. For these meshes, we provide element tags, fibres and sheet directions on the ventricles, all in the same file.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/EPSRC/EP%2FL015226%2F1/">EP/L015226/1</awardNumber>
      <awardTitle>EPSRC Centre for Doctoral Training in Medical Imaging</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/EPSRC/EP%2FM012492%2F1/">EP/M012492/1</awardNumber>
      <awardTitle>Personalised Model Based Optimal Lead Guidance in Cardiac Resynchronisation Therapy</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/EPSRC/NS%2FA000049%2F1/">NS/A000049/1</awardNumber>
      <awardTitle>Wellcome EPSRC Centre for Medical Engineering</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/EPSRC/EP%2FP01268X%2F1/">EP/P01268X/1</awardNumber>
      <awardTitle>Uncertainty Quantification in Prospective and Predictive Patient Specific Cardiac Models</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/750835/">750835</awardNumber>
      <awardTitle>Image-based High-resolution In-silico Modeling of Total Cardiac Function</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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