Dataset DOI: 10.5061/dryad.kkwh70sg0

These meshes are linked to an accepted paper which will be published around mid-August 2025. Once the paper is published and the embargo period has ended, a link will be added to this repository. If you use these models, please cite this repository our paper.

Description of the data and file structure

This repository contains computational meshes of human left atria segmented from late gadolinium enhanced cardiac magnetic resonance imaging (LGE-MRI) for patients receiving a catheter ablation for atrial fibrillation. There are two models per patient (pre-ablation with patterns of fibrotic remodeling, post-ablation with scar created by the procedure) for 82 individuals. These meshes support the replication of our findings while protecting confidential patient information.

Files and variables

Computational meshes are provided in VTK format. The same deidentified numbers used in the publication to identify the holdout patients correspond to the meshes for ID numbers 1-15 in this dataset. Patients in the original cohort were assigned ID numbers 21-87.

We used this format (vtk_bin) in the interest of reproducibility. To reduce the total size of the repository, meshes have been downsampled to an average edge length of 0.5 mm; before running simulations using these meshes, please consider resampling to an appropriate resolution (e.g., ~0.2 mm for reaction-diffuction simulations of electrophysiology). These files can be converted to a machine- and human-readable text format compatible with the openCARP simulation framework using the free software meshtool (available here), e.g.:

$ /path/to/meshtool convert -imsh ID001_PostAbl -ifmt vtk_bin -omsh ID001_PostAbl -ofmt carp_txt

Once each mesh is converted from carp_bin to carp_txt format, the resulting files (.pts, .elem, .lon) can be opened in a text editor and the explicit values of Cartesian coordinates, element specifications, and fiber orientation vectors can be seen.

Attached files are structured as follows.

• holdout_cohort.tgz
  • ID001_PreAbl_rev1.vtk
  • ID001_PostAbl_rev1.vtk
  • ...
  • ID015_PreAbl_rev1.vtk
  • ID015_PostAbl_rev1.vtk
• training_cohort.tgz
  • ID021_PreAbl_rev1.vtk
  • ID021_PostAbl_rev1.vtk
  • ...
  • ID087_PreAbl_rev1.vtk
  • ID087_PostAbl_rev1.vtk

Code/software

We used openCARP (https://opencarp.org/) [1] to run simulations. openCARP is open software licensed under the Academic Public License. Please read and abide by the relevant licenses if you choose to use these tools. More information about the licenses for both of these tools is available at this stable link: https://opencarp.org/download/license.

A good option for visualizing these models is NumeriCor Studio for Academia, which is freely available and has binary installers for Linux, Mac, and Windows. .vtk files can also be used with the free/open source Paraview software: https://www.paraview.org/. 

References

1. Plank, G. et al. The openCARP simulation environment for cardiac electrophysiology. Comput Methods Programs Biomed 208, 106223 (2021). https://doi.org/10.1016/j.cmpb.2021.106223

Human subjects data

This repository contains computational meshes of human left atria segmented from late gadolinium enhanced cardiac magnetic resonance imaging. These meshes support the replication of our findings while protecting confidential patient information. This study was approved by the University of Washington Institutional Review Board. All participants provided written informed consent.