# From Raw Segmentations to Simulation-Ready Cardiac Meshes: An Automated Framework for Anatomical Reconstruction and Virtual Cohort Generation

arXiv: https://arxiv.org/abs/2607.02564 · HTML: https://mlsanity.com/paper/2607.02564/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 56 references that are in the map.
- First posted on arXiv 29 Jun 2026.

## Builds on (most cited first, 13 of 13)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Accelerating 3D Deep Learning with PyTorch3D](https://mlsanity.com/paper/2007.08501/) (2020)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1708.08987/) (2017)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [TotalSegmentator MRI: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in MRI](https://mlsanity.com/paper/2405.19492/) (2024)
- [Multi-Atlas Segmentation of Biomedical Images: A Survey](https://mlsanity.com/paper/1412.3421/) (2014)
- [SDF4CHD: Generative Modeling of Cardiac Anatomies with Congenital Heart Defects](https://mlsanity.com/paper/2311.00332/) (2023)
- [ImageCHD: A 3D Computed Tomography Image Dataset for Classification of Congenital Heart Disease](https://mlsanity.com/paper/2101.10799/) (2021)
- [Point2SSM++: Self-Supervised Learning of Anatomical Shape Models from Point Clouds](https://mlsanity.com/paper/2405.09707/) (2024)
- [Geometric Uncertainty of Patient-Specific Blood Vessels and its Impact on Aortic Hemodynamics](https://mlsanity.com/paper/2410.19472/) (2024)
- [Graph-Convolutional-Beta-VAE for Synthetic Abdominal Aorta Aneurysm Generation](https://mlsanity.com/paper/2506.13628/) (2025)

## Abstract (arXiv)

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.