# Abdominal organ segmentation via deep diffeomorphic mesh deformations

arXiv: https://arxiv.org/abs/2306.15515 · HTML: https://mlsanity.com/paper/2306.15515/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 39 references that are in the map.
- First posted on arXiv 27 Jun 2023.

## Builds on (most cited first, 20 of 20)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Accelerating 3D Deep Learning with PyTorch3D](https://mlsanity.com/paper/2007.08501/) (2020)
- [Pixel2Mesh: Generating 3D Mesh Models from Single RGB Images](https://mlsanity.com/paper/1804.01654/) (2018)
- [Cyclical Learning Rates for Training Neural Networks](https://mlsanity.com/paper/1506.01186/) (2015)
- [AtlasNet: A Papier-Mach'e Approach to Learning 3D Surface Generation](https://mlsanity.com/paper/1802.05384/) (2018)
- [Augmented Neural ODEs](https://mlsanity.com/paper/1904.01681/) (2019)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [Neural Mesh Flow: 3D Manifold Mesh Generation via Diffeomorphic Flows](https://mlsanity.com/paper/2007.10973/) (2020)
- [3DN: 3D Deformation Network](https://mlsanity.com/paper/1903.03322/) (2019)
- [Voxel2Mesh: 3D Mesh Model Generation from Volumetric Data](https://mlsanity.com/paper/1912.03681/) (2019)
- [A Deep-Learning Approach For Direct Whole-Heart Mesh Reconstruction](https://mlsanity.com/paper/2102.07899/) (2021)
- [Vox2Cortex: Fast Explicit Reconstruction of Cortical Surfaces from 3D MRI Scans with Geometric Deep Neural Networks](https://mlsanity.com/paper/2203.09446/) (2022)
- [CorticalFlow++: Boosting Cortical Surface Reconstruction Accuracy, Regularity, and Interoperability](https://mlsanity.com/paper/2206.06598/) (2022)
- [Spatial Correspondence between Graph Neural Network-Segmented Images](https://mlsanity.com/paper/2303.06550/) (2023)

## Built on by (most cited first, 4 of 4)

- [Non-Rigid 3D Shape Correspondences: From Foundations to Open Challenges and Opportunities](https://mlsanity.com/paper/2604.01274/) (2026)
- [Teaching AI the Anatomy Behind the Scan: Addressing Anatomical Flaws in Medical Image Segmentation with Learnable Prior](https://mlsanity.com/paper/2403.18878/) (2024)
- [Implicit Shape-Prior for Few-Shot Assisted 3D Segmentation](https://mlsanity.com/paper/2509.08580/) (2025)
- [KidMesh: Computational Mesh Reconstruction for Pediatric Congenital Hydronephrosis Using Deep Neural Networks](https://mlsanity.com/paper/2602.13299/) (2026)

## Abstract (arXiv)

Abdominal organ segmentation from CT and MRI is an essential prerequisite for surgical planning and computer-aided navigation systems. It is challenging due to the high variability in the shape, size, and position of abdominal organs. Three-dimensional numeric representations of abdominal shapes with point-wise correspondence to a template are further important for quantitative and statistical analyses thereof. Recently, template-based surface extraction methods have shown promising advances for direct mesh reconstruction from volumetric scans. However, the generalization of these deep learning-based approaches to different organs and datasets, a crucial property for deployment in clinical environments, has not yet been assessed. We close this gap and employ template-based mesh reconstruction methods for joint liver, kidney, pancreas, and spleen segmentation. Our experiments on manually annotated CT and MRI data reveal limited generalization capabilities of previous methods to organs of different geometry and weak performance on small datasets. We alleviate these issues with a novel deep diffeomorphic mesh-deformation architecture and an improved training scheme. The resulting method, UNetFlow, generalizes well to all four organs and can be easily fine-tuned on new data. Moreover, we propose a simple registration-based post-processing that aligns voxel and mesh outputs to boost segmentation accuracy.