# Geometrical Cross-Attention and Nonvoid Voxelization for Efficient 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2604.05515 · HTML: https://mlsanity.com/paper/2604.05515/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 31 references that are in the map.
- First posted on arXiv 7 Apr 2026.

## Builds on (most cited first, 21 of 21)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [4D Spatio-Temporal ConvNets: Minkowski Convolutional Neural Networks](https://mlsanity.com/paper/1904.08755/) (2019)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [3D Semantic Segmentation with Submanifold Sparse Convolutional Networks](https://mlsanity.com/paper/1711.10275/) (2017)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [Searching Efficient 3D Architectures with Sparse Point-Voxel Convolution](https://mlsanity.com/paper/2007.16100/) (2020)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [DSVT: Dynamic Sparse Voxel Transformer with Rotated Sets](https://mlsanity.com/paper/2301.06051/) (2023)
- [ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset](https://mlsanity.com/paper/2206.06694/) (2022)
- [OneFormer3D: One Transformer for Unified Point Cloud Segmentation](https://mlsanity.com/paper/2311.14405/) (2023)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [Lumbar spine segmentation in MR images: a dataset and a public benchmark](https://mlsanity.com/paper/2306.12217/) (2023)
- [E2ENet: Dynamic Sparse Feature Fusion for Accurate and Efficient 3D Medical Image Segmentation](https://mlsanity.com/paper/2312.04727/) (2023)
- [Denoising of 3D magnetic resonance images with multi-channel residual learning of convolutional neural network](https://mlsanity.com/paper/1712.08726/) (2017)

## Abstract (arXiv)

Accurate segmentation of 3D medical scans is crucial for clinical diagnostics and treatment planning, yet existing methods often fail to achieve both high accuracy and computational efficiency across diverse anatomies and imaging modalities. To address these challenges, we propose GCNV-Net, a novel 3D medical segmentation framework that integrates a Tri-directional Dynamic Nonvoid Voxel Transformer (3DNVT), a Geometrical Cross-Attention module (GCA), and Nonvoid Voxelization. The 3DNVT dynamically partitions relevant voxels along the three orthogonal anatomical planes, namely the transverse, sagittal, and coronal planes, enabling effective modeling of complex 3D spatial dependencies. The GCA mechanism explicitly incorporates geometric positional information during multi-scale feature fusion, significantly enhancing fine-grained anatomical segmentation accuracy. Meanwhile, Nonvoid Voxelization processes only informative regions, greatly reducing redundant computation without compromising segmentation quality, and achieves a 56.13% reduction in FLOPs and a 68.49% reduction in inference latency compared to conventional voxelization. We evaluate GCNV-Net on multiple widely used benchmarks: BraTS2021, ACDC, MSD Prostate, MSD Pancreas, and AMOS2022. Our method achieves state-of-the-art segmentation performance across all datasets, outperforming the best existing methods by 0.65% on Dice, 0.63% on IoU, 1% on NSD, and relatively 14.5% on HD95. All results demonstrate that GCNV-Net effectively balances accuracy and efficiency, and its robustness across diverse organs, disease conditions, and imaging modalities highlights strong potential for clinical deployment.