# AgileFormer: Spatially Agile Transformer UNet for Medical Image Segmentation

arXiv: https://arxiv.org/abs/2404.00122 · HTML: https://mlsanity.com/paper/2404.00122/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 53 references that are in the map.
- First posted on arXiv 29 Mar 2024.

## Builds on (most cited first, 30 of 43)

- [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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Deformable Convolutional Networks](https://mlsanity.com/paper/1703.06211/) (2017)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Self-Attention with Relative Position Representations](https://mlsanity.com/paper/1803.02155/) (2018)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [MaxViT: Multi-Axis Vision Transformer](https://mlsanity.com/paper/2204.01697/) (2022)
- [Conditional Positional Encodings for Vision Transformers](https://mlsanity.com/paper/2102.10882/) (2021)
- [Road Extraction by Deep Residual U-Net](https://mlsanity.com/paper/1711.10684/) (2017)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [Vision Transformer with Deformable Attention](https://mlsanity.com/paper/2201.00520/) (2022)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [Neighborhood Attention Transformer](https://mlsanity.com/paper/2204.07143/) (2022)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation](https://mlsanity.com/paper/2303.09975/) (2023)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [Mixed Transformer U-Net For Medical Image Segmentation](https://mlsanity.com/paper/2111.04734/) (2021)
- [HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation](https://mlsanity.com/paper/2207.08518/) (2022)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)

## Built on by (most cited first, 3 of 3)

- [SACNet: A Spatially Adaptive Convolution Network for 2D Multi-organ Medical Segmentation](https://mlsanity.com/paper/2407.10157/) (2024)
- [D2-MLP: Dynamic Decomposed MLP Mixer for Medical Image Segmentation](https://mlsanity.com/paper/2409.08905/) (2024)
- [EXR: An Interactive Immersive EHR Visualization in Extended Reality](https://mlsanity.com/paper/2512.05438/) (2025)

## Abstract (arXiv)

In the past decades, deep neural networks, particularly convolutional neural networks, have achieved state-of-the-art performance in a variety of medical image segmentation tasks. Recently, the introduction of the vision transformer (ViT) has significantly altered the landscape of deep segmentation models. There has been a growing focus on ViTs, driven by their excellent performance and scalability. However, we argue that the current design of the vision transformer-based UNet (ViT-UNet) segmentation models may not effectively handle the heterogeneous appearance (e.g., varying shapes and sizes) of objects of interest in medical image segmentation tasks. To tackle this challenge, we present a structured approach to introduce spatially dynamic components to the ViT-UNet. This adaptation enables the model to effectively capture features of target objects with diverse appearances. This is achieved by three main components: (i) deformable patch embedding; (ii) spatially dynamic multi-head attention; (iii) deformable positional encoding. These components were integrated into a novel architecture, termed AgileFormer. AgileFormer is a spatially agile ViT-UNet designed for medical image segmentation. Experiments in three segmentation tasks using publicly available datasets demonstrated the effectiveness of the proposed method. The code is available at hrefhttps://github.com/sotiraslab/AgileFormerhttps://github.com/sotiraslab/AgileFormer.