# CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2103.03024 · HTML: https://mlsanity.com/paper/2103.03024/

## Key facts

- Cited by 227 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 30 references that are in the map.
- First posted on arXiv 4 Mar 2021.

## Builds on (most cited first, 25 of 25)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [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)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [Non-local Neural Networks](https://mlsanity.com/paper/1711.07971/) (2017)
- [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)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [Multi-Scale Context Aggregation by Dilated Convolutions](https://mlsanity.com/paper/1511.07122/) (2015)
- [Pre-Trained Image Processing Transformer](https://mlsanity.com/paper/2012.00364/) (2020)
- [Image Transformer](https://mlsanity.com/paper/1802.05751/) (2018)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [End-to-End Video Instance Segmentation with Transformers](https://mlsanity.com/paper/2011.14503/) (2020)
- [Large Kernel Matters -- Improve Semantic Segmentation by Global Convolutional Network](https://mlsanity.com/paper/1703.02719/) (2017)
- [Multi-organ Segmentation over Partially Labeled Datasets with Multi-scale Feature Abstraction](https://mlsanity.com/paper/2001.00208/) (2020)
- [Inductive Bias of Deep Convolutional Networks through Pooling Geometry](https://mlsanity.com/paper/1605.06743/) (2016)
- [Inter-slice Context Residual Learning for 3D Medical Image Segmentation](https://mlsanity.com/paper/2011.14155/) (2020)

## Built on by (most cited first, 30 of 227)

- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [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)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [CLIP-Driven Universal Model for Organ Segmentation and Tumor Detection](https://mlsanity.com/paper/2301.00785/) (2023)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [ResViT: Residual vision transformers for multi-modal medical image synthesis](https://mlsanity.com/paper/2106.16031/) (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)
- [BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once](https://mlsanity.com/paper/2405.12971/) (2024)
- [Recent advances and clinical applications of deep learning in medical image analysis](https://mlsanity.com/paper/2105.13381/) (2021)
- [MISSFormer: An Effective Medical Image Segmentation Transformer](https://mlsanity.com/paper/2109.07162/) (2021)
- [Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer](https://mlsanity.com/paper/2112.04894/) (2021)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [TransMed: Transformers Advance Multi-modal Medical Image Classification](https://mlsanity.com/paper/2103.05940/) (2021)
- [Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation](https://mlsanity.com/paper/2207.14191/) (2022)
- [Delving into Masked Autoencoders for Multi-Label Thorax Disease Classification](https://mlsanity.com/paper/2210.12843/) (2022)
- [Large AI Models in Health Informatics: Applications, Challenges, and the Future](https://mlsanity.com/paper/2303.11568/) (2023)
- [UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier](https://mlsanity.com/paper/2112.09356/) (2021)
- [ImageCAS: A Large-Scale Dataset and Benchmark for Coronary Artery Segmentation based on Computed Tomography Angiography Images](https://mlsanity.com/paper/2211.01607/) (2022)
- [AFTer-UNet: Axial Fusion Transformer UNet for Medical Image Segmentation](https://mlsanity.com/paper/2110.10403/) (2021)
- [XoFTR: Cross-modal Feature Matching Transformer](https://mlsanity.com/paper/2404.09692/) (2024)
- [UniSeg: A Prompt-driven Universal Segmentation Model as well as A Strong Representation Learner](https://mlsanity.com/paper/2304.03493/) (2023)
- [TriTransNet: RGB-D Salient Object Detection with a Triplet Transformer Embedding Network](https://mlsanity.com/paper/2108.03990/) (2021)
- [A Data-scalable Transformer for Medical Image Segmentation: Architecture, Model Efficiency, and Benchmark](https://mlsanity.com/paper/2203.00131/) (2022)

## Abstract (arXiv)

Convolutional neural networks (CNNs) have been the de facto standard for nowadays 3D medical image segmentation. The convolutional operations used in these networks, however, inevitably have limitations in modeling the long-range dependency due to their inductive bias of locality and weight sharing. Although Transformer was born to address this issue, it suffers from extreme computational and spatial complexities in processing high-resolution 3D feature maps. In this paper, we propose a novel framework that efficiently bridges a bf Convolutional neural network and a bf Transformer bf (CoTr) for accurate 3D medical image segmentation. Under this framework, the CNN is constructed to extract feature representations and an efficient deformable Transformer (DeTrans) is built to model the long-range dependency on the extracted feature maps. Different from the vanilla Transformer which treats all image positions equally, our DeTrans pays attention only to a small set of key positions by introducing the deformable self-attention mechanism. Thus, the computational and spatial complexities of DeTrans have been greatly reduced, making it possible to process the multi-scale and high-resolution feature maps, which are usually of paramount importance for image segmentation. We conduct an extensive evaluation on the Multi-Atlas Labeling Beyond the Cranial Vault (BCV) dataset that covers 11 major human organs. The results indicate that our CoTr leads to a substantial performance improvement over other CNN-based, transformer-based, and hybrid methods on the 3D multi-organ segmentation task. Code is available at defUrlFontrmsmallttfamily urlhttps://github.com/YtongXie/CoTr