This repository complements our survey paper Transformers in Medical Imaging: A Survey, published in Medical Image Analysis.

📢📢🏆🏆🏆 Spotlight: Our article is now among the Top-3 Most Downloaded Articles of the Medical Image Analysis Journal! 🏆🏆🏆

Authors: Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat, Fahad Shahbaz Khan, and Huazhu Fu

`Awesome Transformers in Medical Imaging`

A curated list of awesome Transformers resources in medical imaging (in chronological order), inspired by the other awesome-initiatives. We intend to regularly update the relevant latest papers and their open-source implementations on this page.

We strongly encourage the researchers that want to promote their fantastic work to the community to make pull request to update their paper's information!

Survey

Transformers in Medical Imaging: A survey. [25th Jan., 2022]
. Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat, Fahad Shahbaz Khan, and Huazhu Fu.
[PDF]

Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review. [9th Jan., 2023].
Reza Azad, Amirhossein Kazerouni, Moein Heidari, Ehsan Khodapanah Aghdam, Amirali Molaei, Yiwei Jia, Abin Jose, Rijo Roy, Dorit Merhof [Paper]

Medical image analysis based on transformer: A Review. [13th Aug., 2022].
Zhaoshan Liu, Lei Shen.
[PDF]

Transforming medical imaging with Transformers? A comparative review of key properties, current progresses, and future perspectives. [3rd June, 2022].
Jun Li, Junyu Chen, Yucheng Tang, Ce Wang, Bennett A. Landman, S. Kevin Zhou.
[PDF]

Vision Transformers in Medical Computer Vision -- A Contemplative Retrospection. [29th March, 2022].
Arshi Parvaiz, Muhammad Anwaar Khalid, Rukhsana Zafar, Huma Ameer, Muhammad Ali, Muhammad Moazam Fraz.
[PDF]

Transformers in Medical Image Analysis: A Review. [24th Feb., 2022].
Kelei He, Chen Gan, Zhuoyuan Li, Islem Rekik, Zihao Yin, Wen Ji, Yang Gao, Qian Wang, Junfeng Zhang, Dinggang Shen.
[PDF]

Application of Transformer in Medical Image Segmentation. [25th Oct., 2021].
Wenyin Zhang, Weijie Hao, Yuan Qi and Yong Wu.
[PDF]

Segmentation

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures. [20th Nov., 2020] [BIBM, 2020].
Tim Prangemeier, Christoph Reich, Heinz Koeppl.
[PDF] [Github]

TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation. [8th Feb., 2021].
Jieneng Chen, Yongyi Lu, Qihang Yu, Xiangde Luo, Ehsan Adeli, Yan Wang, Le Lu, Alan L. Yuille, Yuyin Zhou.
[PDF] [Github]

TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation. [16th Feb., 2021] [⚡MICCAI, 2021].
Yundong Zhang, Huiye Liu, Qiang Hu.
[PDF] [Github]

Unsupervised Brain Anomaly Detection and Segmentation with Transformers. [23rd Feb., 2021] [MIDL, 2021].
Walter Hugo Lopez Pinaya, Petru-Daniel Tudosiu, Robert Gray, Geraint Rees, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso.
[PDF]

Convolution-Free Medical Image Segmentation using Transformers. [26th Feb., 2021] [⚡MICCAI, 2021].
Davood Karimi, Serge Vasylechko, Ali Gholipour.
[PDF]

CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation. [4th March, 2021] [⚡MICCAI, 2021].
Yutong Xie, Jianpeng Zhang, Chunhua Shen, Yong Xia.
[PDF] [Github]

SpecTr: Spectral Transformer for Hyperspectral Pathology Image Segmentation. [5th March, 2021].
Boxiang Yun, Yan Wang, Jieneng Chen, Huiyu Wang, Wei Shen, Qingli Li.
[PDF] [Github]

TransBTS: Multimodal Brain Tumor Segmentation Using Transformer. [7th March, 2021] [⚡MICCAI, 2021].
Wenxuan Wang, Chen Chen, Meng Ding, Jiangyun Li, Hong Yu, Sen Zha.
[PDF] [Github]

U-Net Transformer: Self and Cross Attention for Medical Image Segmentation. [10th March, 2021].
Olivier Petit, Nicolas Thome, Clément Rambour, Luc Soler.
[PDF] [Github]

UNETR: Transformers for 3D Medical Image Segmentation . [18th March, 2021].
Ali Hatamizadeh, Yucheng Tang, Vishwesh Nath, Dong Yang, Andriy Myronenko, Bennett Landman, Holger Roth, Daguang Xu.
[PDF] [Github]

Medical Transformer: Universal Brain Encoder for 3D MRI Analysis. [28th April, 2021].
Eunji Jun, Seungwoo Jeong, Da-Woon Heo, Heung-Il Suk.
[PDF]

Pyramid Medical Transformer for Medical Image Segmentation . [29th April, 2021].
Zhuangzhuang Zhang, Baozhou Sun, Weixiong Zhang.
[PDF]

GasHis-Transformer: A Multi-scale Visual Transformer Approach for Gastric Histopathology Image Classification. [29th April, 2021].
Haoyuan Chen, Chen Li, Xiaoyan Li, Ge Wang, Weiming Hu, Yixin Li, Wanli Liu, Changhao Sun, Yudong Yao, Yueyang Teng, Marcin Grzegorzek.
[PDF]

Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentationr. [12th May, 2021].
Hu Cao, Yueyue Wang, Joy Chen, Dongsheng Jiang, Xiaopeng Zhang, Qi Tian, Manning Wang.
[PDF]

Medical Image Segmentation Using Squeeze-and-Expansion Transformers. [20th May, 2021] [⚡IJCAI, 2021].
Shaohua Li, Xiuchao Sui, Xiangde Luo, Xinxing Xu, Yong Liu, Rick Goh.
[PDF] [Github]

A Multi-Branch Hybrid Transformer Network for Corneal Endothelial Cell Segmentation. [21st May, 2021] [⚡MICCAI, 2021].
Yinglin Zhang, Risa Higashita, Huazhu Fu, Yanwu Xu, Yang Zhang, Haofeng Liu, Jian Zhang, Jiang Liu.
[PDF]

DS-TransUNet:Dual Swin Transformer U-Net for Medical Image Segmentation. [12 June, 2021].
Ailiang Lin, Bingzhi Chen, Jiayu Xu, Zheng Zhang, Guangming Lu.
[PDF]

More than Encoder: Introducing Transformer Decoder to Upsample. [20th June, 2021].
Yijiang Li, Wentian Cai, Ying Gao, Xiping Hu.
[PDF]

Multi-Compound Transformer for Accurate Biomedical Image Segmentation. [28th June, 2021] [⚡MICCAI, 2021].
Yuanfeng Ji, Ruimao Zhang, Huijie Wang, Zhen Li, Lingyun Wu, Shaoting Zhang, Ping Luo.
[PDF] [Github]

UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation. [2nd July, 2021] [⚡MICCAI, 2021].
Yunhe Gao, Mu Zhou, Dimitris Metaxas.
[PDF] [Github]

Few-Shot Domain Adaptation with Polymorphic Transformers. [10th July, 2021] [⚡MICCAI, 2021].
Shaohua Li, Xiuchao Sui, Jie Fu, Huazhu Fu, Xiangde Luo, Yangqin Feng, Xinxing Xu, Yong Liu, Daniel Ting, Rick Siow Mong Goh.
[PDF] [Github]

TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation. [12th July, 2021].
Yao Chang, Hu Menghan, Zhai Guangtao, Zhang Xiao-Ping.
[PDF]

TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation. [12th July, 2021].
Bingzhi Chen, Yishu Liu, Zheng Zhang, Guangming Lu, David Zhang.
[PDF]

LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation. [19th July, 2021].
Guoping Xu, Xingrong Wu, Xuan Zhang, Xinwei He.
[PDF] [Github]

Polyp-PVT: Polyp Segmentation with Pyramid Vision Transformers. [16th August, 2021].
Bo Dong, Wenhai Wang, Deng-Ping Fan, Jinpeng Li, Huazhu Fu, Ling Shao.
[PDF] [Github]

Evaluating Transformer-based Semantic Segmentation Networks for Pathological Image Segmentation. [26th August, 2021].
Cam Nguyen, Zuhayr Asad, Yuankai Huo.
[PDF]

Automated Kidney Tumor Segmentation with Convolution and Transformer Network. [30th August, 2021] [👍 MICCAI KiTS Challenge, 2021].
Zhiqiang Shen, Zhiqiang_Shen, Hua Yang, Zhen Zhang, Shaohua Zheng.
[PDF]

nnFormer: Interleaved Transformer for Volumetric Segmentation. [7th Sep., 2021].
Hong-Yu Zhou, Jiansen Guo, Yinghao Zhang, Lequan Yu, Liansheng Wang, Yizhou Yu.
[PDF] [Github]

UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer. [9th, Sep.,].
Haonan Wang, Peng Cao, Jiaqi Wang, Osmar R.Zaiane.
[PDF]