<p align=center> 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

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<p align=center>Awesome Transformers in Medical Imaging</p>

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!

Overview

• Survey papers
• Medical Image Segmentation
• Medical Image Classification
• Medical Image Reconstruction
• Medical Image Registration
• Medical Image Synthesis
• Medical Image Detection
• Clinical Report Generation
• Others

Survey

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

Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review. [9th Jan., 2023].<br> 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].<br> Zhaoshan Liu, Lei Shen.<br> [PDF]

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

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

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

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

Segmentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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