A collection of papers about Transformer in the field of medical image analysis.

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Deep Learning tensorflow pytorch transformer medical-image-processing medical-image-analysis vision-transformer
Overview

Transformer For Medical Image Analysis

Transformer related papers in medical imaging.

Last updated: 10/13/2021

Image Segmentation

Date First Author Title Modality ND Code Paper
09/30/2021 Yunxiang Li GT U-Net: A U-Net Like Group Transformer Network for Tooth Root Segmentation X-ray & Fundus 2D PyTorch MLMI 2021 arXiv
09/15/2021 Xiaohong Huang MISSFormer: An Effective Medical Image Segmentation Transformer CT 2D N/A arXiv
09/07/2021 Hong-Yu Zhou nnFormer: Interleaved Transformer for Volumetric Segmentation CT 3D PyTorch arXiv
07/28/2021 Madeleine K. Wyburd TEDS-Net: Enforcing Diffeomorphisms in Spatial Transformers to Guarantee Topology Preservation in Segmentations MRI 2D PyTorch MICCAI 2021 arXiv
07/19/2021 Guoping Xu LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation CT 2D N/A arXiv
07/12/2021 Bingzhi Chen TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation X-ray & CT ... 2D N/A arXiv
07/12/2021 Chang Yao TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation CT 2D N/A arXiv
07/02/2021 Yunhe Gao UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation CT 2D PyTorch (unofficial) MICCAI 2021 arXiv
06/28/2021 Yuanfeng Ji Multi-Compound Transformer for Accurate Biomedical Image Segmentation Colonoscopy & Pathology ... 2D PyTorch MICCAI 2021 arXiv
06/12/2021 Ailiang Lin DS-TransUNet: Dual Swin Transformer U-Net for Medical Image Segmentation Colonoscopy & Histology ... 2D N/A arXiv
06/02/2021 Shaohua Li Medical Image Segmentation Using Squeeze-and-Expansion Transformers Fundus & Colonoscopy & MRI 2D & 3D PyTorch IJCAI 2021 arXiv
05/12/2021 Hu Cao Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation CT 2D PyTorch arXiv
04/29/2021 Zhuangzhuang Zhang Pyramid Medical Transformer for Medical Image Segmentation Microscopic 2D N/A arXiv
04/28/2021 Eunji Jun Medical Transformer: Universal Brain Encoder for 3D MRI Analysis MRI 3D N/A arXiv
03/18/2021 Ali Hatamizadeh UNETR: Transformers for 3D Medical Image Segmentation CT & MRI 3D PyTorch arXiv
03/10/2021 Olivier Petit U-Net Transformer: Self and Cross Attention for Medical Image Segmentation CT 2D N/A arXiv
03/07/2021 Wenxuan Wang TransBTS: Multimodal Brain Tumor Segmentation Using Transformer MRI 3D PyTorch MICCAI 2021 arXiv
03/05/2021 Boxiang Yun SpecTr: Spectral Transformer for Hyperspectral Pathology Image Segmentation HSI 3D PyTorch arXiv
03/04/2021 Yutong Xie CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation CT 3D PyTorch MICCAI 2021arXiv
02/26/2021 Davood Karimi Convolution-Free Medical Image Segmentation using Transformers CT & MRI 3D N/A arXiv
02/21/2021 Jeya Maria Jose Valanarasu Medical Transformer: Gated Axial-Attention for Medical Image Segmentation Ultrasound & Microscopic 2D PyTorch MICCAI 2021 arXiv
02/16/2021 Yundong Zhang TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation Colonoscopy 2D N/A arXiv
02/08/2021 Jieneng Chen TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation CT & MRI 2D PyTorch arXiv

Image Registration

Date First Author Title Modality ND Code Paper
04/13/2021 Junyu Chen ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration MRI 3D PyTorch MIDL 2021 arXiv

Image Classification

Date First Author Title Modality ND Code Paper
08/20/2021 Christos Matsoukas Is it Time to Replace CNNs with Transformers for Medical Images? Mammograms... 2D PyTorch ICCV 2021 WorkshoparXiv
06/02/2021 Zhuchen Shao TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classication Pathology 2D N/A arXiv
05/23/2021 Zhiqiang Shen COTR: Convolution in Transformer Network for End to End Polyp Detection Colonoscopy 2D N/A arXiv
04/28/2021 Eunji Jun Medical Transformer: Universal Brain Encoder for 3D MRI Analysis MRI 3D N/A arXiv
03/10/2021 Yin Dai TransMed: Transformers Advance Multi-modal Medical Image Classification MRI 3D N/A arXiv

Image Denoising

Date First Author Title Modality ND Code Paper
09/16/2021 Achleshwar Luthra & Harsh Sulakhe Eformer: Edge Enhancement based Transformer for Medical Image Denoising CT 2D N/A ICCV 2021 arXiv
06/08/2021 Dayang Wang TED-net: Convolution-free T2T Vision Transformer-based Encoder-decoder Dilation network for Low-dose CT Denoising CT 2D N/A MLMI 2021 arXiv
02/28/2021 Zhicheng Zhang TransCT: Dual-path Transformer for Low Dose Computed Tomography CT 2D N/A MICCAI 2021 arXiv

Image Synthesis

Date First Author Title Modality ND Code Paper
06/30/2021 Onat Dalmaz ResViT: Residual vision transformers for multi-modal medical image synthesis MRI & CT 3D N/A arXiv
05/28/2021 Xuzhe Zhang PTNet: A High-Resolution Infant MRI Synthesizer Based on Transformer MRI 2D N/A arXiv

Image Reconstruction

Date First Author Title Modality ND Code Paper
05/21/2021 Yilmaz Korkmaz Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers MRI 3D N/A arXiv

Transformer fundamental papers

Date First Author Title Code Paper
03/25/2021 Ze Liu Swin Transformer: Hierarchical Vision Transformer using Shifted Windows PyTorch arXiv
10/22/2020 Alexey Dosovitskiy An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale JAX PyTorch ICLR 2020 arXiv
12/06/2017 Ashish Vaswani Attention Is All You Need TensorFlow NIPS 2017 arXiv
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Comments
  • About ResViT code

    About ResViT code

    Hello, I recently added the code for ResViT in the following repository: https://github.com/icon-lab/ResViT

    in icon-lab, you can also find the code for Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers.

    Have a great day, Onat

    opened by onat-dalmaz 3
  • Adding UNETR Repository

    Adding UNETR Repository

    Hi @junyuchen245 , nice collection of transformers for medical imaging.

    We have open-sourced UNETR in the following repository:

    https://monai.io/research/unetr-btcv-multi-organ-segmentation

    It currently supports multi-organ segmentation task using BTCV dataset, but more segmentation tasks (BRATS, MSD etc.) will be added later.

    It's also now part of MONAI and can be directly imported:

    https://docs.monai.io/en/latest/_modules/monai/networks/nets/unetr.html

    opened by ahatamiz 2
Owner
Junyu Chen
Ph.D. candidate in the Department of Electrical and Computer Engineering & the Department of Radiology and Radiological Science @ Johns Hopkins University
Junyu Chen
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