Transformer For Medical Image Analysis

Transformer related papers in medical imaging.

Please check out our survey paper:
Li, J., Chen, J., Tang, Y., Wang, C., Landman, B. A., & Zhou, S. K. (2023). Transforming medical imaging with Transformers? A comparative review of key properties, current progresses, and future perspectives. Medical image analysis, 102762.

Last updated: 03/17/2022

Image Segmentation

Date	First Author	Title	Modality	ND	Code	Paper
03/10/2022	Lihao Liu	PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation	MRI	3D	N/A
03/10/2022	Lei Zhou	Self Pre-training with Masked Autoencoders for Medical Image Analysis	CT & MRI	3D	N/A
01/30/2022	Jiangyun Li	TransBTSV2: Wider Instead of Deeper Transformer for Medical Image Segmentation	CT & MRI	3D	PyTorch
01/26/2022	Shiqi Huang	RTNet: Relation Transformer Network for Diabetic Retinopathy Multi-lesion Segmentation	DR	2D	N/A	IEEE TMI
01/04/2022	Ali Hatamizadeh	Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images	MRI	3D	PyTorch
01/03/2022	Yixuan Wu	D-Former: A U-shaped Dilated Transformer for 3D Medical Image Segmentation	MRI & CT	3D	N/A
12/17/2021	Yutong Xie	Unified 2D and 3D Pre-training for Medical Image Classification and Segmentation	X-ray & CT	2D & 3D	N/A
12/09/2021	Xiangde Luo	Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer	MRI	2D	PyTorch
11/29/2021	Yucheng Tang	Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis	CT & MRI	3D	PyTorch
11/26/2021	Xiangyu Meng	Exploiting full Resolution Feature Context for Liver Tumor and Vessel Segmentation via Fusion Encoder: Application to Liver Tumor and Vessel 3D reconstruction	CT	2D	N/A
11/26/2021	Himashi Peiris	A Volumetric Transformer for Accurate 3D Tumor Segmentation	CT & MRI	3D	PyTorch
11/15/2021	Dong Yang	T-AutoML: Automated Machine Learning for Lesion Segmentation using Transformers in 3D Medical Imaging	CT	3D	N/A	ICCV 2021
11/08/2021	Hongyi Wang	Mixed Transformer U-Net For Medical Image Segmentation	CT	2D	PyTorch
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
09/15/2021	Xiaohong Huang	MISSFormer: An Effective Medical Image Segmentation Transformer	CT	2D	PyTorch
09/07/2021	Hong-Yu Zhou	nnFormer: Interleaved Transformer for Volumetric Segmentation	CT	3D	PyTorch
07/28/2021	Madeleine K. Wyburd	TEDS-Net: Enforcing Diffeomorphisms in Spatial Transformers to Guarantee Topology Preservation in Segmentations	MRI	2D	PyTorch	MICCAI 2021
07/19/2021	Guoping Xu	LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation	CT	2D	N/A
07/12/2021	Bingzhi Chen	TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation	X-ray & CT ...	2D	N/A
07/12/2021	Chang Yao	TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation	CT	2D	N/A
07/02/2021	Yunhe Gao	UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation	CT	2D	PyTorch	MICCAI 2021
06/28/2021	Yuanfeng Ji	Multi-Compound Transformer for Accurate Biomedical Image Segmentation	Colonoscopy & Pathology ...	2D	PyTorch	MICCAI 2021
06/12/2021	Ailiang Lin	DS-TransUNet: Dual Swin Transformer U-Net for Medical Image Segmentation	Colonoscopy & Histology ...	2D	N/A
06/02/2021	Shaohua Li	Medical Image Segmentation Using Squeeze-and-Expansion Transformers	Fundus & Colonoscopy & MRI	2D & 3D	PyTorch	IJCAI 2021
05/12/2021	Hu Cao	Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation	CT	2D	PyTorch
04/29/2021	Zhuangzhuang Zhang	Pyramid Medical Transformer for Medical Image Segmentation	Microscopic	2D	N/A
04/28/2021	Eunji Jun	Medical Transformer: Universal Brain Encoder for 3D MRI Analysis	MRI	3D	N/A
03/18/2021	Ali Hatamizadeh	UNETR: Transformers for 3D Medical Image Segmentation	CT & MRI	3D	PyTorch
03/10/2021	Olivier Petit	U-Net Transformer: Self and Cross Attention for Medical Image Segmentation	CT	2D	N/A
03/07/2021	Wenxuan Wang	TransBTS: Multimodal Brain Tumor Segmentation Using Transformer	MRI	3D	PyTorch	MICCAI 2021
03/05/2021	Boxiang Yun	SpecTr: Spectral Transformer for Hyperspectral Pathology Image Segmentation	HSI	3D	PyTorch
03/04/2021	Yutong Xie	CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation	CT	3D	PyTorch	MICCAI 2021
02/26/2021	Davood Karimi	Convolution-Free Medical Image Segmentation using Transformers	CT & MRI	3D	N/A
02/21/2021	Jeya Maria Jose Valanarasu	Medical Transformer: Gated Axial-Attention for Medical Image Segmentation	Ultrasound & Microscopic	2D	PyTorch	MICCAI 2021
02/16/2021	Yundong Zhang	TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation	Colonoscopy	2D	N/A
02/08/2021	Jieneng Chen	TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation	CT & MRI	2D	PyTorch
02/08/2021	Walter Hugo Lopez Pinaya	Unsupervised Brain Anomaly Detection and Segmentation with Transformers	MRI	2D	N/A	MIDL 2021

Image Registration

Date	First Author	Title	Modality	ND	Code	Paper
03/10/2022	Lihao Liu	PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation	MRI	3D	N/A
11/19/2021	Junyu Chen	TransMorph: Transformer for unsupervised medical image registration	MRI & CT	3D	PyTorch
09/25/2021	Yungeng Zhang	Learning Dual Transformer Network for Diffeomorphic Registration	MRI	3D	N/A	MICCAI 2021 Springer
04/13/2021	Junyu Chen	ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration	MRI	3D	PyTorch	MIDL 2021

Image Classification & Detection

Date	First Author	Title	Modality	ND	Code	Paper
03/12/2022	Heqin Zhu	DATR: Domain-adaptive transformer for multi-domain landmark detection	X-Ray	2D	N/A
03/10/2022	Lei Zhou	Self Pre-training with Masked Autoencoders for Medical Image Analysis	CT & MRI	3D	N/A
02/13/2022	Sangjoon Park	AI can evolve without labels: self-evolving vision transformer for chest X-ray diagnosis through knowledge distillation	X-ray	2D	Unknown
12/17/2021	Yutong Xie	Unified 2D and 3D Pre-training for Medical Image Classification and Segmentation	X-ray & CT	2D & 3D	N/A
10/27/2021	Behnaz Gheflati	Vision Transformer for Classification of Breast Ultrasound Images	Ultrasound	2D	N/A
08/20/2021	Christos Matsoukas	Is it Time to Replace CNNs with Transformers for Medical Images?	Mammograms...	2D	PyTorch	ICCV 2021 Workshop
06/02/2021	Zhuchen Shao	TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classication	Pathology	2D	N/A
05/23/2021	Zhiqiang Shen	COTR: Convolution in Transformer Network for End to End Polyp Detection	Colonoscopy	2D	N/A
04/28/2021	Eunji Jun	Medical Transformer: Universal Brain Encoder for 3D MRI Analysis	MRI	3D	N/A
03/10/2021	Yin Dai	TransMed: Transformers Advance Multi-modal Medical Image Classification	MRI	3D	N/A

Image Denoising

Date	First Author	Title	Modality	ND	Code	Paper
09/23/2021	Achleshwar Luthra & Harsh Sulakhe	Eformer: Edge Enhancement based Transformer for Medical Image Denoising	CT	2D	N/A	ICCV 2021
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
02/28/2021	Zhicheng Zhang	TransCT: Dual-path Transformer for Low Dose Computed Tomography	CT	2D	N/A	MICCAI 2021

Image Synthesis

Date	First Author	Title	Modality	ND	Code	Paper
10/13/2021	Lingke Kong	Breaking the Dilemma of Medical Image-to-image Translation	MRI	3D	PyTorch	NeurIPS 2021
10/12/2021	Nicolae-Catalin Ristea	CyTran: Cycle-Consistent Transformers for Non-Contrast to Contrast CT Translation	CT	3D	N/A
06/30/2021	Onat Dalmaz	ResViT: Residual vision transformers for multi-modal medical image synthesis	MRI & CT	3D	PyTorch	NeurIPS 2021 Workshop
05/28/2021	Xuzhe Zhang	PTNet: A High-Resolution Infant MRI Synthesizer Based on Transformer	MRI	2D	N/A

Image Reconstruction

Date	First Author	Title	Modality	ND	Code	Paper
01/23/2022	Pengfei Guo	ReconFormer: Accelerated MRI Reconstruction Using Recurrent Transformer	MRI	2D	PyTorch
11/03/2021	Alper Güngör	TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging	MPI	2D	N/A
05/21/2021	Yilmaz Korkmaz	Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers	MRI	3D	TensorFlow	MLMIR 2021

Transformer fundamental papers

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