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Medical Image Segmentation

Last updated: 02/09/2022

Most Interested

Some useful GitHub repositories

  1. Loss functions for image segmentation
  2. Three distance-based segmentation losses
  3. Boundary loss

Some papers

  • Note: BD, boundary loss; CE, cross-entropy loss; HD, Hausdorff distance loss; SDF, signed distance function loss.
Date First Author Title Architecture Modality ND Loss Dataset Paper
10/08/2021 Jiacheng Wang Boundary-aware Transformers for Skin Lesion Segmentation Transformer Image 2D CE+Dice with boundary-wise prior knowledge ISIC 2016 + PH2, ISIC 2018 MICCAI 2021 arXiv PyTorch
07/10/2021 Li Lin BSDA-Net: A Boundary Shape and Distance Aware Joint Learning Framework for Segmenting and Classifying OCTA Images CNN Image 2D MSE with soft label heatmap on the boundary OCTA MICCAI 2021 arXiv PyTorch
06/10/2019 Hoel Kervadec Boundary loss for highly unbalanced segmentation CNN MRI 2D/3D CE+BD WMH MIDL 2019 arXiv PyTorch
06/01/2020 Jun Ma How Distance Transform Maps Boost Segmentation CNNs: An Empirical Study CNN CT/MRI 3D Dice+ BD/HD/SDF MICCAI 2017, 2018 MIDL 2020 arXiv PyTorch
02/08/2021 Jieneng Chen TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation Transformer CT/MRI 2D CE+Dice MICCAI 2015, ACDC arXiv PyTorch
2019 Jieneng Chen Shape-Aware Organ Segmentation by Predicting Signed Distance Maps CNN CT/MRI 2D CE+Dice MICCAI 2015, ACDC AAAI2020 arXiv
2019 Jieneng Chen Reducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks (arxiv) CNN CT/MRI 2D CE+Dice MICCAI 2015, ACDC TMI2019 arXiv

Medical Image Segmentation with Transformer

An survey paper, Transformers in Medical Imaging: A Survey, Jan. 2022.

Some useful github repositories

  1. Awesome Transformers in Medical Imaging

Some papers

  • Note: B, boundary loss; CE, cross-entropy loss.
Date First Author Title Modality ND Loss Dataset Code Paper
01/26/2022 Shiqi Huang RTNet: Relation Transformer Network for Diabetic Retinopathy Multi-lesion Segmentation DR (Image) 2D CE (Multi-class weighted) IDRiD and DDR N/A IEEE TMI arXiv
D01/04/2022 Ali Hatamizadeh Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images MRI 3D Dice BraTS 2021 (1251 subjects, semantic segmentation of brain tumors) PyTorch arXiv
()01/03/2022 Yixuan Wu D-Former: A U-shaped Dilated Transformer for 3D Medical Image Segmentation MRI & CT 3D CE + Dice Synapse (multi-organ segmentation) and ACDC (cardiac diagnosis) N/A arXiv
12/09/2021 Xiangde Luo Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer MRI 2D Dice ACDC PyTorch arXiv
11/29/2021 Yucheng Tang Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis CT & MRI 3D Inpaint + Constrast coding + rotation (for pre-training) 5 CT scan datasets PyTorch arXiv
11/26/2021 Himashi Peiris A Volumetric Transformer for Accurate 3D Tumor Segmentation CT & MRI 3D CE+Dice BraTS PyTorch arXiv
11/15/2021 Dong Yang T-AutoML: Automated Machine Learning for Lesion Segmentation using Transformers in 3D Medical Imaging CT 3D CE+Dice LiTS 2017, Medical Segmentation Decathlon N/A ICCV 2021 arXiv
11/08/2021 Hongyi Wang Mixed Transformer U-Net For Medical Image Segmentation CT 2D CE/Dice Synapse, ACDC PyTorch arXiv
09/15/2021 Xiaohong Huang MISSFormer: An Effective Medical Image Segmentation Transformer CT 2D CE+Dice Synapse, ACDC PyTorch arXiv
09/07/2021 Hong-Yu Zhou nnFormer: Interleaved Transformer for Volumetric Segmentation CT 3D CE+Dice Synapse, ACDC PyTorch arXiv
07/28/2021 Madeleine K. Wyburd TEDS-Net: Enforcing Diffeomorphisms in Spatial Transformers to Guarantee Topology Preservation in Segmentations MRI 2D Dice+Flow Feild Regularisation ACDC PyTorch MICCAI 2021 arXiv
07/19/2021 Guoping Xu LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation CT 2D CE+Dice Synapse, ACDC 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 CE+Dice ISIC-2018, JSRT ... N/A arXiv
07/12/2021 Chang Yao TransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation CT 2D CE Synapse N/A arXiv
07/02/2021 Yunhe Gao UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation CT 2D CE+Dice M&Ms dataset PyTorch MICCAI 2021 arXiv
06/28/2021 Yuanfeng Ji Multi-Compound Transformer for Accurate Biomedical Image Segmentation Colonoscopy & Pathology ... 2D CE+Dice+auxiliary loss Six segmentation datasetsc ... PyTorch MICCAI 2021 arXiv
06/12/2021 Ailiang Lin DS-TransUNet: Dual Swin Transformer U-Net for Medical Image Segmentation Colonoscopy & Histology ... 2D IoU+CE Four seg datasets ... N/A arXiv
06/02/2021 Shaohua Li Medical Image Segmentation Using Squeeze-and-Expansion Transformers Fundus & Colonoscopy & MRI 2D & 3D CE+Dice REFUGE20, Polyp, BraTS19 PyTorch IJCAI 2021 arXiv
05/12/2021 Hu Cao Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation CT 2D CE+Dice Synapse PyTorch arXiv
03/18/2021 Ali Hatamizadeh UNETR: Transformers for 3D Medical Image Segmentation CT & MRI 3D CE+Dice BTCV PyTorch arXiv
03/10/2021 Olivier Petit U-Net Transformer: Self and Cross Attention for Medical Image Segmentation CT 2D Dice TCIA, IMO N/A arXiv
03/07/2021 Wenxuan Wang TransBTS: Multimodal Brain Tumor Segmentation Using Transformer MRI 3D Dice BraTS 2019 PyTorch MICCAI 2021 arXiv
03/04/2021 Yutong Xie CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation CT 3D CE+Dice BCV PyTorch MICCAI 2021arXiv
02/21/2021 Jeya Maria Jose Valanarasu Medical Transformer: Gated Axial-Attention for Medical Image Segmentation Ultrasound & Microscopic 2D CE Brain US, GlaS, MoNuSeg PyTorch MICCAI 2021 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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