harry-urek / hiformer

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation, WACV 2023

Hierarchical Multi-scale Representations for medical image segmentation with state of the art results on synapse multi-organ segmentation, skin lesion segmentation, multiple myeloma cell segmentation. This method designs two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder, then using a Double-Level Fusion (DLF) module, it allows a fine fusion of global and local features. If this code helps with your research please consider citing the following paper:

Moein Heidari*, Amirhossein Kazerouni*, Milad Soltany*, R. Azad, Ehsan Khodapanah Aghdam, Julien Cohen-Adad and Dorit Merhof , "HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation", download link.

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Updates

• October 10, 2022: Accepted in WACV 2023!
• July 14, 2022: First release (Complete implemenation for Synapse Multi-Organ Segmentation dataset.)

This code has been implemented in python language using Pytorch library and tested in ubuntu OS, though should be compatible with related environment. following Environement and Library needed to run the code:

• Python 3
• Pytorch

Prepare data, Train/Test

Please go to "Instructions.ipynb" for complete detail on dataset preparation and Train/Test procedure or follow the instructions below.

1. Download the Synapse Dataset from here.

2. Run the following code to install the Requirements.

   pip install -r requirements.txt

3. Run the below code to train HiFormer on the synapse dataset.

   python train.py --root_path ./data/Synapse/train_npz --test_path ./data/Synapse/test_vol_h5  --model_name hiformer-b --batch_size 10 --eval_interval 20 --max_epochs 400 

   --root_path [Train data path]

   --test_path [Test data path]

   --eval_interval [Evaluation epoch]

   --model_name [Choose from [hiformer-s, hiformer-b, hiformer-l]]

4. Run the below code to test HiFormer on the synapse dataset.

   python test.py --test_path ./data/Synapse/test_vol_h5 --model_name hiformer-b --is_savenii --model_weight './hiformer-b_best.pth'

   --test_path [Test data path]

   --model_name [choose from [hiformer-s, hiformer-b, hiformer-l]]

   --is_savenii [Whether to save results during inference]

   --model_weight [HiFormer trained model path]

Quick Overview

Results

For evaluating the performance of the proposed method, three challenging tasks in medical image segmentaion has been considered. In bellow, results of the proposed approach for synapse multi-organ segmentation is illustrated.

Performance Comparision on Synapse Multi-Organ Segmentation

Methods	DSC↑	HD↓	Aorta	Gallbladder	Kidney(L)	Kidney(R)	Liver	Pancreas	Spleen	Stomach
DARR	69.77	-	74.74	53.77	72.31	73.24	94.08	54.18	89.90	45.96
R50 U-Net	74.68	36.87	87.74	63.66	80.60	78.19	93.74	56.90	85.87	74.16
U-Net	76.85	39.70	89.07	69.72	77.77	68.60	93.43	53.98	86.67	75.58
R50 Att-UNet	75.57	36.97	55.92	63.91	79.20	72.71	93.56	49.37	87.19	74.95
Att-UNet	77.77	36.02	89.55	68.88	77.98	71.11	93.57	58.04	87.30	75.75
R50 ViT	71.29	32.87	73.73	55.13	75.80	72.20	91.51	45.99	81.99	73.95
TransUnet	77.48	31.69	87.23	63.13	81.87	77.02	94.08	55.86	85.08	75.62
SwinUnet	79.13	21.55	85.47	66.53	83.28	79.61	94.29	56.58	90.66	76.60
LeVit-Unet	78.53	16.84	78.53	62.23	84.61	80.25	93.11	59.07	88.86	72.76
DeepLabv3+ (CNN)	77.63	39.95	88.04	66.51	82.76	74.21	91.23	58.32	87.43	73.53
HiFormer-S	80.29	18.85	85.63	73.29	82.39	64.84	94.22	60.84	91.03	78.07
HiFormer-B	80.39	14.70	86.21	65.69	85.23	79.77	94.61	59.52	90.99	81.08
HiFormer-L	80.69	19.14	87.03	68.61	84.23	78.37	94.07	60.77	90.44	82.03

Perceptual visualization results on test data

References

• TransUnet
• Swin Transformer
• CrossViT

Query

All implementations are done by Amirhossein Kazerouni, Milad Soltany and Moein Heidari. For any query, please contact us for more information.

[email protected]

[email protected]

[email protected]

Citation

@inproceedings{heidari2023hiformer,
  title={Hiformer: Hierarchical multi-scale representations using transformers for medical image segmentation},
  author={Heidari, Moein and Kazerouni, Amirhossein and Soltany, Milad and Azad, Reza and Aghdam, Ehsan Khodapanah and Cohen-Adad, Julien and Merhof, Dorit},
  booktitle={Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision},
  pages={6202--6212},
  year={2023}
}