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[MedIA2022]WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image

Home Page: https://www.sciencedirect.com/science/article/pii/S1361841522002705

License: GNU General Public License v3.0

Python 100.00%
medical-image-segmentation abdominal-organ-dataset annotation-efficient-learning dataset deep-learning

word's Introduction

  • This repo provides the codebase and dataset of work WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image. Each download requirement will be approved within two days.
  • Now, we corrected the results of ESPNet+ KD in Table 8 and the dataset descriptions in Table 1 with red font Arxiv and LaTex.
  • Some information about the WORD dataset is presented in the following (the LaTex style tables are here):
Fig. 1. An example in the WORD dataset.
Fig. 2. Volume distribution or each organ in the WORD dataset.
Fig. 3. Comparison results of CNN-based and Transformer-based methods.
Fig. 4. User study based on three junior oncologists independently, each of them comes from a different hospital.

DataSet

Please contact Xiangde (luoxd1996 AT gmail DOT com) for the dataset (the label of the testing set can be downloaded now labelTs). Two steps are needed to download and access the dataset: 1) using your google email to apply for the download permission (Goole Driven, BaiduPan); 2) using your affiliation email to get the unzip password/BaiduPan access code. We will get back to you within two days, so please don't send them multiple times. We just handle the real-name email and your email suffix must match your affiliation. The email should contain the following information:

Name/Homepage/Google Scholar: (Tell us who you are.)
Primary Affiliation: (The name of your institution or university, etc.)
Job Title: (E.g., Professor, Associate Professor, Ph.D., etc.)
Affiliation Email: (the password will be sent to this email, we just reply to the email which is the end of "edu".)
How to use: (Only for academic research, not for commercial use or second-development.)

In addition, this work is still ongoing, the WORD dataset will be extended to larger and more diverse (more patients, more organs, and more modalities, more clinical hospitals' data and MR Images will be considered to include future), any suggestion, comment, collaboration, and sponsor are welcome.

Acknowledgment and Statement

  • This dataset belongs to the Healthcare Intelligence Laboratory at University of Electronic Science and Technology of China and is licensed under the GNU General Public License v3.0.
  • This project has been approved by the privacy and ethical review committee. We thank all collaborators for the data collection, annotation, checking, and user study!
  • This project and dataset were designed for open-available academic research, not for clinical, commercial, second-development, or other use. In addition, if you used it for your academic research, you are encouraged to release the code and the pre-trained model.
  • The interesting and memorable name WORD is suggested by Dr. Jie-Neng, thanks a lot !!!

Citation

It would be highly appreciated if you cite our paper when using the WORD dataset or code:

@article{luo2022word,
  title={{WORD}: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image},
  author={Xiangde Luo, Wenjun Liao, Jianghong Xiao, Jieneng Chen, Tao Song, Xiaofan Zhang, Kang Li, Dimitris N. Metaxas, Guotai Wang, and Shaoting Zhang},
  journal={Medical Image Analysis},
  volume={82},
  pages={102642},
  year={2022},
  publisher={Elsevier}}

word's People

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word's Issues

Rectal cancer data

Hello, thank you for your valuable work. I noticed in your paper that there are samples of rectal cancer mentioned. Are these samples not individually labeled for the cancer site? Could you disclose which samples contain rectal cancer? Thank you very much!

can't reproduce the segmentation results of left femoral head and right femoral head

I've tried training both 2D nnUNetv2 and 3D nnUNetv2 using the WORD dataset. But I found that the segmentation results of Head of femur were not as good as illustrated in the paper. The result of 3D nnUNetv2 were:

target DSC HD95
Head of femur(L) 0.545±0.114 196.485±22.436
Head of femur(R) 0.471±0.138 173.113±35.954

If you have met this situation, I wonder if you can offer me an explanation or guideline. Thank you😀

Scribble train/val split

Hey,

Thank you for your amazing work! I am currently trying to reproduce your scribble experiments. The WORD dataset includes a labelsTr and labelsVal folder for training with the full segmentation, but only a scribblesTr folder for the scribble segmentation. Does that mean that you validated on the full segmentation (labelsVal) during training? Or did you make a separate train/val split for the scribbleTr cases?
I have no problem with either variant. I just need to know in order to reproduce your results :)

Best regards,
Karol

Did you use 5F-CV for evaluation?

Hey,

Did you use five-fold cross-validation during the evaluation in the WORD paper? You only mention that you use the default settings and 5F-CV is part of the default settings, but I want to be sure.

Best,
Karol

share pre-trained 2D network

Hi
In the another issue I asked for pre-trained networks, that you generously shared pre-trained nnUNet3DV2 model with me. Is it possible for you to also share a 2D pre-trained model?

DatasetPassword request

(Alaa )
Primary Affiliation: (King Fahd University of Petroleum & Minerals (KFUPM))
Job Title: (Master Student in AI major)
Affiliation Email: ([email protected],)
How to use: (for academic project under computer vision course.)

Threshold interception in the preprocessing process

Hello, thank you for your valuable work. I want to use your data set to train the segmentation model. I want to use threshold interception in the preprocessing process. I wonder if you know how much the most suitable threshold should be selected?

Scribble-supervision code

Hey,

Thank you for the great dataset! I read the paper and was impressed by your scribble-supervision approach. However, I was unable to find the implementation in this repo. It was stated in the paper that the implementation was public. Could you be so kind as to direct me to the scribble-supervision code?

The relevant parts for me would especially be these:

  • The implementation of nnU-Net V2 with ResUNet 2D backbone
  • The implementation of the pCE + L_ent + L_ivm losses

I would also be grateful if the trained weights for the scribble-supervision model could be made public.

Thank you in advance!

Kind regards,
Karol

share trained networks

Hi
I'm really in need of a neural network which has been trained on your dataset, but as result of lack of appropriate hardware resource its impossible for me to do it. Is it possible for you to share few models that you have trained in your paper?

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