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HaN-Seg

Dataset Information

HaN-Seg is a publicly available head and neck region organ-at-risk (OAR) image segmentation dataset, which contains head and neck (HaN) CT and MR images of 42 patients. These patients underwent CT scans and T1-weighted MR imaging to support image-guided radiation therapy planning. The dataset further includes labels for 30 risk organs, presented in the form of binary segmentation masks. These segmentation masks were obtained through careful curation of manual pixel-by-pixel expert image annotations. It is important to emphasize that these CT and MR images have not been registered with each other.

Dataset Meta Information

Dimensions Modality Task Type Anatomical Structures Anatomical Area Number of Categories Data Volume File Format
3D CT & MR Segmentation 37 organs in head and neck Head and Neck 30 42 .nrrd

Resolution Details

Dataset Statistics spacing (mm) size
min (0.52,0.52,2.0) (512,512,116)
median (0.64,0.64,2.0) (1024,1024,189)
max (1.56,1.56,3.0) (1024,1024,323)

Label Information Statistics

Label Anatomical Structure Cases Coverage Mean Volume (cm³) Median Volume (cm³) Max Volume (cm³)
1 carotid_artery_left 42 100.00% 14.32 3.9 7.18
2 carotid_artery_right 42 100.00% 11.71 3.56 5.94
3 arytenoids 42 100.00% 0.79 0.13 0.46
4 mandible 42 100.00% 89.08 40.38 64.6
5 brainstem 42 100.00% 29.71 14.62 22.68
6 buccal_mucosa 42 100.00% 21.38 4.43 12.83
7 cavity_oral 42 100.00% 161.34 52.94 99.82
8 cochlea_left 42 100.00% 0.26 0.06 0.16
9 cochlea_right 42 100.00% 0.26 0.06 0.16
10 cricopharyngeus 42 100.00% 4.74 1.04 2.58
11 esophagus 42 100.00% 4.8 0.76 2.02
12 Eye_AL (left eyeball) 42 100.00% 1.54 0.38 1.04
13 Eye_AR (right eyeball) 42 100.00% 2.15 0.48 1.08
14 Eye_PL (left eye lens) 42 100.00% 12.82 3.86 7.57
15 Eye_PR (right eye lens) 42 100.00% 9.09 4.55 7.7
16 Gland_Lacrimal_L (left lacrimal gland) 42 100.00% 1.31 0.48 0.87
17 Gland_Lacrimal_R (right lacrimal gland) 42 100.00% 1.51 0.2 0.55
18 Gland_Submand_L (left submandibular gland) 42 100.00% 16.89 2.88 8.2
19 Gland_Submand_R (right submandibular gland) 42 100.00% 16.92 3.57 7.74
20 Gland_Thyroid (thyroid gland) 42 100.00% 45.95 14.2 14.4
21 Glottis 42 100.00% 5.54 1.34 3.28
22 Larynx_SG (supraglottic larynx) 42 100.00% 23.15 4.68 13.29
23 Lips 42 100.00% 47 5.14 23.44
24 Optic_Chasm (optic chiasm) 42 100.00% 1.03 0.06 0.46
25 OpticNrv_L (left optic nerve) 42 100.00% 1.21 0.17 0.71
26 OpticNrv_R (right optic nerve) 42 100.00% 55.19 9.81 27.27
27 Parotid_L (left parotid gland) 42 100.00% 55.75 11.29 26.89
28 Parotid_R (right parotid gland) 42 100.00% 45.06 10.24 28.33
29 Pituitary (pituitary gland) 42 100.00% 13.87 7.44 10.46
30 SpinalCord (spinal cord) 41 97.62% 0.72 0.17 0.34

Visualization

Visualization from official website.

File Structure

The official file structure is as follows, divided into 42 subfolders, organized as follows:

Dataset
│
├── OAR_data.csv
├── patient_data.csv
├── case_xx
│   ├── case_XX_IMG_CT.nrrd
│   ├── case_XX_IMG_MR_T1.nrrd
│   ├── case_XX_OAR_Brainstem.seg.nrrd
│   ├── case_XX_OAR_OpticChiasm.seg.nrrd
│   ├── ...
├── case_xx
│   ├── ...

Authors and Institutions

G. Podobnik (Faculty of Electrical Engineering, University of Ljubljana, Slovenia)

P. Strojan (Institute of Oncology Ljubljana, Slovenia)

P. Peterlin (Institute of Oncology Ljubljana, Slovenia)

B. Ibragimov (Faculty of Electrical Engineering, University of Ljubljana, Slovenia; Department of Computer Science, University of Copenhagen, Denmark)

T. Vrtovec (Faculty of Electrical Engineering, University of Ljubljana, Slovenia)

Source Information

Official Website: https://han-seg2023.grand-challenge.org/

Download Link: https://zenodo.org/record/7442914#.ZBtfBHbMJaQ

Article Address: https://aapm.onlinelibrary.wiley.com/doi/10.1002/mp.16197

Publication Date: January 3rd, 2023

Citation

@article{podobnik2023han,
  title={HaN-Seg: The head and neck organ-at-risk CT and MR segmentation dataset},
  author={Podobnik, Ga{\v{s}}per and Strojan, Primo{\v{z}} and Peterlin, Primo{\v{z}} and Ibragimov, Bulat and Vrtovec, Toma{\v{z}}},
  journal={Medical physics},
  volume={50},
  number={3},
  pages={1917--1927},
  year={2023},
  publisher={Wiley Online Library}
}

Original introduction article is here.