Multi-organ Abdominal CT Reference Standard Segmentations

DenseVNet Multi-organ Segmentation on Abdominal CT

This dataset includes the multi-organ abdominal CT reference segmentations publicly released in conjunction with the IEEE Transactions on Medical Imaging paper "Automatic Multi-organ Segmentation on Abdominal CT with Dense V-networks" [1].

The data comprises reference segmentations for 90 abdominal CT images delineating multiple organs: the spleen, left kidney, gallbladder, esophagus, liver, stomach, pancreas and duodenum.

The abdominal CT images and some of the reference segmentations were drawn from two data sets: The Cancer Image Archive (TCIA) Pancreas-CT data set [2-4] and the Beyond the Cranial Vault (BTCV) Abdomen data set [5-6]. The Pancreas-CT data set comprises abdominal CT acquired at the National Institutes of Health Clinical Center from pre-nephrectomy healthy kidney donors or patients with neither major abdominal pathologies nor pancreatic cancer lesions. Segmentations of the pancreas are included with this data set; images were manually labeled slice-by-slice by a medical student, and verified/modified by an experienced radiologist. The BTCV data set comprises abdominal CT acquired at the Vanderbilt University Medical Center from metastatic liver cancer patients or post-operative ventral hernia patients. Segmentations of the spleen, right and left kidney, gallbladder, esophagus, liver, stomach, aorta, inferior vena cava, portal vein and splenic vein, pancreas, right adrenal gland, left adrenal gland are included in this data set; images were manually labeled by two experienced undergraduate students, and verified by a radiologist on a volumetric basis using the MIPAV software.

Segmentations that were not present in the original data sets were performed interactively using Matlab 2015b and ITK-SNAP 3.2 by an image research fellow under the supervision of a board-certified radiologist with 8 years of experience in gastrointestinal CT and MRI image interpretation. Segmentations that were present in the original data sets were edited to ensure a consistent segmentation protocol across the data set.

Terms of use

The terms of use of this data set include the terms of use of both the TCIA Pancreas-CT data set (see tabs for data links and terms of use) and the Beyond the Cranial Vault (BTCV) Abdomen data set (terms of use; after registration, you can access the data). If you use these reference segmentations, please cite the above manuscript and the references below. Because these data include manual segmentations of images from the Beyond the Cranial Vault challenge test data, they may not be used to develop submissions for the challenge.

References

[1] Gibson E, Giganti F, Hu Y, Bonmati E, Bandula S, Gurusamy K, Davidson B, Pereira SP, Clarkson MJ, Barratt DC. Automatic multi-organ segmentation on abdominal CT with dense v-networks. IEEE Transactions on Medical Imaging, 2018.

[2] Roth HR, Farag A, Turkbey EB, Lu L, Liu J, and Summers RM. (2016). Data From Pancreas-CT. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.tNB1kqBU

[3] Roth HR, Lu L, Farag A, Shin H-C, Liu J, Turkbey EB, Summers RM. DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation. N. Navab et al. (Eds.): MICCAI 2015, Part I, LNCS 9349, pp. 556–564, 2015. http://arxiv.org/pdf/1506.06448.pdf

[4] Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. http://doi.org/10.1007/s10278-013-9622-7

[5] Xu Z, Lee CP, Heinrich MP, Modat M, Rueckert D, Ourselin S, Abramson RG, and Landman BA, "Evaluation of six registration methods for the human abdomen on clinically acquired CT," IEEE Trans. Biomed. Eng., vol. 63, no. 8, pp. 1563–1572, 2016.http://doi.org/10.1109/TBME.2016.2574816

[6] Landman BA, Xu Z, Igelsias JE, Styner M, Langerak TR, and Klein A, "MICCAI multi-atlas labeling beyond the cranial vault - workshop and challenge," 2015, https://doi.org/10.7303/syn3193805

File format Labels are in NIfTI format with the following label definitions. Labels marked with * are only available in the BTCV data set.

spleen

right kidney*

left kidney

gallbladder

esophagus

liver

stomach

aorta*

inferior vena cava*

portal vein and splenic vein*

pancreas

right adrenal gland*

left adrenal gland*

duodenum

Subjects included in the dataset

The data comprises segmentation volumes for 90 cases, and the cropping coordinates (cropping.csv) used in the manuscript. The abdominal CT can be obtained from the links above. The reference standard segmentations may be incomplete outside of the specified cropping region. The cases are listed by their subject identifiers in their original data set:

\(\begin{bmatrix} 1 & TCIA & Pancreas-CT & 0002\\ 2 & TCIA & Pancreas-CT & 0003\\ 3 & TCIA & Pancreas-CT & 0004\\ 4 & TCIA & Pancreas-CT & 0005\\ 5 & TCIA & Pancreas-CT & 0006\\ 6 & TCIA & Pancreas-CT & 0007\\ 7 & TCIA & Pancreas-CT & 0008\\ 8 & TCIA & Pancreas-CT & 0009\\ 9 & TCIA & Pancreas-CT & 0010\\ 10 & TCIA & Pancreas-CT & 0011\\ 11 & TCIA & Pancreas-CT & 0012\\ 12 & TCIA & Pancreas-CT & 0013\\ 13 & TCIA & Pancreas-CT & 0014\\ 14 & TCIA & Pancreas-CT & 0016\\ 15 & TCIA & Pancreas-CT & 0017\\ 16 & TCIA & Pancreas-CT & 0018\\ 17 & TCIA & Pancreas-CT & 0019\\ 18 & TCIA & Pancreas-CT & 0020\\ 19 & TCIA & Pancreas-CT & 0021\\ 20 & TCIA & Pancreas-CT & 0022\\ 21 & TCIA & Pancreas-CT & 0024\\ 22 & TCIA & Pancreas-CT & 0025\\ 23 & TCIA & Pancreas-CT & 0026\\ 24 & TCIA & Pancreas-CT & 0027\\ 25 & TCIA & Pancreas-CT & 0028\\ 26 & TCIA & Pancreas-CT & 0029\\ 27 & TCIA & Pancreas-CT & 0030\\ 28 & TCIA & Pancreas-CT & 0031\\ 29 & TCIA & Pancreas-CT & 0032\\ 30 & TCIA & Pancreas-CT & 0033\\ 31 & TCIA & Pancreas-CT & 0034\\ 32 & TCIA & Pancreas-CT & 0035\\ 33 & TCIA & Pancreas-CT & 0038\\ 34 & TCIA & Pancreas-CT & 0039\\ 35 & TCIA & Pancreas-CT & 0040\\ 36 & TCIA & Pancreas-CT & 0041\\ 37 & TCIA & Pancreas-CT & 0042\\ 38 & TCIA & Pancreas-CT & 0043\\ 39 & TCIA & Pancreas-CT & 0044\\ 40 & TCIA & Pancreas-CT & 0045\\ 41 & TCIA & Pancreas-CT & 0046\\ 42 & TCIA & Pancreas-CT & 0047\\ 43 & TCIA & Pancreas-CT & 0048\\ 44 & Synapse & BeyondTheCranialVault & 0001\\ 45 & Synapse & BeyondTheCranialVault & 0002\\ 46 & Synapse & BeyondTheCranialVault & 0003\\ 47 & Synapse & BeyondTheCranialVault & 0004\\ 48 & Synapse & BeyondTheCranialVault & 0005\\ 49 & Synapse & BeyondTheCranialVault & 0006\\ 50 & Synapse & BeyondTheCranialVault & 0007\\ 51 & Synapse & BeyondTheCranialVault & 0008\\ 52 & Synapse & BeyondTheCranialVault & 0009\\ 53 & Synapse & BeyondTheCranialVault & 0010\\ 54 & Synapse & BeyondTheCranialVault & 0021\\ 55 & Synapse & BeyondTheCranialVault & 0022\\ 56 & Synapse & BeyondTheCranialVault & 0023\\ 57 & Synapse & BeyondTheCranialVault & 0024\\ 58 & Synapse & BeyondTheCranialVault & 0025\\ 59 & Synapse & BeyondTheCranialVault & 0026\\ 60 & Synapse & BeyondTheCranialVault & 0027\\ 61 & Synapse & BeyondTheCranialVault & 0028\\ 62 & Synapse & BeyondTheCranialVault & 0029\\ 63 & Synapse & BeyondTheCranialVault & 0030\\ 64 & Synapse & BeyondTheCranialVault & 0031\\ 65 & Synapse & BeyondTheCranialVault & 0032\\ 66 & Synapse & BeyondTheCranialVault & 0033\\ 67 & Synapse & BeyondTheCranialVault & 0034\\ 68 & Synapse & BeyondTheCranialVault & 0035\\ 69 & Synapse & BeyondTheCranialVault & 0036\\ 70 & Synapse & BeyondTheCranialVault & 0037\\ 71 & Synapse & BeyondTheCranialVault & 0038\\ 72 & Synapse & BeyondTheCranialVault & 0039\\ 73 & Synapse & BeyondTheCranialVault & 0040\\ 74 & Synapse & BeyondTheCranialVault & 0061\\ 75 & Synapse & BeyondTheCranialVault & 0062\\ 76 & Synapse & BeyondTheCranialVault & 0063\\ 77 & Synapse & BeyondTheCranialVault & 0064\\ 78 & Synapse & BeyondTheCranialVault & 0065\\ 79 & Synapse & BeyondTheCranialVault & 0066\\ 80 & Synapse & BeyondTheCranialVault & 0067\\ 81 & Synapse & BeyondTheCranialVault & 0068\\ 82 & Synapse & BeyondTheCranialVault & 0069\\ 83 & Synapse & BeyondTheCranialVault & 0070\\ 84 & Synapse & BeyondTheCranialVault & 0074\\ 85 & Synapse & BeyondTheCranialVault & 0075\\ 86 & Synapse & BeyondTheCranialVault & 0076\\ 87 & Synapse & BeyondTheCranialVault & 0077\\ 88 & Synapse & BeyondTheCranialVault & 0078\\ 89 & Synapse & BeyondTheCranialVault & 0079\\ 90 & Synapse & BeyondTheCranialVault & 0080\\ \end{bmatrix}\)

## DenseVNet腹部CT多器官分割数据集

本数据集包含与发表于《IEEE Transactions on Medical Imaging》的论文《基于密集V网络的腹部CT多器官自动分割》（原文标题：*Automatic Multi-organ Segmentation on Abdominal CT with Dense V-networks*）[1]同步公开的腹部CT多器官参考分割掩码。

该数据集包含90幅腹部CT图像的参考分割掩码，标注覆盖的器官包括脾脏、左肾、胆囊、食管、肝脏、胃、胰腺及十二指肠。

本数据集的腹部CT图像及部分参考分割掩码源自两个公开数据集：**癌症图像档案（The Cancer Image Archive, TCIA）胰腺CT数据集**[2-4]与**颅外腹部数据集（Beyond the Cranial Vault, BTCV）**[5-6]。
其中TCIA胰腺CT数据集的数据采集于美国国立卫生研究院临床中心，受试者为肾切除术前健康肾脏供体，或无重大腹部病变及胰腺癌病灶的患者。该数据集包含胰腺的分割掩码，由医学生逐层手动标注，并由经验丰富的放射科医师审核修正。
BTCV数据集的数据采集于范德堡大学医学中心，受试者为转移性肝癌患者或术后腹壁疝患者。该数据集包含脾脏、左右肾、胆囊、食管、肝脏、胃、主动脉、下腔静脉、门静脉与脾静脉、胰腺、左右肾上腺的分割掩码，由两名有经验的本科生手动标注，并由放射科医师使用MIPAV软件以体素层面进行审核验证。

对于原始数据集中未包含的分割掩码，由一名影像研究助理在拥有8年胃肠CT及MRI影像解读经验的执业放射科医师监督下，使用Matlab 2015b与ITK-SNAP 3.2交互式完成。原始数据集中已有的分割掩码也经过统一编辑，以确保整个数据集采用一致的分割规范。

## 使用条款
本数据集的使用需同时遵循TCIA胰腺CT数据集（数据链接及使用条款见对应标签页）与BTCV腹部数据集（完成注册后方可访问数据，需遵守其使用条款）的相关规定。若您使用本参考分割掩码，请引用上述论文及如下参考文献。由于本数据集包含来自颅外挑战赛测试数据的手动分割掩码，不得将其用于开发该挑战赛的参赛提交作品。

## 参考文献
[1] Gibson E, Giganti F, Hu Y, Bonmati E, Bandula S, Gurusamy K, Davidson B, Pereira SP, Clarkson MJ, Barratt DC. Automatic multi-organ segmentation on abdominal CT with dense v-networks. *IEEE Transactions on Medical Imaging*, 2018.
[2] Roth HR, Farag A, Turkbey EB, Lu L, Liu J, and Summers RM. (2016). Data From Pancreas-CT. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.tNB1kqBU
[3] Roth HR, Lu L, Farag A, Shin H-C, Liu J, Turkbey EB, Summers RM. DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation. N. Navab et al. (Eds.): MICCAI 2015, Part I, LNCS 9349, pp. 556–564, 2015. http://arxiv.org/pdf/1506.06448.pdf
[4] Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, *Journal of Digital Imaging*, Volume 26, Number 6, December, 2013, pp 1045-1057. http://doi.org/10.1007/s10278-013-9622-7
[5] Xu Z, Lee CP, Heinrich MP, Modat M, Rueckert D, Ourselin S, Abramson RG, and Landman BA, "Evaluation of six registration methods for the human abdomen on clinically acquired CT," *IEEE Trans. Biomed. Eng.*, vol. 63, no. 8, pp. 1563–1572, 2016. http://doi.org/10.1109/TBME.2016.2574816
[6] Landman BA, Xu Z, Igelsias JE, Styner M, Langerak TR, and Klein A, "MICCAI multi-atlas labeling beyond the cranial vault - workshop and challenge," 2015, https://doi.org/10.7303/syn3193805

## 文件格式
标签文件采用NIfTI格式，标签定义如下。带*标记的标签仅在BTCV数据集中提供：
- 脾脏
- 右肾*
- 左肾
- 胆囊
- 食管
- 肝脏
- 胃
- 主动脉*
- 下腔静脉*
- 门静脉与脾静脉*
- 胰腺
- 右肾上腺*
- 左肾上腺*
- 十二指肠

## 数据集包含的受试者
本数据集包含90个病例的分割容积数据，以及论文中使用的裁剪坐标文件（cropping.csv）。腹部CT图像可通过上述链接获取。参考标准分割掩码在指定裁剪区域外可能存在不完整的情况。所有病例按其所属原始数据集的受试者ID列出如下：

1 TCIA 胰腺CT 0002
2 TCIA 胰腺CT 0003
3 TCIA 胰腺CT 0004
4 TCIA 胰腺CT 0005
5 TCIA 胰腺CT 0006
6 TCIA 胰腺CT 0007
7 TCIA 胰腺CT 0008
8 TCIA 胰腺CT 0009
9 TCIA 胰腺CT 0010
10 TCIA 胰腺CT 0011
11 TCIA 胰腺CT 0012
12 TCIA 胰腺CT 0013
13 TCIA 胰腺CT 0014
14 TCIA 胰腺CT 0016
15 TCIA 胰腺CT 0017
16 TCIA 胰腺CT 0018
17 TCIA 胰腺CT 0019
18 TCIA 胰腺CT 0020
19 TCIA 胰腺CT 0021
20 TCIA 胰腺CT 0022
21 TCIA 胰腺CT 0024
22 TCIA 胰腺CT 0025
23 TCIA 胰腺CT 0026
24 TCIA 胰腺CT 0027
25 TCIA 胰腺CT 0028
26 TCIA 胰腺CT 0029
27 TCIA 胰腺CT 0030
28 TCIA 胰腺CT 0031
29 TCIA 胰腺CT 0032
30 TCIA 胰腺CT 0033
31 TCIA 胰腺CT 0034
32 TCIA 胰腺CT 0035
33 TCIA 胰腺CT 0038
34 TCIA 胰腺CT 0039
35 TCIA 胰腺CT 0040
36 TCIA 胰腺CT 0041
37 TCIA 胰腺CT 0042
38 TCIA 胰腺CT 0043
39 TCIA 胰腺CT 0044
40 TCIA 胰腺CT 0045
41 TCIA 胰腺CT 0046
42 TCIA 胰腺CT 0047
43 TCIA 胰腺CT 0048
44 Synapse 颅外腹部 0001
45 Synapse 颅外腹部 0002
46 Synapse 颅外腹部 0003
47 Synapse 颅外腹部 0004
48 Synapse 颅外腹部 0005
49 Synapse 颅外腹部 0006
50 Synapse 颅外腹部 0007
51 Synapse 颅外腹部 0008
52 Synapse 颅外腹部 0009
53 Synapse 颅外腹部 0010
54 Synapse 颅外腹部 0021
55 Synapse 颅外腹部 0022
56 Synapse 颅外腹部 0023
57 Synapse 颅外腹部 0024
58 Synapse 颅外腹部 0025
59 Synapse 颅外腹部 0026
60 Synapse 颅外腹部 0027
61 Synapse 颅外腹部 0028
62 Synapse 颅外腹部 0029
63 Synapse 颅外腹部 0030
64 Synapse 颅外腹部 0031
65 Synapse 颅外腹部 0032
66 Synapse 颅外腹部 0033
67 Synapse 颅外腹部 0034
68 Synapse 颅外腹部 0035
69 Synapse 颅外腹部 0036
70 Synapse 颅外腹部 0037
71 Synapse 颅外腹部 0038
72 Synapse 颅外腹部 0039
73 Synapse 颅外腹部 0040
74 Synapse 颅外腹部 0061
75 Synapse 颅外腹部 0062
76 Synapse 颅外腹部 0063
77 Synapse 颅外腹部 0064
78 Synapse 颅外腹部 0065
79 Synapse 颅外腹部 0066
80 Synapse 颅外腹部 0067
81 Synapse 颅外腹部 0068
82 Synapse 颅外腹部 0069
83 Synapse 颅外腹部 0070
84 Synapse 颅外腹部 0074
85 Synapse 颅外腹部 0075
86 Synapse 颅外腹部 0076
87 Synapse 颅外腹部 0077
88 Synapse 颅外腹部 0078
89 Synapse 颅外腹部 0079
90 Synapse 颅外腹部 0080