DICOM converted Slide Microscopy images for the TCGA-HNSC collection
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This dataset corresponds to a collection of images and/or image-derived data available from National Cancer Institute Imaging Data Commons (IDC) [1]. This dataset was converted into DICOM representation and ingested by the IDC team. You can explore and visualize the corresponding images using IDC Portal here: TCGA-HNSC. You can use the manifests included in this Zenodo record to download the content of the collection following the Download instructions below. Collection description The Cancer Imaging Program (CIP) is working directly with primary investigators from institutes participating in TCGA to obtain and load images relating to the genomic, clinical, and pathological data being stored within the TCGA Data Portal. Currently this large PET/CT multi-sequence image collection of head and neck squamous cell carcinoma (HNSC) patients can be matched by each unique case identifier with the extensive gene and expression data of the same case from The Cancer Genome Atlas Data Portal to research the link between clinical phenome and tissue genome. Please see the TCGA-HNSC page to learn more about the images and to obtain any supporting metadata for this collection. Files included A manifest file's name indicates the IDC data release in which a version of collection data was first introduced. For example, collection_id-idc_v8-aws.s5cmd corresponds to the contents of the collection_id collection introduced in IDC data release v8. If there is a subsequent version of this Zenodo page, it will indicate when a subsequent version of the corresponding collection was introduced. tcga_hnsc-idc_v18-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_hnsc-idc_v18-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_hnsc-idc_v18-dcf.dcf: Gen3 manifest (for details see https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids) Note that manifest files that end in -aws.s5cmd reference files stored in Amazon Web Services (AWS) buckets, while -gcs.s5cmd reference files in Google Cloud Storage. The actual files are identical and are mirrored between AWS and GCP. Download instructions Each of the manifests include instructions in the header on how to download the included files. To download the files using .s5cmd manifests: install idc-index package: pip install --upgrade idc-index download the files referenced by manifests included in this dataset by passing the .s5cmd manifest file: idc download manifest.s5cmd. To download the files using .dcf manifest, see manifest header. Acknowledgments Imaging Data Commons team has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN261201500003l. References [1] Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D., Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H. J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P., Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. & Kikinis, R. National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence. RadioGraphics (2023). https://doi.org/10.1148/rg.230180
本数据集对应美国国家癌症研究所影像数据公共库（National Cancer Institute Imaging Data Commons，简称IDC）[1] 提供的图像集合及/或图像衍生数据。本数据集已被转换为医学数字成像和通信（Digital Imaging and Communications in Medicine，简称DICOM）格式，并由IDC团队完成入库。您可通过IDC门户页面浏览并可视化对应图像：TCGA-HNSC。您可借助本Zenodo记录中包含的清单文件，按照下述下载说明下载该数据集的全部内容。 ### 数据集说明 癌症影像项目（Cancer Imaging Program，简称CIP）正与参与癌症基因组图谱（The Cancer Genome Atlas，简称TCGA）项目的各机构首席研究员直接合作，获取并加载TCGA数据门户中存储的、与基因组、临床及病理数据相关的影像资料。当前本数据集包含头颈部鳞状细胞癌（head and neck squamous cell carcinoma，简称HNSC）患者的多序列正电子发射断层显像/计算机断层扫描（PET/CT）影像集合，规模庞大。每一例患者的影像均可通过唯一病例标识符，与癌症基因组图谱数据门户中对应病例的海量基因及表达数据进行匹配，用于研究临床表型与组织基因组之间的关联。 请访问TCGA-HNSC页面，了解本数据集影像的更多相关信息，并获取该数据集的全部支持性元数据。 ### 包含文件 清单文件的名称标注了该版本数据集首次被引入的IDC数据发布版本。例如，`collection_id-idc_v8-aws.s5cmd`对应在IDC数据发布版本v8中首次引入的`collection_id`数据集的内容。若本Zenodo页面后续推出更新版本，将标注对应数据集后续版本的引入时间。 本数据集包含以下清单文件： 1. `tcga_hnsc-idc_v18-aws.s5cmd`：可从公开亚马逊云服务（Amazon Web Services，简称AWS）存储桶下载的数据集文件清单 2. `tcga_hnsc-idc_v18-gcs.s5cmd`：可从公开Google Cloud Storage存储桶下载的数据集文件清单 3. `tcga_hnsc-idc_v18-dcf.dcf`：Gen3格式清单文件（详情请参阅https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids） 请注意，后缀为`-aws.s5cmd`的清单文件指向存储在AWS存储桶中的文件，而`-gcs.s5cmd`后缀的清单文件指向Google Cloud Storage存储桶中的文件。实际文件内容完全一致，且在AWS与谷歌云平台（Google Cloud Platform，简称GCP）间实现了镜像同步。 ### 下载说明 所有清单文件的头部均包含对应文件的下载指引。 1. 使用`.s5cmd`格式清单下载文件： - 安装`idc-index`工具包：执行命令`pip install --upgrade idc-index` - 通过传入`.s5cmd`格式清单文件，下载该清单引用的数据集文件：执行命令`idc download manifest.s5cmd` 2. 使用`.dcf`格式清单下载文件，请参阅清单文件头部的指引。 ### 致谢 影像数据公共库团队的研究经费全部或部分来源于美国国家癌症研究所、美国国立卫生研究院的联邦拨款，相关任务订单编号为HHSN26110071，合同编号为HHSN261201500003l。 ### 参考文献 [1] Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D., Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H. J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P., Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. & Kikinis, R. 美国国家癌症研究所影像数据公共库：迈向影像人工智能的透明化、可重复性与可扩展性. *RadioGraphics* (2023). https://doi.org/10.1148/rg.230180
