DICOM converted Slide Microscopy images for the TCGA-STAD collection

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-STAD. 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 Genome Atlas-Stomach Adenoarcinoma (TCGA-STAD) data collection is part of a larger effort to enhance the TCGA http://cancergenome.nih.gov/ data set with characterized radiological images. The Cancer Imaging Program (CIP) with the cooperation of several of the TCGA tissue-contributing institutions are working to archive a large portion of the radiological images of the genetically-analyzed STAD cases. Please see the TCGA-STAD 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_stad-idc_v18-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_stad-idc_v18-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_stad-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, IDC）[1] 公开的图像及/或图像衍生数据集合。本数据集已转换为DICOM（Digital Imaging and Communications in Medicine）格式，并由IDC团队完成入库。您可通过IDC门户浏览并可视化对应图像：TCGA-STAD。您可借助本Zenodo记录中附带的清单文件，按照下述下载说明下载该集合的全部内容。 数据集说明 本癌症基因组图谱-胃腺癌（The Cancer Genome Atlas-Stomach Adenocarcinoma, TCGA-STAD）数据集是为在已表征的放射学影像基础上完善TCGA（http://cancergenome.nih.gov/）数据集而开展的更大规模项目的组成部分。癌症影像项目（Cancer Imaging Program, CIP）联合多家TCGA组织样本贡献机构，致力于归档经基因分析的STAD病例中的大部分放射学影像。 请访问TCGA-STAD页面以了解更多图像相关信息，并获取本数据集的相关支撑元数据。 包含文件 清单文件名会标注该版本集合数据首次被引入的IDC数据发布版本。例如，collection_id-idc_v8-aws.s5cmd对应于IDC数据发布版本v8中引入的collection_id集合内容。若本Zenodo页面后续更新，将标注对应集合的后续版本引入时间。 - tcga_stad-idc_v18-aws.s5cmd：可从公开亚马逊云科技（Amazon Web Services, AWS）存储桶下载的文件清单 - tcga_stad-idc_v18-gcs.s5cmd：可从公开谷歌云存储（Google Cloud Storage, GCS）存储桶下载的文件清单 - tcga_stad-idc_v18-dcf.dcf：Gen3清单（详情请参见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于AWS存储桶中的文件，而-gcs.s5cmd后缀的清单文件则指向谷歌云存储中的文件。实际文件内容完全一致，且在AWS与谷歌云平台（Google Cloud Platform, 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包含文件的下载指引。 使用.s5cmd格式清单下载文件： 1. 安装idc-index工具包：pip install --upgrade idc-index 2. 通过传入.s5cmd清单文件下载本数据集中引用的文件：idc download manifest.s5cmd。 使用.dcf格式清单下载文件，请参阅清单文件头部说明。 致谢 影像数据公共库团队的全部或部分研究经费由美国国家癌症研究所、美国国立卫生研究院以联邦资金提供，资助任务订单编号为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、可复现性与可扩展性。RadioGraphics, 2023. https://doi.org/10.1148/rg.230180