DICOM converted Slide Microscopy images for the TCGA-COAD 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-COAD. 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-Colon Adenocarcinoma (TCGA-COAD) 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, has archived a large portion of the radiological images of the COAD cases. Please see the TCGA-COAD 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_coad-idc_v10-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_coad-idc_v10-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_coad-idc_v10-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] 收录的图像及/或图像衍生数据。该数据集已被转换为DICOM格式，并由IDC团队完成数据导入。您可通过IDC门户的TCGA-COAD页面浏览并可视化对应图像。您可借助本Zenodo记录中提供的清单文件，按照下述下载说明下载该数据集的全部内容。 数据集说明 本数据集为《癌症基因组图谱-结肠腺癌（The Cancer Genome Atlas-Colon Adenocarcinoma, TCGA-COAD）》，是通过标准化放射影像数据扩充TCGA（http://cancergenome.nih.gov/）数据集的整体项目的一部分。癌症影像项目（Cancer Imaging Program, CIP）联合多家TCGA组织样本贡献机构，已归档了大部分结肠腺癌病例的放射影像数据。请访问TCGA-COAD页面以了解更多图像相关信息，并获取本数据集的配套元数据。 包含文件 清单文件名可标识该数据集版本首次引入的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中首次引入的`collection_id`数据集内容。若本Zenodo页面后续推出更新版本，将同步标注对应数据集更新版本的引入时间。 本记录包含以下清单文件： - `tcga_coad-idc_v10-aws.s5cmd`：可从IDC公共亚马逊云服务（Amazon Web Services, AWS）存储桶下载的文件清单 - `tcga_coad-idc_v10-gcs.s5cmd`：可从IDC公共谷歌云存储（Google Cloud Storage, GCS）存储桶下载的文件清单 - `tcga_coad-idc_v10-dcf.dcf`：Gen3格式清单（详情请参见https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids） 注意：文件名以`-aws.s5cmd`结尾的清单指向存储于亚马逊云服务（AWS）存储桶的文件，而`-gcs.s5cmd`结尾的清单指向谷歌云存储（GCS）中的文件。实际文件内容完全一致，仅在AWS与GCP平台间做了镜像分发。 下载说明 每份清单文件的头部均包含对应文件的下载指引。 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格式清单文件，下载本数据集中的所有目标文件：`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研究经费全部或部分来自美国国家癌症研究所、美国国立卫生研究院的联邦拨款，项目任务订单编号为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. National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence. RadioGraphics, 2023. https://doi.org/10.1148/rg.230180