DICOM converted Slide Microscopy images for the CPTAC-SAR 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: CPTAC-SAR. You can use the manifests included in this Zenodo record to download the content of the collection following the Download instructions below. Collection description This collection contains subjects from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium Sarcomas (CPTAC-SAR) cohort. CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. Radiology and pathology images from CPTAC Phase 3 patients are being collected and made publicly available by The Cancer Imaging Archive to enable researchers to investigate cancer phenotypes which may correlate to corresponding proteomic, genomic and clinical data. Please see the CPTAC-SAR wiki 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. cptac_sar-idc_v15-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets cptac_sar-idc_v15-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets cptac_sar-idc_v15-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共享库（National Cancer Institute Imaging Data Commons, IDC）[1] 提供的图像及/或图像衍生数据集合集。本数据集已被转换为医学数字成像和通信（Digital Imaging and Communications in Medicine, DICOM）格式，并由IDC团队完成入库。您可通过IDC门户访问CPTAC-SAR页面，浏览并可视化对应图像。您可遵循下文的下载说明，使用本Zenodo记录中包含的清单文件下载该合集的内容。 合集说明 本合集源自美国国家癌症研究所临床蛋白质组肿瘤分析委员会肉瘤队列（Clinical Proteomic Tumor Analysis Consortium Sarcomas, CPTAC-SAR）的研究对象。CPTAC是一项全国性项目，旨在通过大规模蛋白质组、基因组分析（即蛋白质基因组学，proteogenomics）加速对癌症分子机制的认知。癌症影像档案库（The Cancer Imaging Archive）正在收集并公开CPTAC第三阶段患者的放射学与病理学图像，以供研究者探究可能与对应蛋白质组、基因组及临床数据相关的癌症表型。 请访问CPTAC-SAR维基页面，了解该合集图像的更多信息并获取相关辅助元数据。 包含文件 清单文件名可标识该合集数据版本首次发布所属的IDC数据发布版本。例如，`collection_id-idc_v8-aws.s5cmd` 对应IDC数据发布版本v8中首次推出的collection_id合集内容。若本Zenodo页面存在后续版本，将标注对应合集后续版本的推出时间。 `cptac_sar-idc_v15-aws.s5cmd`：可从IDC公共亚马逊云科技（Amazon Web Services, AWS）存储桶下载的文件清单 `cptac_sar-idc_v15-gcs.s5cmd`：可从IDC公共谷歌云存储（Google Cloud Storage）存储桶下载的文件清单 `cptac_sar-idc_v15-dcf.dcf`：Gen3格式清单（详情请访问 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`后缀的清单文件指向谷歌云存储中的文件。两类存储桶中的实际文件完全一致，且互为镜像。 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说明。 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，下载本数据集中清单所引用的文件：`idc download manifest.s5cmd` 若使用`.dcf`格式清单下载文件，请参阅清单头部的说明。 致谢 影像数据共享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，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. National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence. RadioGraphics (2023). https://doi.org/10.1148/rg.230180