DICOM converted Slide Microscopy images for the CPTAC-UCEC 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-UCEC. 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 Uterine Corpus Endometrial Carcinoma (CPTAC-UCEC) 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-UCEC 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_ucec-idc_v10-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets cptac_ucec-idc_v10-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets cptac_ucec-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本数据集包含来自美国国家癌症研究所成像数据共享库（National Cancer Institute Imaging Data Commons, IDC）[1]的图像及/或图像衍生数据。本数据集已转换为DICOM（医学数字成像与通信，Digital Imaging and Communications in Medicine）格式，并由IDC团队完成数据摄入。您可通过IDC门户访问CPTAC-UCEC队列以浏览并可视化对应图像。您可借助本Zenodo记录中包含的清单文件，按照下述下载指南下载该数据集的全部内容。 数据集说明 本数据集收录了美国国家癌症研究所临床蛋白质组肿瘤分析协会子宫体子宫内膜癌（Clinical Proteomic Tumor Analysis Consortium Uterine Corpus Endometrial Carcinoma, CPTAC-UCEC）队列的受试者数据。CPTAC是一项全国性研究计划，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。本数据集由癌症成像档案库收集并公开了CPTAC第三阶段受试者的放射学与病理学图像，以供研究者探索与对应蛋白质组、基因组及临床数据相关的癌症表型。 如需了解该数据集图像的更多信息并获取相关支撑元数据，请访问CPTAC-UCEC维基页面。 包含文件 清单文件的命名规则可反映该数据集版本首次发布的IDC数据版本。例如，`collection_id-idc_v8-aws.s5cmd`对应于IDC数据版本v8中首次发布的`collection_id`数据集内容。若本Zenodo记录后续更新版本，将标注对应数据集新版本的发布时间。 - `cptac_ucec-idc_v10-aws.s5cmd`：可从IDC公开亚马逊云服务（Amazon Web Services, AWS）存储桶下载的文件清单 - `cptac_ucec-idc_v10-gcs.s5cmd`：可从IDC公开谷歌云存储（Google Cloud Storage, GCS）存储桶下载的文件清单 - `cptac_ucec-idc_v10-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`的清单文件对应存储于AWS存储桶中的文件，而`-gcs.s5cmd`后缀的清单文件对应存储于谷歌云存储中的文件。两类存储桶中的实际文件完全一致，且为双向镜像同步。 下载指南 所有清单文件的头部均包含对应文件的下载说明。 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`清单文件下载本数据集中清单引用的文件：`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 成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，项目合同编号为HHSN261201500003l，任务订单编号为HHSN26110071。 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成像数据共享库：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