DICOM converted Slide Microscopy images for the TCGA-OV 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-OV. 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-Ovarian Cancer (TCGA-OV) 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 OV cases. Please see the TCGA-OV 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_ov-idc_v10-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_ov-idc_v10-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_ov-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本数据集收录了美国国家癌症研究所影像数据共享库（National Cancer Institute Imaging Data Commons，IDC）[1] 提供的影像及影像衍生数据。本数据集已被转换为DICOM格式，并由IDC团队完成入库。您可通过IDC门户访问TCGA-OV页面，浏览并可视化对应影像。您可遵循下方的下载说明，使用本Zenodo记录中包含的清单文件下载该数据集的全部内容。 数据集说明 癌症基因组图谱-卵巢癌（The Cancer Genome Atlas-Ovarian Cancer，TCGA-OV）数据集是一项更大规模工作的组成部分，该工作旨在为癌症基因组图谱（The Cancer Genome Atlas，TCGA，http://cancergenome.nih.gov/）数据集补充经过标准化表征的放射影像。美国国家癌症研究所癌症影像项目（Cancer Imaging Program，CIP）联合多家TCGA组织样本贡献机构，正在对经基因分析的卵巢癌病例的大部分放射影像进行归档存储。 请访问TCGA-OV页面，了解该数据集影像的更多信息，并获取相关支撑元数据。 包含文件 清单文件的文件名可标识该数据集版本首次被纳入的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`数据集的内容。若本Zenodo页面后续更新，将标注对应数据集新版本的引入时间。 `tcga_ov-idc_v10-aws.s5cmd`：可从IDC公开亚马逊云服务（Amazon Web Services，AWS）存储桶中下载的文件清单 `tcga_ov-idc_v10-gcs.s5cmd`：可从IDC公开谷歌云存储（Google Cloud Storage，GCS）存储桶中下载的文件清单 `tcga_ov-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GCS存储桶中的文件。两类存储桶中的实际文件完全一致，且保持双向同步。 下载说明 每份清单文件的头部均包含对应文件的下载说明。 若使用`.s5cmd`格式清单下载文件，请执行以下步骤： 1. 安装idc-index工具包：`pip install --upgrade idc-index` 2. 通过传入`.s5cmd`清单文件的路径，下载本数据集中清单引用的全部文件：`idc download manifest.s5cmd` 若使用`.dcf`格式清单下载文件，请查阅清单头部的说明。 致谢 本影像数据共享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与美国国立卫生研究院提供的联邦拨款，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影像数据共享库：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