DICOM converted Slide Microscopy images for the TCGA-ESCA 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-ESCA. 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-Esophageal Carcinoma (TCGA-ESCA) data collection is part of a larger effort to enhance the TCGA 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 ESCA cases. Please see the TCGA-ESCA 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_esca-idc_v18-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_esca-idc_v18-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_esca-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本数据集包含可从美国国家癌症研究所影像数据共享库（National Cancer Institute Imaging Data Commons, IDC）[1]获取的影像及/或影像衍生数据。本数据集已转换为医学数字成像和通信（DICOM）格式，并由IDC团队完成数据入库。您可通过IDC门户（链接指向TCGA-ESCA）浏览并可视化对应影像；您可按照下文的下载说明，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。 ## 数据集集合说明 癌症基因组图谱-食管癌（The Cancer Genome Atlas-Esophageal Carcinoma, TCGA-ESCA）数据集集合是一项更大规模工作的组成部分，该工作旨在为TCGA数据集添加经过标注的放射影像。癌症影像项目（Cancer Imaging Program, CIP）联合多家TCGA组织样本贡献机构，正致力于归档经基因分析的食管癌病例的大部分放射影像。 请访问TCGA-ESCA页面以了解更多影像相关信息，并获取本数据集的相关支持元数据。 ## 包含文件 清单文件的名称可标识该数据集版本首次发布所属的IDC数据发布版本。例如，`collection_id-idc_v8-aws.s5cmd`对应于IDC数据发布v8中首次推出的`collection_id`数据集的内容。若本Zenodo页面有后续版本，将标注对应数据集的后续版本发布时间。 1. `tcga_esca-idc_v18-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 2. `tcga_esca-idc_v18-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 3. `tcga_esca-idc_v18-dcf.dcf`：Gen3清单（详情请参阅https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids） 注意，以`-aws.s5cmd`结尾的清单文件指向存储于AWS存储桶中的文件，而以`-gcs.s5cmd`结尾的清单文件则指向GCS中的文件。实际文件内容完全一致，且在AWS与谷歌云平台（GCP）之间互为镜像。 ## 下载说明 所有清单文件的头部均包含如何下载其中所附文件的说明。 ### 基于.s5cmd格式清单下载 1. 安装idc-index工具包：执行命令`pip install --upgrade idc-index` 2. 传入.s5cmd格式的清单文件路径，即可下载本数据集中该清单所引用的文件：`idc download manifest.s5cmd` ### 基于.dcf格式清单下载 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源于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. 美国国家癌症研究所影像数据共享库：实现影像人工智能领域的透明性、可重复性与可扩展性[J]. RadioGraphics, 2023. https://doi.org/10.1148/rg.230180