DICOM converted Slide Microscopy images for the TCGA-LUAD 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-LUAD. 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 Imaging Program (CIP) is working directly with primary investigators from institutes participating in TCGA to obtain and load images relating to the genomic, clinical, and pathological data being stored within the TCGA Data Portal Currently this large CT multi-sequence image collection of lung adenocarcinoma (LUAD) patients can be matched by each unique case identifier with the extensive gene and expression data of the same case from The Cancer Genome Atlas Data Portal to research the link between clinical phenome and tissue genome. Please see the TCGA-LUAD 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_luad-idc_v18-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_luad-idc_v18-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_luad-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本数据集为美国国家癌症研究所影像数据公共库（Imaging Data Commons, IDC）[1] 公开的图像及图像衍生数据合集。本数据集已被转换为DICOM（Digital Imaging and Communications in Medicine）格式，并由IDC团队完成入库。您可通过IDC门户访问TCGA-LUAD页面，浏览并可视化对应图像。您可借助本Zenodo记录中附带的清单文件，按照下方的下载说明下载该合集的内容。 ## 合集说明 癌症影像项目（Cancer Imaging Program, CIP）正与参与癌症基因组图谱（The Cancer Genome Atlas, TCGA）项目的机构首席研究员合作，获取并加载与TCGA数据门户中存储的基因组、临床及病理数据相关的影像资料。当前该大型肺腺癌（lung adenocarcinoma, LUAD）患者多序列计算机断层扫描（Computed Tomography, CT）影像合集，可通过唯一病例标识符与TCGA数据门户中对应病例的海量基因及表达数据进行关联，以研究临床表型与组织基因组之间的关联。 请访问TCGA-LUAD页面，了解更多关于该影像集的信息并获取本合集的相关支持元数据。 ## 包含文件 清单文件的文件名标注了该合集版本首次上线的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中首次上线的`collection_id`合集内容。若本Zenodo页面后续推出更新版本，将标注对应合集的更新上线时间。 本次提供的清单文件包括： 1. `tcga_luad-idc_v18-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 2. `tcga_luad-idc_v18-gcs.s5cmd`：可从IDC公开谷歌云存储（Google Cloud Storage）存储桶下载的文件清单 3. `tcga_luad-idc_v18-dcf.dcf`：Gen3格式清单（详情请参见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`则指向谷歌云平台（Google Cloud Platform, GCP）存储中的文件。实际文件内容完全一致，且在AWS与GCP间实现了镜像同步。 ## 下载说明 每个清单文件的头部均包含对应包含文件的下载说明。 使用.s5cmd格式清单下载文件的步骤如下： 1. 安装idc-index工具包：`pip install --upgrade idc-index` 2. 通过传入.s5cmd格式的清单文件，下载该清单引用的所有文件：`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文档。 ## 致谢 本影像数据公共库团队的研究工作全部或部分获得了美国国家癌症研究所、美国国立卫生研究院提供的联邦资金支持，项目任务编号为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公共库：迈向影像人工智能研究的透明化、可复现性与规模化. RadioGraphics, 2023. https://doi.org/10.1148/rg.230180