DICOM converted Slide Microscopy images for the TCGA-SKCM 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-SKCM. You can use the manifests included in this Zenodo record to download the content of the collection following the Download instructions below. Collection description Melanoma is a cancer in a type of skin cells called melanocytes. Melanocyes are the cells that produce melanin, which colors the skin. When exposed to sun, these cells make more melanin, causing the skin to darken or tan. Melanoma can occur anywhere on the body and risk factors include fair complexion, family history of melanoma, and being exposed to natural or artificial sunlight over long periods of time. Melanoma is most often discovered because it has metastasized, or spread, to another organ, such as the lymph nodes. In many cases, the primary skin melanoma site is never found. Because of this challenge, TCGA is studying primarily metastatic cases (in contrast to other cancers selected for study, where metastatic cases are excluded). For 2011, it was estimated that there were 70,230 new cases of melanoma and 8,790 deaths from the disease. Please see the TCGA-SKCM information page to learn more about the images and to obtain any supporting metadata for this collection. Citation guidelines can be found on the Citing TCGA in Publications and Presentations information page. 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_skcm-idc_v10-aws.s5cmd: manifest of files available for download from public IDC Amazon Web Services buckets tcga_skcm-idc_v10-gcs.s5cmd: manifest of files available for download from public IDC Google Cloud Storage buckets tcga_skcm-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本数据集为可从美国国家癌症研究所影像数据公共平台 (National Cancer Institute Imaging Data Commons, IDC) [1] 获取的影像及/或影像衍生数据集合。本数据集已转换为DICOM格式，并由IDC团队完成入库处理。您可通过IDC门户访问TCGA-SKCM页面，浏览并可视化对应影像。您可借助本Zenodo存档中包含的清单文件，按照下述下载说明下载该队列的全部内容。 ## 队列说明 黑色素瘤是一类起源于黑素细胞的皮肤恶性肿瘤。黑素细胞是生成赋予皮肤颜色的黑色素的细胞，当暴露于日光下时，这类细胞会合成更多黑色素，导致皮肤变黑或晒黑。黑色素瘤可发生于身体任何部位，其危险因素包括白皙肤色、黑色素瘤家族史，以及长期暴露于自然或人工日光照射。黑色素瘤通常在发生转移（即扩散至淋巴结等其他器官）时才被临床发现；在多数病例中，患者的原发性皮肤黑色素瘤病灶始终无法被定位。鉴于这一临床挑战，肿瘤基因组图谱 (The Cancer Genome Atlas, TCGA) 的研究主要聚焦于转移性病例（与其他入选研究的癌症队列不同，后者会排除转移性病例）。据2011年统计数据估算，当年全球新增黑色素瘤病例70230例，因该病死亡病例8790例。 请访问TCGA-SKCM信息页面，以了解该队列影像的更多细节，并获取该数据集的配套元数据。 引用规范可参见“在出版物及演示文稿中引用TCGA”信息页面。 ## 包含文件 清单文件的文件名可标识该队列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`对应于IDC数据发布版本v8中首次推出的`collection_id`队列的内容。若本Zenodo存档存在后续版本，将标注对应队列后续版本的推出时间。 - `tcga_skcm-idc_v10-aws.s5cmd`：可从IDC公共亚马逊云服务 (Amazon Web Services, AWS) 存储桶下载的文件清单 - `tcga_skcm-idc_v10-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 - `tcga_skcm-idc_v10-dcf.dcf`：Gen3清单（详情参见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`后缀的清单文件指向GCS存储桶中的文件。实际文件内容完全一致，且在AWS与GCP平台间实现了镜像同步。 ## 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：执行命令 `pip install --upgrade idc-index` 2. 通过传入本数据集中的`.s5cmd`清单文件，执行命令 `idc download manifest.s5cmd` 即可下载清单中引用的所有文件。 ### 使用.dcf格式清单下载文件 请参见对应清单文件头部的下载说明。 ## 致谢 影像数据公共平台 (IDC) 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，相关项目编号为任务订单HHSN26110071，合同编号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平台：迈向影像人工智能的透明化、可重复性与可扩展性[J]. RadioGraphics, 2023. https://doi.org/10.1148/rg.230180