DICOM converted Slide Microscopy images for the TCGA-READ collection

This dataset corresponds to a collection of images and/or image-derived data available from the National Cancer Institute Imaging Data Commons (IDC). This dataset was converted into DICOM representation and ingested by the IDC team. You can explore and visualize the corresponding images using the IDC Portal. You can use the manifests included in this Zenodo record to download the collection following the Download instructions below.

The Cancer Genome Atlas-Rectum Adenocarcinoma (TCGA-READ) 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 TCGA tissue-contributing institutions, has archived a large portion of the radiological images of the genetically-analyzed READ cases.

Please see the TCGA-READ 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, tcga_read-idc_v22-aws.s5cmd corresponds to the contents of the tcga_read collection introduced in IDC data release v22.

• tcga_read-idc_v25-aws.s5cmd: AWS download manifest
• tcga_read-idc_v25-gcs.s5cmd: GCS download manifest
• tcga_read-idc_v25-dcf.dcf: DCF download manifest

Manifest files ending in -aws.s5cmd reference files in Amazon Web Services (AWS) buckets; -gcs.s5cmd reference files in Google Cloud Storage. The actual files are identical and mirrored between AWS and GCP.

Download instructions

Each manifest file includes instructions in its header on how to download the included files.

To download the files using .s5cmd manifests:

1. Install idc-index: pip install --upgrade idc-index
2. Download the files referenced by a manifest included in this dataset: idc download manifest.s5cmd

To download files using a .dcf manifest, see the manifest header.

For questions or help, contact support@canceridc.dev or post on the IDC Forum.

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. HHSN261201500003I.