HCMI-CMDC: DICOM converted whole slide images from the Human Cancer Models Initiative (HCMI) Cancer Model Development Center (CMDC)

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 Human Cancer Models Initiative (HCMI) is a collaborative international consortium supported by
the National Cancer Institute (NCI), Cancer Research UK (CRUK), the Hubrecht Organoid Technology
(HUB) foundation, and the Wellcome Sanger Institute. HCMI generates novel human cancer culture
models — including organoids, conditionally reprogrammed cells, and other next-generation cancer
models — annotated with genomic and clinical data to accelerate the next generation of cancer
research. NCI contributes to the initiative by supporting four Cancer Model Development Centers
(CMDC).

This collection contains DICOM converted whole slide images from 382 of the 805 cases in the
GDC HCMI-CMDC project
(dbGaP accession
phs001486).
The proprietary format whole slide images were obtained from GDC and converted to DICOM Slide
Microscopy (SM) format using
idc-wsi-conversion. The 810 slides
include H&E-stained (hematoxylin and eosin) frozen section
tumor specimens (633 slides), FFPE tumor specimens (92), frozen section normal specimens (75),
FFPE normal specimens (6), and additional H&E tumor specimens (4).

The collection encompasses a wide variety of cancer types and anatomic sites. The most common
diagnoses in the DICOM-converted subset include infiltrating duct carcinoma (101 patients),
adenocarcinoma NOS (93), glioblastoma (41), malignant melanoma (23), adenocarcinoma metastatic (14),
lobular carcinoma (9), mucinous adenocarcinoma (7), squamous cell carcinoma (6), serous carcinoma
(6), and nephroblastoma (5), among others. Primary sites include colon, pancreas, esophagus, breast,
rectum, brain, skin, lung, stomach, ovary, bladder, uterus, kidney, and liver.

Data organization: DICOM PatientIDs correspond to GDC case IDs and can be used to
link to genomic, transcriptomic, and clinical data in the
GDC portal. Of 805 GDC
cases, 382 have Tissue Slide images; the remaining 423 cases have no slides and are not
represented in this collection. The HCMI initiative pairs these tumor and normal tissue
images with next-generation cancer models (organoids, conditionally reprogrammed cells, and
cell lines); model availability and characterization data can be explored via the
HCMI program page.

HCMI-CMDC data is accessible at the NCI's Genomic Data Commons (GDC) via the
GDC Data Portal.
Learn more about the Human Cancer Models Initiative at the
NCI HCMI program 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, hcmi_cmdc-idc_v22-aws.s5cmd corresponds to the contents of the hcmi_cmdc collection introduced in IDC data release v22.

hcmi_cmdc-idc_v24-aws.s5cmd: AWS download manifest

hcmi_cmdc-idc_v24-gcs.s5cmd: GCS download manifest

hcmi_cmdc-idc_v24-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:

Install idc-index:
pip install --upgrade idc-index

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 [e-mail]
or post on the IDC Forum.