HTAN-TNP-SARDANA: DICOM converted cyclic immunofluorescence and H&E whole slide images from the HTAN SARDANA Trans-Network Project

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 NCI Human Tumor Atlas Network (HTAN) is a multi-institutional effort to collect, analyze, and
publish a database of multi-omic data for a variety of human cancers. The Shared Repositories, Data,
Analysis and Access (SARDANA)
trans-network project (TNP) was
designed to optimize the repeatability, interpretability, and accessibility of data for the atlas.
The SARDANA TNP distributed a set of common tissue samples to participating HTAN centers, allowing
them to generate a spatial cell census using each center's imaging method of choice. Data generated
during the TNP was used to stress-test data standards and informatics systems and compare results
across experimental approaches and organizations.

The main sample imaged in this study is tissue resected from a 69-year-old man with a recent history
of both cutaneous melanoma and gastric marginal zone lymphoma of MALT type. He presented to medical
attention following recurrent syncopal episodes and falls secondary to anemia and orthostatic
hypotension. A colonoscopy identified a large mass in the right colon. Resection of a portion of the
right colon and terminal ileum revealed a 6.2 cm hard, exophytic mass in the cecum immediately
adjacent to the ileocecal valve. In the area of the specimen imaged, the tumor has invaded the
muscularis propria of the bowel wall into the peri-colonic epithelial tissue. There is also a region
of neighboring normal epithelium.

The specimen underwent FFPE processing (formalin fixation and paraffin embedding) followed by serial
sectioning into a collection of 5 um-thick samples for imaging. This dataset comprises one section
imaged with H&E (hematoxylin and eosin brightfield imaging) and an adjacent section imaged with
CyCIF (cyclic immunofluorescence). The CyCIF section was imaged with approximately 20 markers
targeting immune (CD4, CD8a, CD20, CD31, CD45, CD68, CD163, FOXP3, PD1, PDL1), epithelial
(E-Cadherin, CDX2, Cytokeratin), stromal (Smooth Muscle Actin, Vimentin, Desmin, Collagen IV,
Lamin), and proliferation (KI67, PCNA) markers, using Bisbenzimide (DAPI), Alexa Fluor 488, and
Alexa Fluor 647 fluorophores.

The DICOM collection contains 3 series: 240 CyCIF slide microscopy (SM) instances, 6 H&E SM
instances, and 19 presentation state (PR) instances, totaling 265 DICOM instances. The original
OME-TIFF images were converted to DICOM format using the conversion tools developed by the IDC team,
available at idc-wsi-conversion.
Images were processed using the MCMICRO pipeline.
Protocols used in this study are available at protocols.io:
CHTN tissue procurement and fixation,
CHTN tissue cryopreservation.

Files included

A manifest file's name indicates the IDC data release in which a version of collection data was first introduced. For example, htan_tnp_sardana-idc_v22-aws.s5cmd corresponds to the contents of the htan_tnp_sardana collection introduced in IDC data release v22.

htan_tnp_sardana-idc_v24-aws.s5cmd: AWS download manifest

htan_tnp_sardana-idc_v24-gcs.s5cmd: GCS download manifest

htan_tnp_sardana-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.