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  • Annotations for The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC-Tumor-Annotations)

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Summary

Excerpt

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Acknowledgements

We would like to acknowledge the individuals and institutions that have provided data for this collection:

...

Hospital/Institution Name city, state, country - Special thanks to First Last Names, degree PhD, MD, etc from the Department of xxxxxx, Additional Names from same location.

...

This dataset contains image annotations derived from "The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC)”.  This dataset was generated as part of a National Cancer Institute project to augment images from The Cancer Imaging Archive with tumor annotations that will improve their value for cancer researchers and artificial intelligence experts.

Annotation Protocol

For each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences/series. In a typical patient all available time points were annotated. The following annotation rules were followed:

  1. PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.
  2. RECIST 1.1 was otherwise generally followed for MR and CT imaging. A maximum of 5 lesions were annotated per patient scan (timepoint); no more than 2 per organ. The same 5 lesions were annotated at each time point. Lymph nodes were annotated if >1 cm in short axis. Other lesions were annotated if >1 cm. The primary tumor was still annotated if < 1 cm.
  3. Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.
  4. MRIs were annotated using the T1-weighted axial post contrast sequence.
  5. CTs were annotated using all axial post contrast series. 
  6. PET/CTs were annotated on the CT and attenuation corrected PET images, unless there was a diagnostic CT from the same time point, in which case the CT portion of the PET/CT was not annotated.
  7. Lesions were labeled separately.
  8. Seed points were automatically generated, but reviewed by a radiologist.
  9. A “negative” annotation was created for any exam without findings.

At each time point:

  1. Volume calculations were performed for each segmented structure.  These calculations are provided in the Annotation Metadata CSV.
  2. A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.
  3. SNOMED-CT “Anatomic Region Sequence” and “Segmented Property Category Code Sequence” and codes were inserted for all segmented structures.
  4. Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.
    1. “Clinical Trial Time Point ID” was used to encode time point type using one of the following strings as applicable: “pre-dose” or “post-chemotherapy”.
    2. Content Item in “Acquisition Context Sequence” was added containing "Time Point Type" using Concept Code Sequence (0040,A168) selected from:
      1. (255235001, SCT, “Pre-dose”)
      2. (719864002, SCT, "Post-cancer treatment monitoring")

Important supplementary information and sample code

  1. A spreadsheet containing key details about the annotations is available in the Data Access section below.
  2. A Jupyter notebook demonstrating how to use the NBIA Data Retriever Command-Line Interface application and the REST API to access these data can be found in the Additional Resources section below.


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activetrue
titleData Access

Data Access

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Localtab
activetrue
titleData Access

Data Access

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This is a limited access data set. To request access please register an account on the NCTN Data Archive.  After logging in, use the "Request Data" link in the left side menu.  Follow the on screen instructions, and enter NCT00352534 when asked which trial you want to request.  In step 2 of the Create Request form, be sure to select “Imaging Data Requested”. Please contact NCINCTNDataArchive@mail.nih.gov for any questions about access requests.

Data TypeDownload all or Query/FilterLicense

Images, Segmentations, and Radiation Therapy Structures/Doses/Plans (DICOM, XX.X GB)

<< latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>CPTAC-HNSCC Annotations - Segmentations, Seed Points, and Negative Findings Assessments  (DICOM, 26 MB)



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urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_Tumor-Annotations-manifest_07-14-2023.tcia?api=v2



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urlhttps://nbia.cancerimagingarchive.net/nbia-search/?DateRange=07%2F10%2F2023-07%2F24%2F2023&CollectionCriteria=CPTAC-HNSCC&ThirdPartyCriteria=YES



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Clinical data (CSV


CPTAC-HNSCC Annotation Metadata (CSV, 214 KB)


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Click the Versions tab for more info about data releases.

urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/Metadata_Report_CPTAC-HNSCC_2023_07_14.csv?api=v2



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Additional Resources for this Dataset

Note to curators! Use this any time you are linking to NCI's IDC/GDC/PDC resources.  The links below are examples and will need to be tailored to point to the specific dataset (see parameters in URLS).

Nci_crdc additional resources

Note to curators! The link below is an example for NCTN trials and will need to be tailored to the proper URL for the corresponding data on the NCTN Data Archive.

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Note to curators! Below are examples for what to do with other external resources/links that don't fit into the above categories.

The following external resources have been made available by the data submitters.  These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.

  • Software / Code on Github
  • Genomics data in DbGAP
  • Genomics data in Gene Expression Omnibus

Third Party Analyses of this Dataset

TCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection:

Collections Used in this Third Party Analyses 

Below is a list of the Collections used in these analyses:

Source Data TypeDownloadLicense
Original CPTAC-HNSCC Images used to create Segmentations and Seed Points (DICOM, 20.3 GB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_SourceImages_SEGSandSeedpoints-manifest-07-14-2023.tcia?api=v2


(Download requires NBIA Data Retriever)

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Original CPTAC-HNSCC Images used to create Negative Assessment reports (DICOM, 11.6 GB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_SourceImages_NegativeAssessments-manifest-07-14-2023.tcia?api=v2


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Tcia restricted license



Localtab
titleDetailed Description

Detailed Description

Pathology Image Statistics


Image Statistics

Radiology Image Statistics

ModalitiesModalities

RTSTRUCT

Number of Patients

101

Number of Studies

261

Number of Series

715

Number of Images

715

Images Size (GB)
<< Add any additional information that didn't fit or belong in the Summary section. >>
26 MB



Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy

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Info
titleData Citation

DOI goes here. Create using Datacite with information from Collection Approval form

Info
titlePublication Citation

We ask on the proposal form if they have ONE traditional publication they'd like users to cite.

Info
titleAcknowledgement

Required acknowledgements only (ex:The CPTAC program requests that publications using data from this program...). If they just want to thank someone, that goes in the Acknowledgement section underneath the Summary.Rozenfeld, M., & Jordan, P. (2023). Annotations for The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC-Tumor-Annotations) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/PFEC-T641


Info
titleTCIA Citation

Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC.https://doi.org/10.1007/s10278-013-9622-7

Other Publications Using This Data

TCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA's Helpdesk.


Localtab
titleVersions

Version

X

1 (Current): Updated

yyyy

2023/

mm

07/

dd

24

Data TypeDownload all or Query/FilterLicense

Images, Segmentations, and Radiation Therapy Structures/Doses/Plans (DICOM, XX.X GB)

<< latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>

CPTAC-HNSCC Annotations - Segmentations, Seed Points, and Negative Findings Assessments  (DICOM, 26 MB)



Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_Tumor-Annotations-manifest_07-14-2023.tcia?api=v2
tcia-button-generator



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labelSearch
url
(Download requires the 
https://nbia.cancerimagingarchive.net/nbia-search/?DateRange=07%2F10%2F2023-07%2F24%2F2023&CollectionCriteria=CPTAC-HNSCC&ThirdPartyCriteria=YES



(Download requires NBIA Data Retriever)

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CPTAC-HNSCC Annotation Metadata (CSV, 214 kb)


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restricted-license

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Tissue Slide Images (SVS, XX.X
button-generator
labelSearch
urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/Metadata_Report_CPTAC-HNSCC_2023_07_14.csv?api=v2



Tcia cc by 4


Original CPTAC-HNSCC Images used to create Segmentations and Seed Points (DICOM, 20.3 GB)


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Tcia button generator
labelSearch
urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_SourceImages_SEGSandSeedpoints-manifest-07-14-2023.tcia?api=v2


(Download requires NBIA Data Retriever)

tcia-cc-by-4

Tcia restricted license

Nctn_with_collab license only

Nctn_no_collab license only

Clinical data (CSV


Original CPTAC-HNSCC Images used to create Negative Assessment reports (DICOM, 11.6 GB)


Tcia button generator
labelSearch
urlhttps://wiki.cancerimagingarchive.net/download/attachments/157288486/CPTAC-HNSCC_SourceImages_NegativeAssessments-manifest-07-14-2023.tcia?api=v2


(Download requires NBIA Data Retriever)

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-license

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