Summary
Excerpt |
---|
Put Collection Abstract here. If it's really long ask them to help you break it up such that the most important summary stuff is here and the rest goes in the Detailed Description tab. |
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 Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA)”. 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 ProtocolFor 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: - PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.
- 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. If the primary lesion measures < 1 cm, it was still annotated.
- Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.
- MRIs were annotated using axial T1-weighted post contrast sequences that best demonstrated the tumor.
- CTs were annotated using all axial post contrast series. If not available, the axial non-contrast series were annotated.
- 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.
- Lesions were labeled separately.
- Seed points were automatically generated, but reviewed by a radiologist.
- A “negative” annotation was created for any exam without findings.
At each time point: - Volume calculations were performed for each segmented structure. These calculations are provided in the Annotation Metadata CSV.
- A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.
- SNOMED-CT “Anatomic Region Sequence” and “Segmented Property Category Code Sequence” and codes were inserted for all segmented structures.
- Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.
- “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”.
- Content Item in “Acquisition Context Sequence” was added containing "Time Point Type" using Concept Code Sequence (0040,A168) selected from:
- (255235001, SCT, “Pre-dose”)
- (719864002, SCT, "Post-cancer treatment monitoring")
- A spreadsheet containing key details about the annotations is available in the Data Access section below.
- 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.
|
Localtab Group |
---|
Localtab |
---|
active | true |
---|
title | Data Access |
---|
| Data Access |
|
Localtab Group |
---|
Localtab |
---|
active | true |
---|
title | Data Access |
---|
| Data AccessNote to curators! This macro is for collections that are restricted due to facial reconstruction possibility. Note to curators! This macro is for collections that are restricted because of a PI's embargo request General restricted license access |
---|
Note to curators! Only use the appropriate macro for your collection above, or the text below in the case of NCTN trials. It will need to be tailored with the correct NCT#. 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 Type | Download all or Query/Filter | License |
---|
Images, Segmentations, and Radiation Therapy Structures/Doses/Plans CPTAC-PDA Annotations - Segmentations, Seed Points, and Negative Findings Assessments (DICOM, XX0.X 01 GB) << latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>
|
Tcia button generator |
---|
Tcia button generator |
---|
|
(Download requires NBIA Data Retriever) Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
| Tissue Slide Images (SVS, XX.X GB) | url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_Tumor-Annotations-manifest_07-05-2023.tcia?api=v2 |
---|
| tcia-button-generator |
|
Tcia button generator |
---|
label | Search |
---|
url | https://nbia.cancerimagingarchive.net/nbia-search/?MinNumberOfStudiesCriteria=1&CollectionCriteria=CPTAC-PDA&ThirdPartyCriteria=YES |
---|
|
|
(Download requires Aspera pluginNBIA Data Retriever) | Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
| Clinical data CPTAC-PDA Annotation Metadata (CSV) |
Tcia button generator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/Metadata_Report_CPTAC-PDA_2023_07_14.csv?api=v2 |
---|
|
|
| Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
|
Click the Versions tab for more info about data releases. Additional Resources for this DatasetNote 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-resourcesDataset - The NCI Cancer Research Data Commons (CRDC) provides access to proteomic, genomic and clinical data related to these subjects.
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. Nctn additional resources |
---|
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 DatasetTCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection: <add links to TCIA Analysis Result DOIs here>Collections Used in this Third Party AnalysisBelow is a list of the Collections used in these analyses: Source Data Type | Download | License |
---|
Original CPTAC-PDA Images used to create Segmentations and Seed Points (DICOM, 18.0 GB) |
Tcia button generator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_SourceImages_SEGSandSeedpoints-manifest-07-05-2023.tcia?api=v2 |
---|
|
|
(Download requires NBIA Data Retriever) | | Original CPTAC-PDA Images used to create Negative Assessment reports (DICOM, 1.54 GB) |
Tcia button generator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_SourceImages_NegativeAssessments-manifest-07-05-2023.tcia?api=v2 |
---|
|
|
(Download requires NBIA Data Retriever) | |
|
Localtab |
---|
title | Detailed Description |
---|
| Detailed DescriptionImage Statistics | Radiology Image Statistics | Pathology Image Statistics |
|
---|
Modalities | RTSTRUCTModalities | Number of Patients | 103 | Number of Studies | 119 | Number of Series | 534 | Number of Images | 534 | Images Size (GB) |
<< Add any additional information that didn't fit or belong in the Summary section. >>
|
Localtab |
---|
title | Citations & Data Usage Policy |
---|
| Citations & Data Usage Policy Tcia limited license policy |
---|
Info |
---|
| DOI goes here. Create using Datacite with information from Collection Approval form |
Info |
---|
title | Publication Citation |
---|
| We ask on the proposal form if they have ONE traditional publication they'd like users to cite. |
Info |
---|
| 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 Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA-Tumor-Annotations) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/BW9V-BX61 |
Info |
---|
| 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 DataTCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. |
Localtab |
---|
| Version X 1 (Current): Updated yyyy2023/mm07/dd24
Data Type | Download all or Query/Filter | License |
---|
Images, Segmentations, and Radiation Therapy Structures/Doses/Plans CPTAC-PDA Annotations - Segmentations, Seed Points, and Negative Findings Assessments (DICOM, | XXX << latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>
|
Tcia button generator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_Tumor-Annotations-manifest_07-05-2023.tcia?api=v2 |
---|
|
| tcia-button-generator
Tcia button generator |
---|
label | Search |
---|
url | https://nbia.cancerimagingarchive.net/nbia-search/?MinNumberOfStudiesCriteria=1&CollectionCriteria=CPTAC-PDA&ThirdPartyCriteria=YES |
---|
|
|
(Download | requires the | | CPTAC-PDA Annotation Metadata (CSV) | | restrictedlicense Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
Tissue Slide Images (SVS, XX.X generator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/Metadata_Report_CPTAC-PDA_2023_07_14.csv?api=v2 |
---|
|
|
| | Original CPTAC-PDA Images used to create Segmentations and Seed Points (DICOM, 18.0 GB) | |
Tcia button generator |
---|
label | Search |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_SourceImages_SEGSandSeedpoints-manifest-07-05-2023.tcia?api=v2 |
---|
|
|
(Download requires NBIA Data Retriever) | | Original CPTAC-PDA Images used to create Negative Assessment reports (DICOM, 1.54 GB) | | restrictedlicensegenerator |
---|
url | https://wiki.cancerimagingarchive.net/download/attachments/157288334/CPTAC-PDA_SourceImages_NegativeAssessments-manifest-07-05-2023.tcia?api=v2 |
---|
|
|
(Download requires NBIA Data Retriever) |
Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
Clinical data (CSV) | tcia-button-generator Nctn_with_collab license only |
---|
Nctn_no_collab license only |
---|
<< One or two sentences about what you changed since last version. No note required for version 1. >>
|
|