Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add DICOM Stack data set #9

Merged
merged 44 commits into from
Apr 12, 2022

Conversation

adam-grant-hendry
Copy link
Contributor

See PR #5 for original discussion (which was accidentally deleted).

This dataset will be used to test improved volume rendering and DICOM stack reading per pyvista/pyvista-support issue #500.

Skin Cancer

The Cancer Imaging Archive (TCIA) is a service which de-identifies and hosts a large archive of medical images of cancer accessible for public download. The data are organized as “collections”; typically patients’ imaging related by a common disease (e.g. lung cancer), image modality or type (MRI, CT, digital histopathology, etc) or research focus. DICOM is the primary file format used by TCIA for radiology imaging. Supporting data related to the images such as patient outcomes, treatment details, genomics and expert analyses are also provided when available.

This dataset is a member of the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium Sarcomas (CPTAC-SAR) cohort. CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. Radiology and pathology images from CPTAC patients are being collected and made publicly available by The Cancer Imaging Archive to enable researchers to investigate cancer phenotypes which may correlate to corresponding proteomic, genomic and clinical data.

This data has been published under the Creative Commons Attribution 3.0 Unported License and must adhere to the CPTAC Data Use Agreement. Per the TCIA Data Usage Policy (see License file), all oral or written presentations, disclosures, or publications must acknowledge the specific dataset(s) or applicable accession number(s) and the NIH-designated data repositories through which the investigator accessed any data. The appropriate citations are included in the Citations file. The metadata for this dataset is included in metadata.csv. Questions may be directed to help@cancerimagingarchive.net.

Title: Forearm Sarcoma
DataDescription URI: https://doi.org/10.7937/TCIA.2019.9bt23r95
Number of Images: 3
Total Size: 1.51 MB
File Format: DICOM

Files:
DICOM_Stack.zip
LICENSE.txt
CITATION.txt
metadata.csv

akaszynski and others added 14 commits April 9, 2021 10:48
This dataset will be used to test improved volume rendering and DICOM
stack reading per pyvista/pyvista-support issue #500.

The Cancer Imaging Archive (TCIA) is a service which de-identifies and
hosts a large archive of medical images of cancer accessible for public
download. The data are organized as “collections”; typically patients’
imaging related by a common disease (e.g. lung cancer), image modality
or type (MRI, CT, digital histopathology, etc) or research focus. DICOM
is the primary file format used by TCIA for radiology imaging.
Supporting data related to the images such as patient outcomes,
treatment details, genomics and expert analyses are also provided when
available.

This dataset is a member of the National Cancer Institute's Clinical
Proteomic Tumor Analysis Consortium Sarcomas (CPTAC-SAR) cohort. CPTAC
is a national effort to accelerate the understanding of the molecular
basis of cancer through the application of large-scale proteome and
genome analysis, or proteogenomics. Radiology and pathology images from
CPTAC patients are being collected and made publicly available by The
Cancer Imaging Archive to enable researchers to investigate cancer
phenotypes which may correlate to corresponding proteomic, genomic and
clinical data.

This data has been published under the `Creative Commons Attribution 3.0
Unported License` and must adhere to the CPTAC Data Use Agreement. Per
the TCIA Data Usage Policy (see License file), all oral or written
presentations, disclosures, or publications must acknowledge the
specific dataset(s) or applicable accession number(s) and the
NIH-designated data repositories through which the investigator
accessed any data. The appropriate citations are included in the
CITATIONS file. The metadata for this dataset is included in
metadata.csv. Questions may be directed to
<help@cancerimagingarchive.net>.

Title: Forearm Sarcoma
DataDescription URI: https://doi.org/10.7937/TCIA.2019.9bt23r95
Number of Images: 3
Total Size: 1.51 MB
File Format: DICOM
@adam-grant-hendry
Copy link
Contributor Author

@akaszynski @MatthewFlamm @banesullivan If you would, please review this PR at your earliest convenience. Once accepted, I will submit my PR to solve issue #500.

Copy link
Member

@akaszynski akaszynski left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is good to go. Thanks @adam-grant-hendry!

@akaszynski akaszynski merged commit d73e8f6 into pyvista:master Apr 12, 2022
@MatthewFlamm
Copy link
Contributor

This PR modified Data/FORGE.omf. I'm not sure if that was intended.

@adam-grant-hendry
Copy link
Contributor Author

adam-grant-hendry commented Apr 12, 2022

@MatthewFlamm No, that was not intended. The reason PR #5 failed was because of a botched attempt to cherry-pick my commit on top of the latest master branch.

I noticed the commit message git wanted to commit was Add forge data, so I cancelled that commit, deleted my branch, and manually recreated it on top of master since the change was simple.

What did it change?

@adam-grant-hendry
Copy link
Contributor Author

@MatthewFlamm I see now. It appears Data/FORGE.omf was removed by @banesullivan in bd3721. IIRC, that was the base of my original branch, so perhaps I accidentally re-introduced the file.

I'll submit another PR to correct this.

@adam-grant-hendry adam-grant-hendry deleted the feat/dicomstack branch April 12, 2022 20:01
@akaszynski
Copy link
Member

I've removed Data/FORGE.omf in 72402e9.

@adam-grant-hendry
Copy link
Contributor Author

Thank you @akaszynski !

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

4 participants