BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing...
-
Upload
kathlyn-casey -
Category
Documents
-
view
231 -
download
4
Transcript of BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing...
![Page 1: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/1.jpg)
BioInformaticsandData
Sharing
![Page 2: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/2.jpg)
1. Data Sharing: Mechanism• QIN is strongly focused on data sharing
(image and metadata)
http://www.cancerimagingarchive.net/
• TCIA is preferred archive
• CTP is preferred tool for De-ID and Xfer to TCIA for curation and sharing
![Page 3: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/3.jpg)
1. Data Sharing: Format
• Preferred format is DICOM– For images of course– For segmentation maps, DICOM-Seg– For contours, DICOM-RT– (DCE group is using Matlab & NRRD?)– Tools are available to convert
![Page 4: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/4.jpg)
1. Data Sharing Status• 12 data sets in TCIA currently
0 20 40 60 80 100 120 140 160
QIN BRAIN
QIN LUNG
QIN LUNG LSC
QIN PHANTOM
QIN PROSTATE
QIN-BREAST
QIN-HEADNECK
QIN-SARCOMA
BWH
IOWA
MAASTRO
MOFFITT
OHSU
UOFWASH
UPMC
VANDERBILT
![Page 5: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/5.jpg)
1. Data Sharing Status
MR (13), CT (5), PET/CT (5), PET (2)
[# subjects]
![Page 6: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/6.jpg)
1. MetaData Sharing
• While DICOM addresses image data, there is no good standard for clinical data—e.g. survival therapy, tumor type and grade
• BIDS Breakout group: We wish to collect the type of information like that that is used by each QIN. Please be sure to send a person to at least 1 BIDS break out session with this information.
![Page 7: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/7.jpg)
1. Tool Sharing
License Maturity
Type Operating System
![Page 8: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/8.jpg)
1. Tool Sharing• Spans all major modalities except ultrasound
and X-ray• Predominantly vendor/hardware independent• Wide array of capabilities
![Page 9: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/9.jpg)
1. Tool Sharing
• Whitepaper is being considered that would– Characterize tool sharing today– Define best ways to encourage tool sharing– Define best ways to encourage joint tool
development
![Page 10: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/10.jpg)
2. Preferred Measures
• Many segmentation measures have been used for grand challenge– “Weigh in” on preferred segmentation measures– Preferred measures for ‘soft’ segmentation– Preferred measures for non-geometric data
![Page 11: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/11.jpg)
2. Preferred Measures
• Preferred labels– DICOM-Seg has some and should be preferred– ID gaps in DICOM-Seg
![Page 12: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/12.jpg)
2. Preferred Measures
• Methods and tools for assessing other types of measures like textures are nearly absent. Small group is forming to address this need.
![Page 13: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/13.jpg)
3. Infrastructure for Decision Support
• Common need to have infrastructure to ease pain of deploying decision support for clinical trials
![Page 14: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/14.jpg)
Next Year Activities: Data Sharing
• Define use case for Segmentation Grand Challenge at MICCAI.– To include both image data and ROI metadata with
tissue labels
![Page 15: BioInformatics and Data Sharing. 1. Data Sharing: Mechanism QIN is strongly focused on data sharing (image and metadata)](https://reader038.fdocuments.net/reader038/viewer/2022102800/56649ee55503460f94bf3cc4/html5/thumbnails/15.jpg)
Decision Support Use Case
• Take TCGA data and simulate send from 2 or more ‘source sites’ using CTP to central site
• Central site receives, IDs trial, and executes series of steps on the images
• User(s) at each site view web page with ‘results’ of analysis
• Likely task is segmentation of pre-op tumor, and perhaps CBV or ADC or T2 texture predicting grade or MGMT or 1p19q or ??
“Stretch Goal”