ctiip coordination. contract period of performance digital pathology and integrative query –july...
DESCRIPTION
Timeline – Digital Pathology Support native WSI format in caMicroscope –Delivered to QA – March 2015 Tools and libraries to support the creation, consumption and management of PathAIM –Delivered to QA – August 2015 Support analytical services –Delivered to QA – November 2015 Pilot a data mashup and integrative query system –Delivered to QA – DecemberTRANSCRIPT
CTIIP Coordination
Contract Period of Performance• Digital Pathology and Integrative Query
– July 24, 2014 – January 23, 2016• DICOM WG-30
– June 26, 2014 – June 25, 2015• Pilot Challenges
– December 18, 2014 – June 17, 2016• Co-clinical and animal model data
– April 15, 2015 – April 14, 2016
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Timeline – Digital Pathology• Support native WSI format in caMicroscope
– Delivered to QA – March 2015• Tools and libraries to support the creation, consumption
and management of PathAIM – Delivered to QA – August 2015
• Support analytical services– Delivered to QA – November 2015
• Pilot a data mashup and integrative query system– Delivered to QA – December 2015
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Timeline - Pilot Challenges• Evaluation of existing challenge platforms, standards, tools and
technologies– Report due March 31, 2015
• Develop MedICI system to support imaging (radiology and digital pathology) challenges– Development March to October 2015– Deliver to QA – September 2015
• Demonstrate the ability to host/execute pilot challenges using the challenge management system– Deploy Challenge Management System – September 2015– Execute first challenge – October / November 2015– Fine-tune system – November 2015 – January 2016– QA refinements – March 2016– Execute two more challenges – March to June 2016
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Timeline – Co-clinical/animal model• Submit Whole Slide Images and Demographics
– May – October 2015• PathAIM mark up and annotations
– June – October 2015• Prepare CMGI Images
– May – July 2015• Mark up In-Vivo Images
– July – August 2015• Submit CMGI images
– July – November 2015• Identify and prepare human BrCa cases
– July – September 2015 • Submit human BrCA Images
– November 2015 – April 2016
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Dependencies / Linking of ProjectsCreation of PathAIM annotations and markups for animal images
• DigPath– Tools and libraries to support the creation, consumption and management of
PathAIM • Delivered to QA – August 2015
• Co-Clinical– Submit Whole Slide Images and Demographics
• May – October 2015– PathAIM mark up and annotations
• June – October 2015
UC Davis team to provide input on markup and annotations for animal imagesUC Davis team = user acceptance testing during development
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• DigPath– Pilot a data mashup and integrative query system
• Delivered to QA – December 2015• Co-clinical
– Submit Whole Slide Images and Demographics• May – October 2015
– PathAIM mark up and annotations• June – October 2015
– Prepare CMGI Images• May – July 2015
– Mark up In-Vivo Images• July – August 2015
– Submit CMGI images• July – November 2015
• Need to agree where to store the data to make them accessible to the query system.
Dependencies / Linking of ProjectsProviding animal model/co-clinical data for integrated queries
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• Pilot Challenges– Execute two more challenges
• March to June 2016• Co-clinical
– PathAIM mark up and annotations• June – October 2015
– Mark up In-Vivo Images• July – August 2015
– Submit CMGI images• July – November 2015
– Submit human BrCA Images• November 2015 – April 2016
Dependencies / Linking of ProjectsProviding animal model/co-clinical data for pilot challenge
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Dependencies / Linking of ProjectsDICOM for animal model images
• Co-clinical– Submit CMGI images
• July – November 2015• DICOM WG-30
– Collecting images now– Images can be used as test cases
• DCB funded project develops DICOM wrapper tool– Coordination with DCB team (Rubin/Beck) needed
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Working with the QA team• Digital Pathology
– QA Engineer Reza Mehri– Requirements before we go in QA
• Design Document• Requirements Definition Document• Architectural Review Checklist (ARC)
– https://wiki.nci.nih.gov/display/sysdeploy/CTIIP+Digital+Pathology+ARC
• Provision Target Environment (PTE)– https://
wiki.nci.nih.gov/display/sysdeploy/CTIIP+Digital+Pathology+PTE– App scan for security vulnerabilities– 508 compliance scan– Use the same QA server for Dig Path and Pilot Challenges?
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Working with the technical writer• Carolyn Klinger
– Goal = make the CTIIP wiki public– User Documentation– Installation Guides
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Coordination Meetings• Once a month have all teams meet in a one-hour
meeting to– Report progress– Discuss interactions and data delivery– Feedback on tools
• Find a timeslot
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Resources• CTIIP wiki
– https://wiki.nci.nih.gov/x/XQJjCg