Difference between revisions of "2011 Winter Project Week:MIDAS for data hosting"

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==Key Investigators==
 
==Key Investigators==
 
* Kitware: Zach Mullen
 
* Kitware: Zach Mullen
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* Iowa: Hans Johnson
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* UIowa: Hans Johnson
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.
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Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.
  
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Two driving applications:
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Motivation:
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* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
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* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
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* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)
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* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
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* Don't download any duplicated test data more than once
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History
 
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* June 2001, UNC released the patent on vessel extraction method from [Aylward, Bullitt 1996...]
 
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* TubeTK released under Apache 2.0 license: includes rights to patents
 
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
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* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
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** Workflow: brain envelop segmentation, seeding, extraction
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* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
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* Integration with VMTK
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* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
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* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
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* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
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* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
  
 
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
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This work will be delivered to the NA-MIC Kit as follows:
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* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
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* Test data in the Slicer4 repository will be replaced by a reference
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* All software written during the project week will be contributed to TubeTK, and algorithms will be incorporated into 3D Slicer as CLI applications.
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* That site will also host the Slicer Easy Upload page.
  
 
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Latest revision as of 15:08, 10 January 2011

Home < 2011 Winter Project Week:MIDAS for data hosting

Key Investigators

  • Kitware: Zach Mullen
  • UIowa: Hans Johnson

Objective

Make use of the MIDAS data archiving system to host data related to tests such as baseline and comparison images.

Motivation:

  • Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
  • Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
  • Don't download any duplicated test data more than once

Approach, Plan

  • MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
  • The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
  • Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
  • MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

Progress

  • MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
  • Easy Upload page has a working prototype and requires further improvements and customization for Slicer
  • MIDASDesktop: svn repo is here https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp

Delivery Mechanism

  • Test data will be hosted publicly (with any necessary access control) on midas.kitware.com
  • Test data in the Slicer4 repository will be replaced by a reference
  • That site will also host the Slicer Easy Upload page.
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