View source for ITK Release 4/Data Collection

= Overview =

== Testing Data ==

* '''Testing Data'''
** (Slides Set 1:[[Media:ITKv4-Testing-Data-Nov-2010.ppt|PPT]],[[Media:ITKv4-Testing-Data-Nov-2010.odp|ODP]],[[Media:ITKv4-Testing-Data-Nov-2010.pdf|PDF]])
** (Slides Set 2: )

== MIDAS Structure ==

* Communities (recursive)
** Collection
*** Items
**** Resources
***** Bitstreams
**** Bitstreams

= Expected Data =

* Maintain data using original acquisition format (Bill's suggestion)?
 

{| border="1"
|- bgcolor="#abcdef"
! Group !! Expected Amount of Data !! File Formats !! Features
|-
| Raghu Machiraju || 10 Gb ||  TIFF, LSM, MetaImage ||
|-
| Ziv Yaniv ||  10 Gb || DICOM, MetaImage (e.g. segmentation label maps), bmp/jpg/avi (2D frame grabbed US and x-ray fluoroscopy images)||
|-
| Brad Lowekamp || 10 Gb || TIFF ? ||
|-
| Hans Johnson ||  4 Gb || GE45, Phillips, Siemens, Dicom, Analyze, Nifti, etc Migration from :  http://www.nitrc.org/projects/brainstestdata/  || Dictionary of expected meta-information (spacing, size, data-type, etc)
|-
| Sean Megason ||  10 Tb || TIFF, LSM [[File:Megason-A2D2proposal-SCORExx.pdf]]  ||
|-
| Marcel Pratwsaw ||  10 Gb || ??  ||
|-
| Marc Niethammer || 10 Gb || TIFF || Point spread functions (and image, or 12 (key,value) pair parameters
|-
|}

= MetaData =

==Medical==
* physical quantities associated with image acquisition apparatus (e.g. camera calibration for endoscopy and x-ray, US calibration).
* reason for scan (e.g. suspected liver tumor), should be in header but often is not.
* contrast phase (e.g. pre contrast, arterial phase).
* respiratory phase (e.g. end inspiration, end expiration).
* apparatus used to acquire images when not specified in DICOM (e.g. xyz frame grabber).
* rigid transformation data acquired with a tracker (pose of US/endoscope relative to tracking system, required for positioning multiple 2D images in 3D space)
* calibration data of other equipment used in experiment (calibration of tracked pointer)

= Structure =

== Suggested Organization ==

<graphviz>
digraph G {
ITK_DATA 
ITK_DATA -> Microscopy_Community
Microscopy_Community -> Raghu_Machiraju
Microscopy_Community -> Sean_Megason
Microscopy_Community -> Brad_Lowekamp
Microscopy_Community -> Marc_Niethammer
ITK_DATA -> Radiology_Community
Radiology_Community -> Hans_Johnson
Radiology_Community -> Ziv_Yaniv
ITK_DATA -> Remote_Sensing_Community
Remote_Sensing_Community -> JPEG2000_Tests
}
</graphviz>

== Strawman of data organization ==

Filename scheme

   AllSubjects/Subject/ScanDateTime/Modality/Subject_ScanDate_Modality.nii.gz

ScanDate is in the form  YYYYMMDDTT  where we only keep 2 digits of time.

so you would have  e.g.

  ITKTestCTdata1/0001/2010122200/T1/0001_2010122200_T1.nii.gz

= MIDAS Installations =

* http://www.insight-journal.org/midas/
** http://www.insight-journal.org/midas/community/view/22 (Miscellaneous collection of ITK related data)
* http://www.insight-journal.org/rire/ (RIRE: Retrospective Registration Evaluation)
** http://www.insight-journal.org/midas/community/view/16
* http://midas.kitware.com/
** http://midas.kitware.com/community/view/7 (ITK Testing Data)
** http://midas.kitware.com/community/view/22 (Tutorials: Virtual Appliances > 2Gb)

= Integration with CTest =

* http://review.source.kitware.com/#change,301

== XNAT ==

* http://central.xnat.org/app/template/Index.vm

= Data Licenses =

* http://www.kitware.com/blog/home/post/72
** Public Domain Dedication and License (PDDL) — “Public Domain for data/databases” http://www.opendatacommons.org/licenses/pddl/
** Attribution License (ODC-By) — “Attribution for data/databases” http://www.opendatacommons.org/licenses/by/
** Open Database License (ODC-ODbL) — “Attribution Share-Alike for data/databases” http://www.opendatacommons.org/licenses/odbl/

* Designed by the Scientific Commons at http://www.opendatacommons.org/