1. PLUS overview (PerkLab ultrasound library and applications)
Tamas Ungi, Andras Lasso
Laboratory for Percutaneous Surgery,
Queen’s University
August 4, 2011

2. Introduction PLUS – PerkLab ultrasound
History: implementation is based on two SynchroGrab versions
QueensOpenIGTLibs in Queen’s repository Last commit: October 7, 2008 (Revision: 30) svn+ssh://image.cs.queensu.ca/image/svn/QueensOpenIGTLibs/trunk/VTKLibs/Ultrasound
4D Ultrasound module in NAMIC sandbox repository Last commit: August 16, 2009 (Revision: 4993) trunk/4DUltrasound-WithGating/
Team:
Csaba Pinter (project management, PLUS core, free-hand calibration development)
Tamas Heffter (PLUS core, iCAL development)
Thomas K. Chen (calibration algorithm development)
Alexis Boucharin (fiducial segmentation)
Tamas Ungi (Ascension, OpenIGTLink communication development)
Andras Lasso (review, coordination with other projects)
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

3. What’s new
Support for new hardware: brachy stepper, EM tracker, new Ultrasonix SDK versions, CIVCO stepper
New applications: fCal, volume reconstruction, diagnostics, OpenIGTLinkBroadcaster
Enhancements: temporal calibration – a.k.a. synchronization, …
Bugfixes
Automatic tests
But: Some old hardware and applications are not tested or not integrated. Tested on Windows only.
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

4. (PLUS applications or custom apps)
Software platform
Language: C++
Build system: CMake
Automatic testing and dashboard: CTest, CDash
External libraries:
Required: ITK, VTK
Optional: OpenIGTLink (for communication with 3D Slicer and IGSTK), device drivers
Supported operating systems:
Windows XP (32-bit), Windows 7 (64-bit): regularly tested
Linux: not tested, everything should work except Windows drivers and RS-232 serial communication
Applications
(PLUS applications or custom apps)
PLUS library
ITK
VTK
Open
IGTLink
SDKs and drivers
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

5. Supported hardware /1 Image acquisition
Ultrasonix US capture via Ulterius SDK (Windows only): supports SDK versions 1.2, 2.0, 5.6 (latest) – tested
ImagingControls USB framegrabber (Windows only) – tested
Simulator: replay saved image sequences from metafile (for testing without hardware) – tested
Not integrated (source code is in the repository, but not used):
Ultrasonix US capture via Porta SDK (Windows only)
Video for Windows (Windows only): generic framegrabber
Linux video (Linux only)
Matrox imaging library
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

6. Supported hardware /2 Position tracking
NDI Certus tracker (Windows only) – tested
Brachytherapy steppers/stabilizers (Windows only):
Burdette Medical Systems target guide – tested
CMS Accuseed DS-300 – tested
CIVCO – under testing
Ascension 3DG electromagnetic tracker (Windows only) – tested
Polaris tracker – not tested
Flock of birds tracker – not tested
Not integrated: Micron tracker
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

7. Applications fCAL iCAL Tracked US capturing
fCAL: Free-hand calibration (compute image plane to marker transform), using double-N calibration phantom, with GUI – under testing
Tracked ultrasound capturing: synchronized image and position acquisition, with GUI – tested
Volume reconstruction (from tracked ultrasound capture files), console app – tested
iCAL: Calibration and diagnostics of brachytherapy stepper, with GUI – tested
Image acquisition and tracking diagnostic – tested
OpenIGTLinkBroadcaster: for live data transfer to 3D Slicer, console app – work in progress
Synchrograb 4D (4D Ultrasound) - not fully integrated
Tracked US capturing
iCAL
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

8. Development process /1
Source code repository, releases, documentation, issue tracker:
Recently moved (from internal SVN / Mantis / MediaWiki)
Collaborators (people at UBC, Robarts, …) can get access
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

9. Development process /2 Automatic nightly build and test: CTest/CDash
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

10. Coordinate systems

11. Ultrasound image orientation
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

12. Ultrasound image orientation
Plus stores all images in MF
By default, Touch displays UF
See Assembla Wiki for details
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

13. Sequence metafile (.mha)
Extension to the meta I/O standard
Slices readable by many existing applications
Extra information for tracking/reconstruction
Frame number
Unfiltered and filtered timestamp
Probe and Reference tracking transforms
Used by all applications of Plus
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

14. Configuration XML file
Defines input parameters for all components of Plus, grouped as “Device set” for easy selection in GUI applications.
Main sections
USDataCollection
Tracker (e.g. Certus, Ascension) + Tools (probe, reference, stylus)
Image source (e.g. SonixVideo, Frame grabber)
Synchronization
USCalibration
Calibration phantom definition
Volume reconstruction
Output spacing
Slice clipping
Probe calibration …
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011

15. Planned developments
Finalize Free-hand US calibration application (Sept)
OpenIGTLink interface for most functions (Aug)
Tracked RF image acquisition (Aug)
Brachytherapy stepper sagittal transducer calibration (Sept)
Support Terason ultrasound image acquisition (Sept)
Support/bugfixes (continuous)
Laboratory for Percutaneous Surgery (The Perk Lab) – Copyright © Queen’s University, 2011