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An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images Jonathan.

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Presentation on theme: "An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images Jonathan."— Presentation transcript:

1 http://www.media.queensu.ca1 An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images Jonathan Boisvert, David Gobbi, Siddharth Vikal, Robert Rohling, Gabor Fichtinger and Purang Abolmaesumi Medical Image Analysis (MedIA) Laboratory http://www.media.queensu.ca Queen’s University Kingston, Ontario, Canada

2 http://www.media.queensu.ca2 Introduction Ultrasound is a very common interventional image modality Ultrasound is a very common interventional image modality Open-interface machines makes it even more attractive to IGT developers Open-interface machines makes it even more attractive to IGT developers Often used with motion tracking devices. Often used with motion tracking devices. Problem: Problem: Acquisition, synchronization and transfer to existing IGT systems is more difficult than it should be. Acquisition, synchronization and transfer to existing IGT systems is more difficult than it should be.

3 http://www.media.queensu.ca3 Integrated navigation software such as: Integrated navigation software such as: CustusX 1, IGSonic 2, SonoNav 3 or Stradx 4. CustusX 1, IGSonic 2, SonoNav 3 or Stradx 4. Software frameworks such as: Software frameworks such as: IGSTK 5 IGSTK 5 Slicer specific software development Slicer specific software development A module for Slicer 2 initially developed by Boctor et al. 6 A module for Slicer 2 initially developed by Boctor et al. 6 Prior work

4 http://www.media.queensu.ca4 Sophisticated registration, data- fusion and visualization capabilities Sophisticated registration, data- fusion and visualization capabilities Modular architecture Modular architecture Multi-platform Multi-platform Support for the new OpenIGTLink protocol Support for the new OpenIGTLink protocol Open-source software platform: Slicer

5 http://www.media.queensu.ca5 Ultrasound Image Acquisition Ultrasound Image Acquisition 3D Tracking 3D Tracking Synchronization Synchronization Ultrasound Volumes Reconstruction Ultrasound Volumes Reconstruction Open-Source Open-Source Standardized communication with independent IGT platforms. Standardized communication with independent IGT platforms. Objectives

6 http://www.media.queensu.ca6 Architecture : SynchroGrab Provide real-time ultrasound processing capabilities. Provide real-time ultrasound processing capabilities. Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer). Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

7 http://www.media.queensu.ca7 Architecture : SynchroGrab Provide real-time ultrasound processing capabilities. Provide real-time ultrasound processing capabilities. Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer). Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

8 http://www.media.queensu.ca8 Architecture : SynchroGrab Provide real-time ultrasound processing capabilities. Provide real-time ultrasound processing capabilities. Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer). Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

9 http://www.media.queensu.ca9 Architecture : SynchroGrab Provide real-time ultrasound processing capabilities. Provide real-time ultrasound processing capabilities. Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer). Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

10 http://www.media.queensu.ca10 Architecture : SynchroGrab Provide real-time ultrasound processing capabilities. Provide real-time ultrasound processing capabilities. Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer). Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

11 http://www.media.queensu.ca11 SonixRP SonixRP Open interface Open interface Access to pre-scan converted images, post-scan converted images, imaging parameters, RF raw-data, etc. Access to pre-scan converted images, post-scan converted images, imaging parameters, RF raw-data, etc. New vtk class “vtkSonixVideoSource” New vtk class “vtkSonixVideoSource” Easy integration Easy integration Highly reusable Highly reusable Ultrasound image acquisition

12 http://www.media.queensu.ca12 Inherit from vtkVideoSource Inherit from vtkVideoSource Support many data types: Support many data types: BPreScan, BPost 8 bit, BPost 32 bit, RF 16 bit, MPost 8 bit, Color+ B 32 bits BPreScan, BPost 8 bit, BPost 32 bit, RF 16 bit, MPost 8 bit, Color+ B 32 bits vtkSonixVideoSource *sonixGrabber = vtkSonixVideoSource::New(); sonixGrabber->SetSonixIP("127.0.0.1"); sonixGrabber->SetImagingMode(BMode); sonixGrabber-> SetAcquisitionDataType(udtBPost); sonixGrabber->Record(); sonixGrabber->Stop(); sonixGrabber->Rewind(); // Process the first image here sonixGrabber->Seek(1) // Process the second image here sonixGrabber->Delete(); vtkSonixVideoSource *sonixGrabber = vtkSonixVideoSource::New(); sonixGrabber->SetSonixIP("127.0.0.1"); sonixGrabber->SetImagingMode(BMode); sonixGrabber-> SetAcquisitionDataType(udtBPost); sonixGrabber->Record(); sonixGrabber->Stop(); sonixGrabber->Rewind(); // Process the first image here sonixGrabber->Seek(1) // Process the second image here sonixGrabber->Delete(); Using vtkSonixVideoSource

13 http://www.media.queensu.ca13 Object oriented Object oriented Extensible Extensible Multi-threaded Multi-threaded Circular buffers for transformations synchronization Circular buffers for transformations synchronization 3D Tracking

14 http://www.media.queensu.ca14 Tracking and ultrasound imaging Tracking and ultrasound imaging not performed at the same frequency. not performed at the same frequency. Need to interpolate the poses (using spherical linear interpolation) Need to interpolate the poses (using spherical linear interpolation) Synchronization

15 http://www.media.queensu.ca15 Data preprocessing Data preprocessing Hardware latency, pose computation, ultrasound image processing, and copy to user-space memory. Hardware latency, pose computation, ultrasound image processing, and copy to user-space memory. OS related OS related Context switching, memory swapping, etc. Context switching, memory swapping, etc. Compensate for the mean lag Compensate for the mean lag Synchronization

16 http://www.media.queensu.ca16 vtkTaggedImageFilter vtkTaggedImageFilter Compute the transformation associated with an image. Compute the transformation associated with an image. Two inputs: a vtkTrackerTool and a vtkImageAlgorithm object Two inputs: a vtkTrackerTool and a vtkImageAlgorithm object vtkTaggedImageFilter *tagger = vtkTaggedImageFilter::New(); tagger->SetInput(sonixGrabber->GetOutput()); tagger->SetTrackerTool(trackerTool); tagger->SetTemporalLag(xxx); tagger->Update(); currentTransforms = tagger->GetTransform(); currentImage = tagger->GetOutput(); vtkTaggedImageFilter *tagger = vtkTaggedImageFilter::New(); tagger->SetInput(sonixGrabber->GetOutput()); tagger->SetTrackerTool(trackerTool); tagger->SetTemporalLag(xxx); tagger->Update(); currentTransforms = tagger->GetTransform(); currentImage = tagger->GetOutput(); Synchronization

17 http://www.media.queensu.ca17 Synchronized images and transformation Synchronized images and transformation Combined to produce 3D volumes Combined to produce 3D volumes Pixel-based reconstruction Pixel-based reconstruction Pixel nearest neighbors (PNN) Pixel nearest neighbors (PNN) Pixel trilinear interpolation (PTL) Pixel trilinear interpolation (PTL) 3D Reconstruction

18 http://www.media.queensu.ca18 SynchroGrab --calibration-file 071508_162653.Calibration.results --save-images --use-tracker-transforms --nb-frames 150 --fps 5 Saving : usImage0.png Current rigid transform: 0.0933926 0.982412 0.152506 - 394.844 0.976081 -0.0744842 -0.208865 296.167 -0.196327 0.171225 -0.96587 -1923.87 0 0 0 1 Saving : usImage1.png Current rigid transform: 0.0934317 0.982387 0.152642 - 394.833 0.976065 -0.0744826 -0.208939 296.161 -0.196386 0.171371 -0.965833 -1923.89 0 0 0 1 Saving : usImage2.png Current rigid transform: 0.093352 0.982413 0.152529 - 394.84 0.976048 -0.0744086 -0.209039 296.141 -0.196509 0.171252 -0.965829 -1923.86 0 0 0 1 …. Saving : usImage0.png Current rigid transform: 0.0933926 0.982412 0.152506 - 394.844 0.976081 -0.0744842 -0.208865 296.167 -0.196327 0.171225 -0.96587 -1923.87 0 0 0 1 Saving : usImage1.png Current rigid transform: 0.0934317 0.982387 0.152642 - 394.833 0.976065 -0.0744826 -0.208939 296.161 -0.196386 0.171371 -0.965833 -1923.89 0 0 0 1 Saving : usImage2.png Current rigid transform: 0.093352 0.982413 0.152529 - 394.84 0.976048 -0.0744086 -0.209039 296.141 -0.196509 0.171252 -0.965829 -1923.86 0 0 0 1 …. Collecting images  Just start the application using the command line

19 http://www.media.queensu.ca19 SynchroGrab --calibration-file 071508_162653.Calibration.results --reconstruct-volume --nb-frames 150 --fps 5 --use-tracker-transforms Reconstructing volumes   Just start the application using the command line

20 http://www.media.queensu.ca20 SynchroGrab --calibration-file 071508_162653.Calibration.results --oigtl-transfert-images --nb-frames 150 --fps 5 Communication with Slicer Real-time acquisition using SynchroGrab. Visualization with Slicer 3.

21 http://www.media.queensu.ca21 Communication with Slicer

22 http://www.media.queensu.ca22 SynchroGrab SynchroGrab Acquisition and synchronization of tracking and ultrasound data Acquisition and synchronization of tracking and ultrasound data Can be used as a stand-alone command-line application. Can be used as a stand-alone command-line application. Can be used in conjunction to an OpenIGTLink compliant software. Can be used in conjunction to an OpenIGTLink compliant software. Development of temporal calibration protocols Development of temporal calibration protocols Future support for 3D probes Future support for 3D probes Conclusion & Future work

23 http://www.media.queensu.ca23 1.T. Lango, G. A. Tangen, R. Marvik, B. Ystgaard, Y. Yavuz, J. H. Kaspersen, O. V. Solberg, and T. A. N. Hernes. Navigation in laparoscopy–prototype research platform for improved image-guided surgery. Minim Invasive Ther Allied Technol, 17(1):17–33, 2008. 2.BrainLAB (AG, Heimstetten, Germany). IGSonic. http://www.brainlab.com http://www.brainlab.com 3.Medtronic(Louisville, CO, U.S.). SonoNav. http://www.medtronicnavigation.com http://www.medtronicnavigation.com 4.Graham Treece, Richard Prager and Andrew Gee. Stradx/Stradwin. http://mi.eng.cam.ac.uk/~rwp/stradwin/ http://mi.eng.cam.ac.uk/~rwp/stradwin/ 5.Andinet Enquobahrie, Patrick Cheng, Kevin Gary, Luis Ibanez, David Gobbi, Frank Lindseth, Ziv Yaniv, Stephen Aylward, Julien Jomier, and Kevin Cleary. The image-guided surgery toolkit IGSTK: an open source C++ software toolkit. J Digit Imaging, 20 Suppl 1:21–33, 2007. 6.E. M. Boctor, A. Viswanathan, S. Pieper, M. A. Choti, R. H. Taylor, R. Kikinis, and G. Fichtinger. CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API. Proceedings of the SPIE, volume 5367, pages 247–256, May 2004 References

24 http://www.media.queensu.ca24 Natural Sciences and Engineering Research Council (NSERC), Natural Sciences and Engineering Research Council (NSERC), Canadian Institutes of Health Research (CIHR), Canadian Institutes of Health Research (CIHR), National Alliance in Medical Image Computing (NIH5U54EB005149- 03), National Alliance in Medical Image Computing (NIH5U54EB005149- 03), Fonds québécois de recherche sur la nature et les technologies. Fonds québécois de recherche sur la nature et les technologies. Acknowledgments

25 http://www.media.queensu.ca25 Questions

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