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The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging.

Clarkson MJ, Zombori G, Thompson S, Totz J, Song Y, Espak M, Johnsen S, Hawkes D, Ourselin S - Int J Comput Assist Radiol Surg (2014)

Bottom Line: NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data.NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps.These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects.

View Article: PubMed Central - PubMed

Affiliation: Centre For Medical Image Computing, University College London, Engineering Front Building, Malet Place, London, UK, m.clarkson@ucl.ac.uk.

ABSTRACT

Purpose: To perform research in image-guided interventions, researchers need a wide variety of software components, and assembling these components into a flexible and reliable system can be a challenging task. In this paper, the NifTK software platform is presented. A key focus has been high-performance streaming of stereo laparoscopic video data, ultrasound data and tracking data simultaneously.

Methods: A new messaging library called NiftyLink is introduced that uses the OpenIGTLink protocol and provides the user with easy-to-use asynchronous two-way messaging, high reliability and comprehensive error reporting. A small suite of applications called NiftyGuide has been developed, containing lightweight applications for grabbing data, currently from position trackers and ultrasound scanners. These applications use NiftyLink to stream data into NiftyIGI, which is a workstation-based application, built on top of MITK, for visualisation and user interaction. Design decisions, performance characteristics and initial applications are described in detail. NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data.

Results: NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps. NiftyIGI was tested, receiving stereo high-definition laparoscopic video at 30 fps, tracking data from 4 rigid bodies at 20-30 fps and ultrasound data at 20 fps with rendering refresh rates between 2 and 20 Hz with no loss of user interaction.

Conclusion: These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects. Code and documentation for the NifTK platform are available from http://www.niftk.org . NiftyLink is provided open-source under a BSD license and available from http://github.com/NifTK/NiftyLink . The code for this paper is tagged IJCARS-2014.

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An example of a basic Tracked Pointer system using NifTK. a The NDI active pointer is placed within a plastic pelvis phantom (physical layout). bniftkNDICertus from the NiftyGuide suite of applications sends tracking data to c NiftyIGI which displays 2D outlines and 3D views via the standard MITK Display. The NifTK Tracked Pointer plugin moves the red wireframe pointer representation as tracking updates, visualised in the bottom right-hand quadrant of NiftyIGI
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Fig5: An example of a basic Tracked Pointer system using NifTK. a The NDI active pointer is placed within a plastic pelvis phantom (physical layout). bniftkNDICertus from the NiftyGuide suite of applications sends tracking data to c NiftyIGI which displays 2D outlines and 3D views via the standard MITK Display. The NifTK Tracked Pointer plugin moves the red wireframe pointer representation as tracking updates, visualised in the bottom right-hand quadrant of NiftyIGI

Mentions: A basic use of image guidance technology is to display the location of a tracked physical pointer, along with a registered pre-operative model. NiftyIGI was set up as follows: An NDI Optotrak Certus was used to track a single NDI 6-IRED active pointer, calibrated via the NDI 6-Degree Architect software. A custom made VTK surface representing the 6 IREDs, and pointer tip was used for visualisation. A plastic pelvis phantom and fiducial markers were attached to a solid acetal base. The phantom and attached fiducial markers were CT scanned resulting in an image that was cropped to voxels with millimetres voxel spacing. An iso-surface was extracted using the VTK 5.10 marching cubes implementation. CT points for 6 fiducials were saved as an mitk::PointSet file using the MITK PointSet Interaction Plugin. Corresponding points for the physical location were saved using the NiftyIGI Tracked Pointer Plugin. The mitk::PointSets were registered [1] and applied to the CT surface model. The NiftyIGI Tracked Pointer Plugin was used to update the location of the pointer model and visualise the pointer as it moved. Hence, a basic IGS system is realised, see Fig. 5. A further example is shown in Fig. 6, using an NDI Polaris Vicra tracker and a porcine ribcage phantom.Fig. 5


The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging.

Clarkson MJ, Zombori G, Thompson S, Totz J, Song Y, Espak M, Johnsen S, Hawkes D, Ourselin S - Int J Comput Assist Radiol Surg (2014)

An example of a basic Tracked Pointer system using NifTK. a The NDI active pointer is placed within a plastic pelvis phantom (physical layout). bniftkNDICertus from the NiftyGuide suite of applications sends tracking data to c NiftyIGI which displays 2D outlines and 3D views via the standard MITK Display. The NifTK Tracked Pointer plugin moves the red wireframe pointer representation as tracking updates, visualised in the bottom right-hand quadrant of NiftyIGI
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4338364&req=5

Fig5: An example of a basic Tracked Pointer system using NifTK. a The NDI active pointer is placed within a plastic pelvis phantom (physical layout). bniftkNDICertus from the NiftyGuide suite of applications sends tracking data to c NiftyIGI which displays 2D outlines and 3D views via the standard MITK Display. The NifTK Tracked Pointer plugin moves the red wireframe pointer representation as tracking updates, visualised in the bottom right-hand quadrant of NiftyIGI
Mentions: A basic use of image guidance technology is to display the location of a tracked physical pointer, along with a registered pre-operative model. NiftyIGI was set up as follows: An NDI Optotrak Certus was used to track a single NDI 6-IRED active pointer, calibrated via the NDI 6-Degree Architect software. A custom made VTK surface representing the 6 IREDs, and pointer tip was used for visualisation. A plastic pelvis phantom and fiducial markers were attached to a solid acetal base. The phantom and attached fiducial markers were CT scanned resulting in an image that was cropped to voxels with millimetres voxel spacing. An iso-surface was extracted using the VTK 5.10 marching cubes implementation. CT points for 6 fiducials were saved as an mitk::PointSet file using the MITK PointSet Interaction Plugin. Corresponding points for the physical location were saved using the NiftyIGI Tracked Pointer Plugin. The mitk::PointSets were registered [1] and applied to the CT surface model. The NiftyIGI Tracked Pointer Plugin was used to update the location of the pointer model and visualise the pointer as it moved. Hence, a basic IGS system is realised, see Fig. 5. A further example is shown in Fig. 6, using an NDI Polaris Vicra tracker and a porcine ribcage phantom.Fig. 5

Bottom Line: NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data.NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps.These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects.

View Article: PubMed Central - PubMed

Affiliation: Centre For Medical Image Computing, University College London, Engineering Front Building, Malet Place, London, UK, m.clarkson@ucl.ac.uk.

ABSTRACT

Purpose: To perform research in image-guided interventions, researchers need a wide variety of software components, and assembling these components into a flexible and reliable system can be a challenging task. In this paper, the NifTK software platform is presented. A key focus has been high-performance streaming of stereo laparoscopic video data, ultrasound data and tracking data simultaneously.

Methods: A new messaging library called NiftyLink is introduced that uses the OpenIGTLink protocol and provides the user with easy-to-use asynchronous two-way messaging, high reliability and comprehensive error reporting. A small suite of applications called NiftyGuide has been developed, containing lightweight applications for grabbing data, currently from position trackers and ultrasound scanners. These applications use NiftyLink to stream data into NiftyIGI, which is a workstation-based application, built on top of MITK, for visualisation and user interaction. Design decisions, performance characteristics and initial applications are described in detail. NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data.

Results: NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps. NiftyIGI was tested, receiving stereo high-definition laparoscopic video at 30 fps, tracking data from 4 rigid bodies at 20-30 fps and ultrasound data at 20 fps with rendering refresh rates between 2 and 20 Hz with no loss of user interaction.

Conclusion: These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects. Code and documentation for the NifTK platform are available from http://www.niftk.org . NiftyLink is provided open-source under a BSD license and available from http://github.com/NifTK/NiftyLink . The code for this paper is tagged IJCARS-2014.

Show MeSH
Related in: MedlinePlus