NAMIC Wiki - User contributions [en]

AHM2009:JHU

2008-11-27T19:27:30Z

Dgobbi: /* Outreach */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:TRProstateModuleCalibrationInterface.png|thumb|280px|Workflow page for "Calibration" step.]]
|}

== Overview ==

We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy. The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==

There are several Slicer features that are crucial to image-guided therapy that are utilized in this module:

'''Oriented volumes and image slice reformatting'''

Each volume acquired during the biopsy procedure has its own orientation, since images are acquired according to the orientation of the instrument, which is at an oblique angle to the MR scanner's coordinate axes. What we have added is that, for each workflow step, a particular volume is specified as the "primary" and, when overlays are performed e.g. for verification, Slicer displays the primary image in its original orientation and reslices the others. The displayed slice orientation automatically changes to match the primary whenever the workflow step changes.

'''Multiple fiducial lists'''

This module maintains two Slicer fiducial lists: for registration, and for targeting. Like the image orientation, we have added automatic switching between display of fiducials according to the workflow step.

'''Communication with hardware devices'''

The module uses optical encoders that are attached to the joints of the biopsy device to verify that the position of the device matches that of the plan.

==Software & documentation==

* The TRProstateBiopsy module is in the "Queens" directory of the NAMICSandBox
* Tutorial is forthcoming

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==

* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

AHM2009:JHU

2008-11-27T19:26:34Z

Dgobbi: /* Software & documentation */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:TRProstateModuleCalibrationInterface.png|thumb|280px|Workflow page for "Calibration" step.]]
|}

== Overview ==

We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy. The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==

There are several Slicer features that are crucial to image-guided therapy that are utilized in this module:

'''Oriented volumes and image slice reformatting'''

Each volume acquired during the biopsy procedure has its own orientation, since images are acquired according to the orientation of the instrument, which is at an oblique angle to the MR scanner's coordinate axes. What we have added is that, for each workflow step, a particular volume is specified as the "primary" and, when overlays are performed e.g. for verification, Slicer displays the primary image in its original orientation and reslices the others. The displayed slice orientation automatically changes to match the primary whenever the workflow step changes.

'''Multiple fiducial lists'''

This module maintains two Slicer fiducial lists: for registration, and for targeting. Like the image orientation, we have added automatic switching between display of fiducials according to the workflow step.

'''Communication with hardware devices'''

The module uses optical encoders that are attached to the joints of the biopsy device to verify that the position of the device matches that of the plan.

==Software & documentation==

* The TRProstateBiopsy module is in the "Queens" directory of the NAMICSandBox
* Tutorial is forthcoming

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==
* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

AHM2009:JHU

2008-11-27T19:25:07Z

Dgobbi: /* Detailed Information about the Pipeline */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:TRProstateModuleCalibrationInterface.png|thumb|280px|Workflow page for "Calibration" step.]]
|}

== Overview ==

We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy. The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==

There are several Slicer features that are crucial to image-guided therapy that are utilized in this module:

'''Oriented volumes and image slice reformatting'''

Each volume acquired during the biopsy procedure has its own orientation, since images are acquired according to the orientation of the instrument, which is at an oblique angle to the MR scanner's coordinate axes. What we have added is that, for each workflow step, a particular volume is specified as the "primary" and, when overlays are performed e.g. for verification, Slicer displays the primary image in its original orientation and reslices the others. The displayed slice orientation automatically changes to match the primary whenever the workflow step changes.

'''Multiple fiducial lists'''

This module maintains two Slicer fiducial lists: for registration, and for targeting. Like the image orientation, we have added automatic switching between display of fiducials according to the workflow step.

'''Communication with hardware devices'''

The module uses optical encoders that are attached to the joints of the biopsy device to verify that the position of the device matches that of the plan.

==Software & documentation==
* url for downloading all the software
* url for the end-user tutorial

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==
* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

AHM2009:JHU

2008-11-27T19:24:28Z

Dgobbi: /* Detailed Information about the Pipeline */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:TRProstateModuleCalibrationInterface.png|thumb|280px|Workflow page for "Calibration" step.]]
|}

== Overview ==

We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy. The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==

There are several Slicer features that are crucial to image-guided therapy that are utilized in this module:

===Oriented volumes and image slice reformatting===

Each volume acquired during the biopsy procedure has its own orientation, since images are acquired according to the orientation of the instrument, which is at an oblique angle to the MR scanner's coordinate axes. What we have added is that, for each workflow step, a particular volume is specified as the "primary" and, when overlays are performed e.g. for verification, Slicer displays the primary image in its original orientation and reslices the others. The displayed slice orientation automatically changes to match the primary whenever the workflow step changes.

===Multiple fiducial lists===

This module maintains two Slicer fiducial lists: for registration, and for targeting. Like the image orientation, we have added automatic switching between display of fiducials according to the workflow step.

===Communication with hardware devices===

The module uses optical encoders that are attached to the joints of the biopsy device to verify that the position of the device matches that of the plan.

==Software & documentation==
* url for downloading all the software
* url for the end-user tutorial

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==
* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

File:TRProstateModuleCalibrationInterface.png

2008-11-27T19:08:05Z

Dgobbi:

AHM2009:JHU

2008-11-27T19:07:38Z

Dgobbi: /* JHU Roadmap Project */

AHM2009:JHU

2008-11-27T18:47:44Z

Dgobbi: /* Overview */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== Overview ==

We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy. The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==
* Illustrate the components and workflow of the pipeline using your own data
* Demonstrate parameters/steps that need to be adjusted using someone else's data

==Software & documentation==
* url for downloading all the software
* url for the end-user tutorial

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==
* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

AHM2009:JHU

2008-11-27T18:47:10Z

Dgobbi: /* Overview */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==JHU Roadmap Project==

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== Overview ==

* We have created a module that provides a workflow interface for MR-guided transrectal prostate biopsy.
* The MR images are captured with the help of an endorectal coil which is mounted on the same shaft as the biopsy needle.
* The steps in the workflow are as follows:
** Calibration, to register the image to the biopsy device via MR fiducials.
** Targeting, to mark biopsy targets (manually) and compute needle trajectory and depth (automatically).
** Verification, to use post-biopsy images to verify biopsy locations against the planned targets.
* This module provides a demonstration of how Slicer modules can be created for specific interventional devices.

==Detailed Information about the Pipeline==
* Illustrate the components and workflow of the pipeline using your own data
* Demonstrate parameters/steps that need to be adjusted using someone else's data

==Software & documentation==
* url for downloading all the software
* url for the end-user tutorial

==Team==
* DBP: Affiliation & logo
* Core 1: Affiliation & logo
* Core 2: Affiliation & logo
* Contact: name, email

==Outreach==
* Publication Links to the PubDB.
* Planned outreach activities (including presentations, tutorials/workshops) at conferences

File:SynchroGrab MICCAI2008 Workshop.ppt

2008-09-13T16:09:18Z

Dgobbi: uploaded a new version of "Image:SynchroGrab MICCAI2008 Workshop.ppt"

Ultrasound acquisition with VTK, presentation by Jonathan Boisvert at MICCAI 2008 workshop.

File:SynchroGrab MICCAI2008 Workshop.ppt

2008-09-13T15:27:23Z

Dgobbi: Ultrasound acquisition with VTK, presentation by Jonathan Boisvert at MICCAI 2008 workshop.

Ultrasound acquisition with VTK, presentation by Jonathan Boisvert at MICCAI 2008 workshop.

Miccai 2008 Prostate Workshop

2008-09-12T20:57:17Z

Dgobbi:

=Workshop title=
Prostate image analysis and computer-assisted intervention

----

=Place, Time=

{|align="right"
|[[Image:mrusprostate.gif|left|250px|MR-US registration]]
[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}

*at MICCAI 2008
*Room 906, Kimmel Cengter, 60 Washington Square South
New York, NY 10012, http://www.nyu.edu/kimmel.center/
*9am-1pm, September 10, 2008

=Registration=

Fee: $100-150 (see registration site for detail)

Please visit the registration site for the main MICCAI conference.
https://www.registrationassistant.com/p/rg.asp?Event=234DD6A3C6421F5F40C1B

Those who are not attending the main conference can also register for the workshop only at the registration site.

=Keywords=
Prostate, Image guided therapy, medical Image analysis, Focused ultrasound, novel image acquisition, robotics, device,

=Sponsor=
National Center for Image Guided Therapy, Brigham and Women’s Hospital and Harvard Medical School

=General Organizers=

Clare Tempany, MD

Professor of Radiology

Vice Chairman of Radiology Research

Brigham & Women's Hospital

Nobuhiko Hata, PhD

Technical Director, Image guided Therapy Program

Assistant Professor of Radiology

Brigham and Women’s Hospital and Harvard Medical School

=Workshop secretary=
Nobuhiko Hata, hata@bwh.harvard.edu
617-732-5809
Department of Radiology, Brigham and Women’s Hostapil
75 Francis St, Boston, MA
www.nicgt.org

=Presentation Format=
Oral presentation with computer screen projection, 12 minutes for talk, 3 minutes for discussion

=Objectives=
The objective of this workshop is discuss state-of-art in medical image processing and computer assisted intervention of prostate, In this half-day workshop, we will share our recent advances and identify translational technologies useful in clinical application of prostate diagnosis and threpy. We will also identify possible synergies among the participants and potential future collaboration.

=Final Program =

==9:00-9:15am: Introduction==
*Welcome and Clinician's perspective on prostate imaging and intervention, Clare Tempnay, Brigham and Women's Hospital

==9:15 - 11:00am: Intervention==
*Ultrasound Image-guided Robotic Brachytherapy Systems for Prostate Seed Implant [[Media:miccaiws-podder-abst.pdf|(abstract)]]
:T.K. Podder, I. Buzurovic, K. Yan, Y. Hu, R. Valicenti, A. Dicker, Y. Yu, Department of Radiation Oncology, Kimmel Cancer Center,Jefferson Medical College, Thomas Jefferson University
*Haptic Device for MR-guided Transrectal Prostate Biopsy [[Media:miccaiws-tse.pdf|(abstract)]]
:Z. T. H. Tse 1, H. Elhawary1, M. Rea 1,2, A. Zivanovic1 ,C. Besant1, D. McRobbie2, I. Young3, N. de Souza4, B.L. Davies1 and M. Lamperth1, 1 Department of Mechanical Engineering, Imperial College London, UK, 2Faculty of Medicine, Clinical Sciences Centre, Charing Cross Hospital, London, UK, 3 Department of Electrical and Electronic Engineering, Imperial College London, UK, 4Cancer Research UK Clinical Magnetic Resonance Research Group, Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
*Intraoperative Prostate Tracking with Slice-to-Volume Registration in MRI[[Media:miccaiws-gill.pdf|(abstract)]]
:Sean Gill, Purang Abolmaesumi, Siddharth Vikal, Parvin Mousavi and Gabor Fichtingera,b,* (a) School of Computing, Queen’s University, (b) Department of Electrical and Computer Engineering, Queen’s University, Kingston, Ontario, Canada
*Software / Hardware Integration for MRI-guided Robotic Prostate Intervention using Open IGT Link [[Media:miccaiws-tokuda.pdf|(abstract)]]
:Junichi Tokuda, Gregory S. Fischer, Csaba Csoma, David G. Gobbi, Jack Blevins, Gabor Fichtinger, Clif Burdette4, Clare M. Tempany1, and Nobuhiko Hata1, 1 Department of Radiology, Brigham and Women’s Hospital, Boston, MA, USA , 2 EngineeringResearch Center for Computer Integrated Surgery, Johns Hopkins University, Baltimore, MD, USA , 3 School of Computing, Queen’s University, Kingston, Ontario, Canada , 4 Acoustic MedSystems, Inc., Champaign, IL, USA
*Optimized Biopsy Procedures for Estimating Gleason Score and Prostate Cancer Volume [[Media:miccaiws-ou.pdf|(abstract)]]
:Yangming Ou1, Dinggang Shen2, Yong Fan1, Jianchao Zeng3, Leon Sun4, Christos Davatzikos1 , 1 Section of Biomedical Image Analysis (SBIA), Univ. of Pennsylvania, 2 Dept. of Radiology, Univ. of North Carolina – Chapel Hill, 3 Dept. of Electrical and Computer Engineering, Howard Univ., 4 Division of Urologic Surgery, Duke Univ. Medical Center
*Prostate contouring in MRI guided biopsy [[Media:miccaiws-vikal.pdf|(abstract)]]
:Siddharth Vikala, Steven Hakerb, Clare Tempanyb, Gabor Fichtingera,(a) Queen’s University, Kingston, ON, Canada , (b) Brigham & Women’s Hospital, Boston, MA, USA
*Ultrasonic detection and imaging of two common types of prostate-brachytherapy seeds using singular spectrum analysis [[Media:miccaiws-mamou.pdf|(abstract)]]
:Jonathan Mamou and Ernest J. Feleppa, Lizzi Center for Biomedical Engineering Riverside Research Institute, New York, NY

==11:00am-11:15am: Coffee Break==

==11:15am-1:00pm Imaging==
*Imaging of the prostate with vibro-elastography: preliminary patient results [[Media:miccaiws-wen.pdf|(abstract)]]
:Xu Wen, S. E. Salcudean, J. Morris, and I. Spadinger1, Department of Electrical and Computer Engineering, University of British Columbia, Canada, 2 Radiation Oncology, British Columbia Cancer Agency, Canada,3 Medical Physics, British Columbia Cancer Agency, Canada
*Multi-protocol Prostate MR Image Analysis: Image Segmentation, Registration, and Computer-aided Diagnosis [[Media:miccaiws-madabhushi.pdf|(abstract)]]
:Anant Madabhushi, Jonathan Chappelow, Satish Viswanath, Pallavi Tiwari, Rob Toth, Mark by Rosen, Michael Feldman, John E , Tomaszewski2, Elizabeth Genega3, Neil Rofsky3, Robert Lenkinski3, and Nicolas Bloch3 , 1 Laboratory for Computational Imaging and Bioinformatics (LCIB), Department of Biomedical Engineering, Rutgers University, 2 Hospital at the University of Pennsylvania, 3Beth Israel Deaconess Medical Center.
*Fast automatic correction of non-rigid motion artefacts in MRI of the abdomen [[Media:miccaiws-dowling.pdf|(abstract)]]
:Jason Dowling,1, Pierrick Bourgeat1, David Raffelt1, Jurgen Fripp1, Peter Greer2,3, Jacqueline Patterson2, James Denham2,3, Peter Stanwell4, Sébastien Ourselin1,5 , Olivier Salvado1, 1 Australian e-Health Research Centre, CSIRO ICT Centre, Australia , 2 Calvary Mater Newcastle Hospital, Australia, University of Newcastle, Australia 4 Brigham & Women's Hospital, Harvard Medical School, Boston, USA , 5 Centre for Medical Image Computing, University College London, UK
*Automated detection of prostate cancer using wavelet transform features of ultrasound RF time series [[Media:miccaiws-aboofazeli.pdf|(abstract)]]
:Mohammad Aboofazeli, Parvin Mousavi, Mehdi Moradi, Purang Abolmaesumi School of Computing, Queen’s University, Kingston, Ontario, Canada K7L 3N6
*Ultrasonic tissue-type imaging of prostate cancer [[Media:miccaiws-feleppassa.pdf|(abstract)]]
:Ernest J. Feleppa1, Christopher R. Porter2, Shreedevi Dasgupta1, Deborah Sparks2 1 Lizzi Center for Biomedical Engineering Riverside Research Institute , Department of Urology Virginia Mason Medical Center, Seattle, WA
*3D Prostate Segmentation in Ultrasound Images using Image Deformation and Shape Fitting [[Media:miccaiws-mahdavi.pdf|(abstract)]]
:Seyedeh Sara Mahdavi, Septimiu E. Salcudean, James Morris, Ingrid Spadinger, Department of Electrical and Computer Engineering, University of British Columbia,Vancouver Cancer Centre, British Columbia Cancer Agency, Vancouver
*Summary of Presentation and Discussions- Nobuhiko Hata, PhD, Brigham and Women's Hospital

=Confirmed attendees (as of 8/21/08)=
*Nobuhiko Hata, Brigham and Women's Hospital
*Clare Tempnay, Brigham and Women's Hospital
*Junichi Tokuda, Brigham and Women's Hospital
*Gabor Fichtinger, Queen's University
*Yangming Ou, University of Pennsylvania
*Tarun K. Podder, PhD, Jefferson Medical College, Thomas Jefferson University
*Mohammad Aboofazeli
*Tim Carter
*Shreedevi Dasgupta
*Jason Dowling
*Ernest Feleppa
*Gregory Fischer
*Ioana Fleming
*Neil Glossop
*Helen Hong
*Anant Madabhushi, Director, Laboratory for Computational Imaging and Bioinformatics, Dept. of Biomedical Engineering,Rutgers The State University of New Jersey
*Mehdi Moradi
*Yangming Ou
*Tim Salcudean
*Tsz Ho Tse
*Marc Verstraeten
*Xu Wen

=Call For Abstracts (closed)=

*Abstracts will be peer-reviewed by a scientific program committee.
*The abstracts should comprise at least one page up to a maximum of two pages. The abstracts will be published as part of the conference proceedings.
*Authors should submit a PDF file that will print on a PostScript printer. Electronic submission is required.
*The abstracts should be submitted to the conference secretary, Nobuhiko Hata, by email (hata@bwh.harvard.edu).
*Important Dates
* (Extended) abstracts due: July 20, 2008

=Proceedings and meeting notes=
The attendants will receive the abstracts of talks at the workshop. The attendants will also receive notes from the discussion after the workshop.

[[invitation]]

OpenIGTLink/Workshop/miccai2008

2008-09-12T20:48:07Z

Dgobbi: Fix date

[[OpenIGTLink | << OpenIGTLink]]

==About the workshop==
*Title: MICCAI 2008 Workshop on Systems & Architecture for Computer Assisted Intervention
*Date: Sep 6, 2008
*Place: New York University, New York, NY
*Official Web page: [http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 http://smarts.lcsr.jhu.edu/CAI-Workshop-2008]

==Software and hardware integration strategy for image guided therapy using Open IGT Link==
by Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

* Power Point Presentation file:
**Please click [[media:OpenIGTLink_MICCAI2008_Workshop.ppt|here]].

Events

2008-09-12T20:46:59Z

Dgobbi: /* 2008 */

__NOTOC__
== Introduction ==

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| NA-MIC organizes a variety of events. The engineering core holds a weekly telephone conference. Workshops address specific research focus areas. Training events aim at training NA-MIC participants and outsiders in NA-MIC technologies. Project weeks are intended for making progress in a variety of projects. The majority of NA-MIC events are hands-on and open to collaborators and interested scientists.
| style="background: #ebeced" colspan="2" align="center"| Example of a Training Event
|-
| style="background: #ebeced"| [[Image:Munich2008-Danielle.jpg|250px]]
| style="background: #ebeced"| The Munich 2008 training workshop in full swing. For more information about the workshop, click [[2008_June_Workshop_Germany|'''here''']].
|}
 

== [[TCON:Main|'''Telephone Conferences''']] ==

== Upcoming Events ==

== 2008 ==
* October 15-16, 2008: '''[[Robarts_Training_Session | NA-MIC kit training event at The University of Western Ontario]]''', London, Ontario, Canada
* December 1, 2008:[[Events:RSNA2008| Tutorial at RSNA]], [http://rsna2008.rsna.org/ RSNA conference website]
* December 8-12, 2008:[[2008_IGT_Project_Week|IGT Hands-on Project Week]], Boston
* Fall Semester 2008 Ibanez and Schroeder teach [http://public.kitware.com/OpenSourceSoftwarePractice/index.php/Main_Page Open Source Software Course] at Rensselaer Polytechnic Institute

== 2009 ==
* '''[[AHM_2009|January 5-9, 2009, AHM,]] [[2009_EAB|EAB,]] [[2009_Winter_Project_Week|Winter Project Week]]'''
* January 8, 2009:[[Events:TutorialContestJan2009| Tutorial Contest:]] announcement of the winners.

== Standing Events ==

* [[TCON:Main|A list of all upcoming and past teleconferences is available here]].
* [[Engineering:Programming_Events|Hands on Project Events]]
* [[Slicer:Developer_Meetings|Slicer developer meetings are here]].

== Past Events ==

=== 2008 ===
* September 10, 2008: '''[[Miccai_2008_Tutorial| Interfacing third-party software with the NA-MIC Kit]]''': Tutorial at MICCAI 2008, New York City
* September 10, 2008: '''[[Miccai_2008_Prostate_Workshop| Prostate image analysis and computer-assisted intervention]]''': Workshop at MICCAI 2008, New York City
* September 6, 2008: '''[[Miccai_2008_Systems_and_Architecture_Workshop| Systems & architecture for computer assisted intervention]]''': Workshop at MICCAI 2008, New York City
* September 6, 2008: '''[[Miccai_2008_Segmentation_Workshop| Segmentation in the Clinic Challenge]]''': Workshop at MICCAI 2008, New York City
* September 3, 2008: '''[[Stanford_2008_Slicer_Workshop| Slicer Training in Stanford]]'''
* August 21-22, 2008: [[Events:August2008XNATDesktop|Visit by WashU Developers to Boston for Discussions of XND]]
* August 15, 2008: [[Events:NCI_Workshop_August_2008|August 15 2008, NA-MIC Workshop at NCI]]
* August 13-14, 2008: [[Events:August_2008_NCBC_AHM|August 13-14 2008, NCBC all hands meeting]]
* July 30 - August 1, 2008: [[2008_July_RFA_Experiment_Georgetown | RFA Interventional Experiment at Georgetown University]]
* August 1, 2008: [[Events:August2008XNATDesktop| Planning tcon for XNAT Desktop Slicer interface]]
* Steve Pieper presented NA-MIC and Slicer Module development at the [http://www.ipam.ucla.edu/programs/mbi2008/ IPAM MBI] Summer School [[Media:Pieper-UCLA-MBI-2008-07-17.ppt|(Slides)]]
* July 10 or 11, 2008: [[2008 July Slicer Introduction to Princess Margaret Hospital|Slicer Introduction to Princess Margaret Hospital]]
* July 23, 2008: [[2008_July_Slicer_IGT_VV_Link_Session_II|Slicer IGT Integration with Brainlab via VVLink]]
* June 23-27, 2008: '''[[2008_Summer_Project_Week|Summer Project Week]]'''
* June 26, 2008: [[2008_June_IGT_Tumor_Growth_Model_Demo_SPL|June 26, 2008, 4pm, Tumor Growth Model Software Demo at SPL]]
* June 16-17, 2008: '''[[2008 June Workshop Germany |Training Event in Germany]]'''
* May 21, 2008: [[2008_Core_1_UNC_Utah_DTI| Core 1 UNC & Utah Technical Meeting about DTI tool development at Utah]]
* May 22-23, 2008: [[2008_Core_1_Core_3_mtg|Cores 1-3 Technical Meeting at Utah]]
* March - June, 2008: [[3D_Ultrasound_Module_in_Slicer_3|Slicer IGT training for graduate students at SJTU, Shanghai, China (every Thursday 10 am - noon)]]
* May 21, 2008: Kilian Pohl presented on segmentation tools in 3D Slicer at the [http://www.dkfz.de/en/mbi/index.html Division of Medical and Biological Informatics, DKFZ, Germany] ([[media:Pohl_dkfz_08.pdf | Slides]])
* Noon, May 12, 2008: [[Events:May12_2008_FirstMondaySeminar | Brigham and Women's Hospital, First Monday Seminar Talk given by Drs. Ichiro Sakuma and Nassir Navab]]
* May 8, 2008: [[Events:2008_05_08_Collaboration_UWA_Perth|Conference Call to Explore Collaboration with Adam Wittek, UWA Perth]]
*May 2, 2008: [[2008_5_2_Hata_Talk_U_Michigan | Nobuhiko Hata's talk at Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI ]]
* [[Slicer3:Slicer3_Workshop_UNC_Chapel_Hill_2008| April 14, 2008: Full day Slicer 3 Users and Plug-in Workshop]] hosted by UNC-Chapel Hill faculty
* April 7, 2008: [[2008_David_Hawkes|2008 Dr. David Hawkes of UCL's visit to SPL]]
* March 31- Apr 11, 2008: [[2008_Platel_visit_from_TUE|2008 Dr. Platel's, IGT grp leader from Technical University Eindhoven, to SPL]]
* March 24-27, 2008: [[2008_Engineering_review_at_Utah|2008 Engineering review at Utah]]
* [[Events:HST-563-March2008|March 19, 2008: Harvard-MIT Division of Health Sciences and Technology (HST), Lecture on Interventional MRI by Hata, Kikinis, HST 563]]
* March 12, 2008: Steve Pieper presented on the NA-MIC Kit and 3D Slicer at the [http://www.cisst.org/wiki/Seminar_2008_03_12_3D_Slicer Johns Hopkins CISST] ([[media:Pieper-JHU-seminar-2008-03-12.ppt | Slides]])
* March 10-11, 2008: [[IGT:March_2008_IGT_Workshop|IGI Workshop, Rockville, MD]]
* Discussion of NA-MIC Kit for Cardiac EP with [http://www.bidmc.harvard.edu/cmr BIDMC].
* [[Slicer3:Spring-2008-User-Training|February 20th, 2008, Spring 2008 Slicer3 User Training Workshop ]] at the SPL 1249 Boylston St, Boston
* [[Slicer3:MiniRetreat February 5-7, 2008 | February 5-7, 2008, Slicer3 Mini-Retreat, Boston]]
* '''[[AHM_2008|January 7-11, 2008, AHM,]] [[2008_EAB|EAB,]] [[2008_Winter_Project_Week|Winter Project Week]]

=== 2007 ===
*[[2007_December_Slicer_IGT_Programming|December 12-14, 2007, Slicer IGT Programming Event]]
*[http://www.insightsoftwareconsortium.org/wiki/index.php/2007_MICCAI_Open_Workshop Nov 2, 2007: Third Annual Open Source Workshop at MICCAI]
*[[2007_October_Collaboration_Visit_Robert_Israel|October 14-20, 2007, Robert Israel Collaboration Visit to SPL]]
*2007 October 16-17: [http://nbirn.net/about/current/ahm2007.shtm BIRN AHM] Query Atlas and Qdec interfaces in Slicer 3 presented at the BIRN AHM.
** [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Module:QueryAtlas See this page] for links to QueryAtlas slides, movies and example datasets.
** [http://wiki.na-mic.org/Wiki/index.php/Image:Slicer3QDEC_AHM2007.ppt See this page] for links to Qdec slides.
*[[SanteFe.Tractography.Conference | October 1-2, 2007, Contrasting Tractography Methods Conference, Santa Fe]]
*[[Engineering:September 12, 2007 | September 12, 2007, Engineering End of Summer Meeting]]
*[[GPU.Enabled.Tools.Meeting | September 11, 2007, GPU-enabling of NA-MIC Algorithms, Boston]]
* Aug 21, 2007: [[DBP2:UNC:Cortical Thickness Roadmap | UNC DBP Roadmap Tcon]]
* '''[[2007_Programming/Project_Week_MIT|June 25-29, 2007, Summer Programming/Project Week at MIT]]'''
* [[Training:OHBM2007_Training_Workshop|June 9, 2007, OHBM DTI Training Workshop, Chicago]]
*[[2007_Pohl_at_CCB|June 1, 2007, Pohl Talk at CCB: A Hierarchical Segmentation Algorithm for MR Brain Images]]
* '''[[2007_Core_1_Meeting|May 29-31, 2007, Annual Core 1 Workshop, Boston]]'''
* April 24 Steve Pieper presented Slicer3 and the NA-MIC Kit to the [http://gray.mgh.harvard.edu/content/index.php Medical Physics group at MGH] [http://wiki.na-mic.org/Wiki/images/9/9c/Pieper-MGH-medical-physics-2007-04-24.ppt (slides)]
* [[Slicer3:MiniRetreat March 29, 30, 2007| March 29, 30, 2007, Slicer3 Mini-Retreat, Boston]]
* Feb 21-22 Vince Calhoun from MIND is visiting at MIT and MGH [http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1349 Talk announecement]
* Feb 3 and 10, 2007: [http://mri.radiology.uiowa.edu/mediawiki/index.php/ITK_Programming_Short_Course_-_Feb_2007 Iowa ITK Programming Short Course]
* [[Slicer3:MiniRetreat February 7-8, 2007| Feb 7-8, 2007, Slicer3 Mini-Retreat, Boston]]
* Jan 29 2007: [[P41-2007-Joint-Retreat | CFIT NAC P41 2007 Joint Retreat]]
* [[2007-01-16 Core 5, Core 6 Summit]]
* '''[[AHM_2007|Jan 10-11-12, 2007: Third All Hands Meeting, EAB, Project Half Week]]'''

=== 2006 ===

* [[Slicer3:Alpha-release|2006 December 12: Slicer3 retreat at Kitware]]
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]
* [[Slicer3:Usability#Report_from_Usability_Session_with_PNL_at_BWH_11.2F15.2F06|November 15, 2006: Usability session with PNL at BWH ]]
* [[Training:User_Workshop_Fall_HCNR_2006|November 1, 2006: NA-MIC Training Workshop at the Harvard Center for Neurodegeneration and Repair, Boston. ]]
* [[Oct-26-2006-MIND-visit_Visiting_the_MIND_institute|October 26, 2006: New DBP MIND Institute Visit]]
* October 23-26, 2006 [http://www.nbirn.net/press/current/ahm2006.shtm <nowiki>| BIRN All Hands Meeting</nowiki>]
* [[IGT:October_2006_IGT_Workshop|October 19-20 2006, NCIGT and NA-MIC Workshop on Open System Architectures for Image-Guided Therapy]]
* [[Core1-3-meeting-2006|October 17 2006: Coordination meeting]] between Core 1 and Core 3 to plan the specifics for the third and last year of the current DBP's
* [http://www.insightsoftwareconsortium.org/wiki/index.php/2006_MICCAI_Open_Workshop MICCAI_2006 October 1, 2006: Open Source Workshop at MICCAI 2006, Copenhagen]
* [[2006_September_Slicer3_Update|September 19-20, 2006 Slicer 3 Update Meeting in Boston]]
* September 14-15, 2006: We have been invited to participate in [http://usms.nist.gov/workshops/bioimaging.htm NIH Workshop on Standards in Change Measurement]. This workshop will potentially set the stage for additional workshops that focus on Image Guided Interventions and Open Source standards.
* Sept-06-2006, [http://www.ibmisps.org/pdf/InformationparticipantsANGLAIS.pdf 2006 IBMISPS conference:] [[Media:Kikinis-IBMISPS-09-06-2006.ppt|talk]] by [[media:Kikinis-FOSS.ppt|R. Kikinis on FOSS]] ([[2006 FOSS Abstract Kikinis]])
* [[NIH:_2006_All_NCBC_Meeting|July 17-19, 2006, All NCBC All Hands Meeting at NIH]]
* [[Training:NLM_Workshop_2006|July 19, 2006: NA-MIC Training Workshop at NLM]]
* [http://bsp.csie.nctu.edu.tw/lssa06/ July 13-14, 2006: 2nd IEEE-NLM International Life Science Systems and Applications Workshop, Lister Hill Auditorium, NIH, chaired by Stephen Wong, co-sponsored by IEEE, NLM, and NAMIC]
* July 2nd: Ron Kikinis [[Media:NA-MIC-Kit-07-01-2006.ppt| presentation]] (28MB ppt file) at the [http://www.future-cad.org/fcad/Docs/CFP_for_2nd_Int_Sympo_2006_ver3.2.pdf The 2nd International Symposium on Intelligent Assistance in Diagnosis of Multi-Dimensional Medical Images ]
* '''[[2006_Programming/Project_Week_MIT|June 26-30, 2006, Summer Programming/Project Week at MIT]]'''
* [[Georgia_Tech_visit_to_UNC%2C_June_8-9|June 8-9, 2006, Georgia Tech visit to UNC: Shape Analysis Discussion]]
* [[Slicer:Slicer3-June-5-2006-Retreat|June 5, 2006, Slicer 3 Retreat]]
* May 30, 2006 [http://www.cimit.org/forum/forum.html CIMIT Forum] with Steve Pieper and Luis Ibanez ([[Media:CIMIT-BIRN-update-2006-05-30.ppt| Steve's Slides]])([[Media:CIMIT-2006-IGSTK-InsightJournal.ppt| Luis' Slides]])
* [[Training:DTI_Workshop|May 26, 2006 UNC-Chapel Hill NA-MIC DTI Analysis Training Workshop]]
* [[Algorithms:Core1Visit_May06|May 23-24, 2006: NA-MIC Core 1 meeting at UNC]]
* [[DBP:Harvard:Collaboration:GTech#Progress|May 15 2006: Delphine Nain at the PNL]]
* [[Slicer:StevePieper_RonKikinis_VisitToDartmouth_051906|May 19, 2006: Steve Pieper and Ron Kikinis Visit to Dartmouth]]
* [[Training:NIH_Workshop_2006|April 27, 2006: NA-MIC Training Workshop at NIH]]
* April 24, 2006 [http://www.nimh.nih.gov/neuroinformatics/springagenda2006.cfm The Human Brain Project: Linking Within and Beyond] Natcher Conference Center, NIH Campus, Bethesda, Maryland: National Alliance for Medical Image Computing: Science & Technology of One National Center for Biomedical Computing [[Media:NA-MIC_Kit_revised.ppt| (this is a slightly modified version of the presentation)]]
* [[DBP:Harvard:Collaboration:Toronto|April 12-13, 2006: James Kennedy and Aristotle Voineskos at the PNL]]
* [[Training:MIND_Institute_Workshop_Spring_2006|April 10-11, 2006: NA-MIC Training Workshop at MIND Institute, New Mexico]]
* Steve Pieper presented the NA-MIC Kit at [http://www.biomedicalimaging.org ISBI] 2006 on April 7, 2006 ([[Media:NA-MIC-2006-04-07-ISBI.ppt| Slides]], [[Media:Pieper-ISBI-2006-revised.pdf| Paper]]).
* [[Slicer3:_Alpha1_Meeting|April 3-4, 2006: Design Review and Work meeting on Slicer3 (alpha1 release)]]
* [[DBP:Sylvain_Doug_visit_Dartmouth_Feb_22_2006|Feb 22, 2006: Sylvain Bouix to visit Dartmouth]]
* [[Engineering:Slicer3_and_GPU|Feb 22-24, 2006: Meeting at Kitware to discuss Slicer3 (thurs) and GPU programming (fri)]]
* [[IGT:Workshop_Feb_2006|Feb 20-23, 2006: IGT and FUS Workshops]]
* [[Training:User_Workshop_SPL_Winter_HCNR_2005|January 24, 2006: HCNR User Training Workshop at the Surgical Planning Lab in Boston]]
* '''[[AHM_2006:AHM_2006|January 8-13, 2006: The Second All-Hands-Meeting and Programming Event in Salt Lake City, Utah]]'''

=== 2005 ===

* [[DBP:Marek_Kubicki_visit_Dartmouth_December_20_2005|December 20, 2005: Marek Kubicki visit to Dartmouth]]
* [[Collaboration:GT-UCI|December 17, 2005: Jim Fallon from UC Irvine visit to Georgia Tech for work on Rule-Based Segmentation]]
* [[DBP:Andy_Saykin_visit_BWH_December_14_2005|December 14, 2005: Andy Saykin and Group visit to Brigham and Women's Hospital]]
* [[DBP:Dartmouth_Harvard_Slicer_Training_12_01_2005|December 1, 2005 Dartmouth Group Slicer Training Followup at Harvard, 1249 Boylston]]
* [http://rsna2005.rsna.org/rsna2005/V2005/index.cvn November 27-December 2, RSNA 2005, Chicago: Slicer session at the Open source imaging tools workshop ]
* [[DBP:Harvard:Collaboration:GTech#Progress|November 18 2005: Ramsey Al-Hakim at the PNL]]
* [[Collaboration:GT-Kitware|November 17-18, 2005: John Melonakos at Kitware -- Bayesian Classification Filter addition to ITK]]
* [[IGT:2005_Nov_16_IGT_Consortium_Kickoff|November 16, 2005: IGT Consortium Kickoff]]
* [[Collaboration:UNC-UCI|November 16, 2005: Jim Fallon and Martina from UC Irvine visit to UNC on DTI tools and clinical projects]]
* [[Engineering:Slicer3.0_November_15_2005|November 15, 2005, noon-5pm: Slicer 3.0 Meeting at SPL, Boston]]
* [[Dissemination:MICCAI_Workshop_2005|ISC and NA-MIC Workshop on Open Source Toolkits, Applications, and their uses in Medical Image Analysis at MICCAI]]
* October 29, 2005 (Thursday): Informal NA-MIC Lunch at MICCAI, Palm Springs, CA
* [[2005_AHM:_3D_Slicer/Freesurfer_Workshop|October 20, 2005: Slicer Training Workshop, AHM BIRN San Diego, California]]
* [[Dissemination:EPFL_Workshop_2005|October 5-7, 2005, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland: Advanced ITK and Slicer Workshop]]
* [[Collaboration:UNC-PNL|October 7, 2005, UNC visit at the Psychiatry NeuroImaging Laboratory]]
* [[Training:User_Workshop_SPL_Fall_2005|September 30, 2005. User Training Workshop at the SPL on Boylston St, Boston.]]
* [[Engineering:Core_3_Programming_Week#1_Feedback|September 26-27-28, 2005. DBP and Engineering Session on Feedback from Programming Week Projects, and Planning the next 6-months]]
* [[Training:User_Workshop_MGH_Summer_2005|September 16, 2005. User Training Workshop at MGH.]]
* [[Dissemination:CSB2005|August 11 2005 Invited Lecture about NA-MIC.]]
* [[Collaboration:Workshop_July_20_2005|July 20, 2005. UNC visit of Georgia Tech for collaborative work on shape and DTI algorithms.]]
* [[Engineering:Programmers_Week_Summer_2005|June 27-July 1, 2005. Programming Week in Boston]]
* [[Dissemination:NCRR_NIBIB_PI_Meeting_June_22-23_2005|June 22-23, 2005, NCRR/NIBIB PI Meeting]]
* [[Collaboration:Workshop_June_16-19_2005|June 16-19, 2005. Georgia Tech visit of UC-Irvine for collaborative work on anatomically accurate algorithms.]]
* [[Dissemination:Workshop_May_26-27_2005|May 26-27, 2005. User Training and Dissemination Workshop at Dartmouth]]
* [[DBP:Andy_Saykin_visit_BWH_April_21_2005|April 21-22, 2005: Andy Saykin visit to Brigham and Women's Hospital and MIT]]
* March 25, 2005. University of Utah visit of Harvard VA for collaborative work on DTMRI.
* [[FBIRN:retreat2005|March 21-23,2005: fBIRN Retreat in Irvine with User Tutorials for Slicer, Brains2 Wednesday on March 23]]
* [[AHM_2005:Main|February 20-22, 2005 AHM in SLC]]
* [[Dissemination:Workshop_Feb17-18_2005|February 17-18, 2005 Dissemination Workshop at UCSD]]
* January 26, 2005. Slicer User Workshop at BWH: [[Slicer:User_Workshop_Jan26|Information for Atendees]]
* January 24-25, 2005. Dissemination Workshop at [[Dissemination:Workshop_Jan24-25_Boston|Agenda]], [[Dissemination:Workshop_Jan2005_Interested_Attendee_List|List of Participants]], [[Talk:Dissemination:Workshop_Jan24-25_Boston_Feedback|Attendee Feedback]]
* January 17-18, 2005. [http://www.imaginggenetics.uci.edu First International Imaging Genetics Conference] at the Beckman Center of the National Academy of Sciences in Irvine, CA.

=== 2004 ===

* December 9-10, 2004. Dissemination Workshop at SPL, BWH:[[Dissemination:Workshop_Dec9-10_Boston|Agenda]], [[Dissemination:Workshop_Dec9-10_Boston_Presentations|Presentations]], [[Dissemination:Workshop_Dec9:10_Attendees_List|List of Participants]], [[Dissemination:Workshop_Dec9:10_Summary|Summary]],[[Talk:Dissemination:Workshop_Dec9-10_Boston_Feedback|Attendee Feedback]]
* November 16, 2004. Dissemination Meeting: [[Dissemination:Kickoff_Agenda|Agenda]], [[Dissemination:Kickoff_Summary|Summary]]
* [[Kickoff:Main|October 15, 2004. NA-MIC Kickoff Meeting]]

Miccai 2008 Systems and Architecture Workshop

2008-09-12T20:42:25Z

Dgobbi:

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

'''Software and hardware integration strategy for image guided therapy using Open IGT Link'''. [[media:OpenIGTLink_MICCAI2008_Workshop.ppt|(PowerPoint)]]

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

'''An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images'''. [[media:SynchroGrab_MICCAI2008_Workshop.ppt|(PowerPoint)]]

Jonathan Boisvert (Queen's University), David G. Gobbi (Queen's University), Siddharth Vikal (Queen's University), Robert Rohling (University of British Columbia), Purang Abolmaesumi (Queen’s University)

'''SimITK and SimVTK: ITK and VTK in Simulink'''. [[media:SimITKVTK_MICCAI2008_Workshop.ppt|(PowerPoint)]]

David G. Gobbi, Parvin Mousavi, Karen M. Li, Jing Xiang, Adam Campigotto, Adrien LaPointe, Gabor Fichtinger, Purang Abolmaesumi (Queen's University)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Events

2008-09-12T20:37:52Z

Dgobbi: /* 2008 */

__NOTOC__
== Introduction ==

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| NA-MIC organizes a variety of events. The engineering core holds a weekly telephone conference. Workshops address specific research focus areas. Training events aim at training NA-MIC participants and outsiders in NA-MIC technologies. Project weeks are intended for making progress in a variety of projects. The majority of NA-MIC events are hands-on and open to collaborators and interested scientists.
| style="background: #ebeced" colspan="2" align="center"| Example of a Training Event
|-
| style="background: #ebeced"| [[Image:Munich2008-Danielle.jpg|250px]]
| style="background: #ebeced"| The Munich 2008 training workshop in full swing. For more information about the workshop, click [[2008_June_Workshop_Germany|'''here''']].
|}
 

== [[TCON:Main|'''Telephone Conferences''']] ==

== Upcoming Events ==

== 2008 ==
* October 15-16, 2008: '''[[Robarts_Training_Session | NA-MIC kit training event at The University of Western Ontario]]''', London, Ontario, Canada
* December 1, 2008:[[Events:RSNA2008| Tutorial at RSNA]], [http://rsna2008.rsna.org/ RSNA conference website]
* December 8-12, 2008:[[2008_IGT_Project_Week|IGT Hands-on Project Week]], Boston
* Fall Semester 2008 Ibanez and Schroeder teach [http://public.kitware.com/OpenSourceSoftwarePractice/index.php/Main_Page Open Source Software Course] at Rensselaer Polytechnic Institute

== 2009 ==
* '''[[AHM_2009|January 5-9, 2009, AHM,]] [[2009_EAB|EAB,]] [[2009_Winter_Project_Week|Winter Project Week]]'''
* January 8, 2009:[[Events:TutorialContestJan2009| Tutorial Contest:]] announcement of the winners.

== Standing Events ==

* [[TCON:Main|A list of all upcoming and past teleconferences is available here]].
* [[Engineering:Programming_Events|Hands on Project Events]]
* [[Slicer:Developer_Meetings|Slicer developer meetings are here]].

== Past Events ==

=== 2008 ===
* September 10, 2008: '''[[Miccai_2008_Tutorial| Interfacing third-party software with the NA-MIC Kit]]''': Tutorial at MICCAI 2008, New-York City
* September 10, 2008: '''[[Miccai_2008_Prostate_Workshop| Prostate image analysis and computer-assisted intervention]]''': Workshop at MICCAI 2008, New-York City
* September 5, 2008: '''[[Miccai_2008_Systems_and_Architecture_Workshop| Systems & architecture for computer assisted intervention]]''': Workshop at MICCAI 2008, New York City
* September 3, 2008: '''[[Stanford_2008_Slicer_Workshop| Slicer Training in Stanford]]'''
* September 6, 2008: '''[[Miccai_2008_Segmentation_Workshop| Segmentation in the Clinic Challenge]]''': Workshop at MICCAI 2008, New-York City
* August 21-22, 2008: [[Events:August2008XNATDesktop|Visit by WashU Developers to Boston for Discussions of XND]]
* August 15, 2008: [[Events:NCI_Workshop_August_2008|August 15 2008, NA-MIC Workshop at NCI]]
* August 13-14, 2008: [[Events:August_2008_NCBC_AHM|August 13-14 2008, NCBC all hands meeting]]
* July 30 - August 1, 2008: [[2008_July_RFA_Experiment_Georgetown | RFA Interventional Experiment at Georgetown University]]
* August 1, 2008: [[Events:August2008XNATDesktop| Planning tcon for XNAT Desktop Slicer interface]]
* Steve Pieper presented NA-MIC and Slicer Module development at the [http://www.ipam.ucla.edu/programs/mbi2008/ IPAM MBI] Summer School [[Media:Pieper-UCLA-MBI-2008-07-17.ppt|(Slides)]]
* July 10 or 11, 2008: [[2008 July Slicer Introduction to Princess Margaret Hospital|Slicer Introduction to Princess Margaret Hospital]]
* July 23, 2008: [[2008_July_Slicer_IGT_VV_Link_Session_II|Slicer IGT Integration with Brainlab via VVLink]]
* June 23-27, 2008: '''[[2008_Summer_Project_Week|Summer Project Week]]'''
* June 26, 2008: [[2008_June_IGT_Tumor_Growth_Model_Demo_SPL|June 26, 2008, 4pm, Tumor Growth Model Software Demo at SPL]]
* June 16-17, 2008: '''[[2008 June Workshop Germany |Training Event in Germany]]'''
* May 21, 2008: [[2008_Core_1_UNC_Utah_DTI| Core 1 UNC & Utah Technical Meeting about DTI tool development at Utah]]
* May 22-23, 2008: [[2008_Core_1_Core_3_mtg|Cores 1-3 Technical Meeting at Utah]]
* March - June, 2008: [[3D_Ultrasound_Module_in_Slicer_3|Slicer IGT training for graduate students at SJTU, Shanghai, China (every Thursday 10 am - noon)]]
* May 21, 2008: Kilian Pohl presented on segmentation tools in 3D Slicer at the [http://www.dkfz.de/en/mbi/index.html Division of Medical and Biological Informatics, DKFZ, Germany] ([[media:Pohl_dkfz_08.pdf | Slides]])
* Noon, May 12, 2008: [[Events:May12_2008_FirstMondaySeminar | Brigham and Women's Hospital, First Monday Seminar Talk given by Drs. Ichiro Sakuma and Nassir Navab]]
* May 8, 2008: [[Events:2008_05_08_Collaboration_UWA_Perth|Conference Call to Explore Collaboration with Adam Wittek, UWA Perth]]
*May 2, 2008: [[2008_5_2_Hata_Talk_U_Michigan | Nobuhiko Hata's talk at Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI ]]
* [[Slicer3:Slicer3_Workshop_UNC_Chapel_Hill_2008| April 14, 2008: Full day Slicer 3 Users and Plug-in Workshop]] hosted by UNC-Chapel Hill faculty
* April 7, 2008: [[2008_David_Hawkes|2008 Dr. David Hawkes of UCL's visit to SPL]]
* March 31- Apr 11, 2008: [[2008_Platel_visit_from_TUE|2008 Dr. Platel's, IGT grp leader from Technical University Eindhoven, to SPL]]
* March 24-27, 2008: [[2008_Engineering_review_at_Utah|2008 Engineering review at Utah]]
* [[Events:HST-563-March2008|March 19, 2008: Harvard-MIT Division of Health Sciences and Technology (HST), Lecture on Interventional MRI by Hata, Kikinis, HST 563]]
* March 12, 2008: Steve Pieper presented on the NA-MIC Kit and 3D Slicer at the [http://www.cisst.org/wiki/Seminar_2008_03_12_3D_Slicer Johns Hopkins CISST] ([[media:Pieper-JHU-seminar-2008-03-12.ppt | Slides]])
* March 10-11, 2008: [[IGT:March_2008_IGT_Workshop|IGI Workshop, Rockville, MD]]
* Discussion of NA-MIC Kit for Cardiac EP with [http://www.bidmc.harvard.edu/cmr BIDMC].
* [[Slicer3:Spring-2008-User-Training|February 20th, 2008, Spring 2008 Slicer3 User Training Workshop ]] at the SPL 1249 Boylston St, Boston
* [[Slicer3:MiniRetreat February 5-7, 2008 | February 5-7, 2008, Slicer3 Mini-Retreat, Boston]]
* '''[[AHM_2008|January 7-11, 2008, AHM,]] [[2008_EAB|EAB,]] [[2008_Winter_Project_Week|Winter Project Week]]

=== 2007 ===
*[[2007_December_Slicer_IGT_Programming|December 12-14, 2007, Slicer IGT Programming Event]]
*[http://www.insightsoftwareconsortium.org/wiki/index.php/2007_MICCAI_Open_Workshop Nov 2, 2007: Third Annual Open Source Workshop at MICCAI]
*[[2007_October_Collaboration_Visit_Robert_Israel|October 14-20, 2007, Robert Israel Collaboration Visit to SPL]]
*2007 October 16-17: [http://nbirn.net/about/current/ahm2007.shtm BIRN AHM] Query Atlas and Qdec interfaces in Slicer 3 presented at the BIRN AHM.
** [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Module:QueryAtlas See this page] for links to QueryAtlas slides, movies and example datasets.
** [http://wiki.na-mic.org/Wiki/index.php/Image:Slicer3QDEC_AHM2007.ppt See this page] for links to Qdec slides.
*[[SanteFe.Tractography.Conference | October 1-2, 2007, Contrasting Tractography Methods Conference, Santa Fe]]
*[[Engineering:September 12, 2007 | September 12, 2007, Engineering End of Summer Meeting]]
*[[GPU.Enabled.Tools.Meeting | September 11, 2007, GPU-enabling of NA-MIC Algorithms, Boston]]
* Aug 21, 2007: [[DBP2:UNC:Cortical Thickness Roadmap | UNC DBP Roadmap Tcon]]
* '''[[2007_Programming/Project_Week_MIT|June 25-29, 2007, Summer Programming/Project Week at MIT]]'''
* [[Training:OHBM2007_Training_Workshop|June 9, 2007, OHBM DTI Training Workshop, Chicago]]
*[[2007_Pohl_at_CCB|June 1, 2007, Pohl Talk at CCB: A Hierarchical Segmentation Algorithm for MR Brain Images]]
* '''[[2007_Core_1_Meeting|May 29-31, 2007, Annual Core 1 Workshop, Boston]]'''
* April 24 Steve Pieper presented Slicer3 and the NA-MIC Kit to the [http://gray.mgh.harvard.edu/content/index.php Medical Physics group at MGH] [http://wiki.na-mic.org/Wiki/images/9/9c/Pieper-MGH-medical-physics-2007-04-24.ppt (slides)]
* [[Slicer3:MiniRetreat March 29, 30, 2007| March 29, 30, 2007, Slicer3 Mini-Retreat, Boston]]
* Feb 21-22 Vince Calhoun from MIND is visiting at MIT and MGH [http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1349 Talk announecement]
* Feb 3 and 10, 2007: [http://mri.radiology.uiowa.edu/mediawiki/index.php/ITK_Programming_Short_Course_-_Feb_2007 Iowa ITK Programming Short Course]
* [[Slicer3:MiniRetreat February 7-8, 2007| Feb 7-8, 2007, Slicer3 Mini-Retreat, Boston]]
* Jan 29 2007: [[P41-2007-Joint-Retreat | CFIT NAC P41 2007 Joint Retreat]]
* [[2007-01-16 Core 5, Core 6 Summit]]
* '''[[AHM_2007|Jan 10-11-12, 2007: Third All Hands Meeting, EAB, Project Half Week]]'''

=== 2006 ===

* [[Slicer3:Alpha-release|2006 December 12: Slicer3 retreat at Kitware]]
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]
* [[Slicer3:Usability#Report_from_Usability_Session_with_PNL_at_BWH_11.2F15.2F06|November 15, 2006: Usability session with PNL at BWH ]]
* [[Training:User_Workshop_Fall_HCNR_2006|November 1, 2006: NA-MIC Training Workshop at the Harvard Center for Neurodegeneration and Repair, Boston. ]]
* [[Oct-26-2006-MIND-visit_Visiting_the_MIND_institute|October 26, 2006: New DBP MIND Institute Visit]]
* October 23-26, 2006 [http://www.nbirn.net/press/current/ahm2006.shtm <nowiki>| BIRN All Hands Meeting</nowiki>]
* [[IGT:October_2006_IGT_Workshop|October 19-20 2006, NCIGT and NA-MIC Workshop on Open System Architectures for Image-Guided Therapy]]
* [[Core1-3-meeting-2006|October 17 2006: Coordination meeting]] between Core 1 and Core 3 to plan the specifics for the third and last year of the current DBP's
* [http://www.insightsoftwareconsortium.org/wiki/index.php/2006_MICCAI_Open_Workshop MICCAI_2006 October 1, 2006: Open Source Workshop at MICCAI 2006, Copenhagen]
* [[2006_September_Slicer3_Update|September 19-20, 2006 Slicer 3 Update Meeting in Boston]]
* September 14-15, 2006: We have been invited to participate in [http://usms.nist.gov/workshops/bioimaging.htm NIH Workshop on Standards in Change Measurement]. This workshop will potentially set the stage for additional workshops that focus on Image Guided Interventions and Open Source standards.
* Sept-06-2006, [http://www.ibmisps.org/pdf/InformationparticipantsANGLAIS.pdf 2006 IBMISPS conference:] [[Media:Kikinis-IBMISPS-09-06-2006.ppt|talk]] by [[media:Kikinis-FOSS.ppt|R. Kikinis on FOSS]] ([[2006 FOSS Abstract Kikinis]])
* [[NIH:_2006_All_NCBC_Meeting|July 17-19, 2006, All NCBC All Hands Meeting at NIH]]
* [[Training:NLM_Workshop_2006|July 19, 2006: NA-MIC Training Workshop at NLM]]
* [http://bsp.csie.nctu.edu.tw/lssa06/ July 13-14, 2006: 2nd IEEE-NLM International Life Science Systems and Applications Workshop, Lister Hill Auditorium, NIH, chaired by Stephen Wong, co-sponsored by IEEE, NLM, and NAMIC]
* July 2nd: Ron Kikinis [[Media:NA-MIC-Kit-07-01-2006.ppt| presentation]] (28MB ppt file) at the [http://www.future-cad.org/fcad/Docs/CFP_for_2nd_Int_Sympo_2006_ver3.2.pdf The 2nd International Symposium on Intelligent Assistance in Diagnosis of Multi-Dimensional Medical Images ]
* '''[[2006_Programming/Project_Week_MIT|June 26-30, 2006, Summer Programming/Project Week at MIT]]'''
* [[Georgia_Tech_visit_to_UNC%2C_June_8-9|June 8-9, 2006, Georgia Tech visit to UNC: Shape Analysis Discussion]]
* [[Slicer:Slicer3-June-5-2006-Retreat|June 5, 2006, Slicer 3 Retreat]]
* May 30, 2006 [http://www.cimit.org/forum/forum.html CIMIT Forum] with Steve Pieper and Luis Ibanez ([[Media:CIMIT-BIRN-update-2006-05-30.ppt| Steve's Slides]])([[Media:CIMIT-2006-IGSTK-InsightJournal.ppt| Luis' Slides]])
* [[Training:DTI_Workshop|May 26, 2006 UNC-Chapel Hill NA-MIC DTI Analysis Training Workshop]]
* [[Algorithms:Core1Visit_May06|May 23-24, 2006: NA-MIC Core 1 meeting at UNC]]
* [[DBP:Harvard:Collaboration:GTech#Progress|May 15 2006: Delphine Nain at the PNL]]
* [[Slicer:StevePieper_RonKikinis_VisitToDartmouth_051906|May 19, 2006: Steve Pieper and Ron Kikinis Visit to Dartmouth]]
* [[Training:NIH_Workshop_2006|April 27, 2006: NA-MIC Training Workshop at NIH]]
* April 24, 2006 [http://www.nimh.nih.gov/neuroinformatics/springagenda2006.cfm The Human Brain Project: Linking Within and Beyond] Natcher Conference Center, NIH Campus, Bethesda, Maryland: National Alliance for Medical Image Computing: Science & Technology of One National Center for Biomedical Computing [[Media:NA-MIC_Kit_revised.ppt| (this is a slightly modified version of the presentation)]]
* [[DBP:Harvard:Collaboration:Toronto|April 12-13, 2006: James Kennedy and Aristotle Voineskos at the PNL]]
* [[Training:MIND_Institute_Workshop_Spring_2006|April 10-11, 2006: NA-MIC Training Workshop at MIND Institute, New Mexico]]
* Steve Pieper presented the NA-MIC Kit at [http://www.biomedicalimaging.org ISBI] 2006 on April 7, 2006 ([[Media:NA-MIC-2006-04-07-ISBI.ppt| Slides]], [[Media:Pieper-ISBI-2006-revised.pdf| Paper]]).
* [[Slicer3:_Alpha1_Meeting|April 3-4, 2006: Design Review and Work meeting on Slicer3 (alpha1 release)]]
* [[DBP:Sylvain_Doug_visit_Dartmouth_Feb_22_2006|Feb 22, 2006: Sylvain Bouix to visit Dartmouth]]
* [[Engineering:Slicer3_and_GPU|Feb 22-24, 2006: Meeting at Kitware to discuss Slicer3 (thurs) and GPU programming (fri)]]
* [[IGT:Workshop_Feb_2006|Feb 20-23, 2006: IGT and FUS Workshops]]
* [[Training:User_Workshop_SPL_Winter_HCNR_2005|January 24, 2006: HCNR User Training Workshop at the Surgical Planning Lab in Boston]]
* '''[[AHM_2006:AHM_2006|January 8-13, 2006: The Second All-Hands-Meeting and Programming Event in Salt Lake City, Utah]]'''

=== 2005 ===

* [[DBP:Marek_Kubicki_visit_Dartmouth_December_20_2005|December 20, 2005: Marek Kubicki visit to Dartmouth]]
* [[Collaboration:GT-UCI|December 17, 2005: Jim Fallon from UC Irvine visit to Georgia Tech for work on Rule-Based Segmentation]]
* [[DBP:Andy_Saykin_visit_BWH_December_14_2005|December 14, 2005: Andy Saykin and Group visit to Brigham and Women's Hospital]]
* [[DBP:Dartmouth_Harvard_Slicer_Training_12_01_2005|December 1, 2005 Dartmouth Group Slicer Training Followup at Harvard, 1249 Boylston]]
* [http://rsna2005.rsna.org/rsna2005/V2005/index.cvn November 27-December 2, RSNA 2005, Chicago: Slicer session at the Open source imaging tools workshop ]
* [[DBP:Harvard:Collaboration:GTech#Progress|November 18 2005: Ramsey Al-Hakim at the PNL]]
* [[Collaboration:GT-Kitware|November 17-18, 2005: John Melonakos at Kitware -- Bayesian Classification Filter addition to ITK]]
* [[IGT:2005_Nov_16_IGT_Consortium_Kickoff|November 16, 2005: IGT Consortium Kickoff]]
* [[Collaboration:UNC-UCI|November 16, 2005: Jim Fallon and Martina from UC Irvine visit to UNC on DTI tools and clinical projects]]
* [[Engineering:Slicer3.0_November_15_2005|November 15, 2005, noon-5pm: Slicer 3.0 Meeting at SPL, Boston]]
* [[Dissemination:MICCAI_Workshop_2005|ISC and NA-MIC Workshop on Open Source Toolkits, Applications, and their uses in Medical Image Analysis at MICCAI]]
* October 29, 2005 (Thursday): Informal NA-MIC Lunch at MICCAI, Palm Springs, CA
* [[2005_AHM:_3D_Slicer/Freesurfer_Workshop|October 20, 2005: Slicer Training Workshop, AHM BIRN San Diego, California]]
* [[Dissemination:EPFL_Workshop_2005|October 5-7, 2005, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland: Advanced ITK and Slicer Workshop]]
* [[Collaboration:UNC-PNL|October 7, 2005, UNC visit at the Psychiatry NeuroImaging Laboratory]]
* [[Training:User_Workshop_SPL_Fall_2005|September 30, 2005. User Training Workshop at the SPL on Boylston St, Boston.]]
* [[Engineering:Core_3_Programming_Week#1_Feedback|September 26-27-28, 2005. DBP and Engineering Session on Feedback from Programming Week Projects, and Planning the next 6-months]]
* [[Training:User_Workshop_MGH_Summer_2005|September 16, 2005. User Training Workshop at MGH.]]
* [[Dissemination:CSB2005|August 11 2005 Invited Lecture about NA-MIC.]]
* [[Collaboration:Workshop_July_20_2005|July 20, 2005. UNC visit of Georgia Tech for collaborative work on shape and DTI algorithms.]]
* [[Engineering:Programmers_Week_Summer_2005|June 27-July 1, 2005. Programming Week in Boston]]
* [[Dissemination:NCRR_NIBIB_PI_Meeting_June_22-23_2005|June 22-23, 2005, NCRR/NIBIB PI Meeting]]
* [[Collaboration:Workshop_June_16-19_2005|June 16-19, 2005. Georgia Tech visit of UC-Irvine for collaborative work on anatomically accurate algorithms.]]
* [[Dissemination:Workshop_May_26-27_2005|May 26-27, 2005. User Training and Dissemination Workshop at Dartmouth]]
* [[DBP:Andy_Saykin_visit_BWH_April_21_2005|April 21-22, 2005: Andy Saykin visit to Brigham and Women's Hospital and MIT]]
* March 25, 2005. University of Utah visit of Harvard VA for collaborative work on DTMRI.
* [[FBIRN:retreat2005|March 21-23,2005: fBIRN Retreat in Irvine with User Tutorials for Slicer, Brains2 Wednesday on March 23]]
* [[AHM_2005:Main|February 20-22, 2005 AHM in SLC]]
* [[Dissemination:Workshop_Feb17-18_2005|February 17-18, 2005 Dissemination Workshop at UCSD]]
* January 26, 2005. Slicer User Workshop at BWH: [[Slicer:User_Workshop_Jan26|Information for Atendees]]
* January 24-25, 2005. Dissemination Workshop at [[Dissemination:Workshop_Jan24-25_Boston|Agenda]], [[Dissemination:Workshop_Jan2005_Interested_Attendee_List|List of Participants]], [[Talk:Dissemination:Workshop_Jan24-25_Boston_Feedback|Attendee Feedback]]
* January 17-18, 2005. [http://www.imaginggenetics.uci.edu First International Imaging Genetics Conference] at the Beckman Center of the National Academy of Sciences in Irvine, CA.

=== 2004 ===

* December 9-10, 2004. Dissemination Workshop at SPL, BWH:[[Dissemination:Workshop_Dec9-10_Boston|Agenda]], [[Dissemination:Workshop_Dec9-10_Boston_Presentations|Presentations]], [[Dissemination:Workshop_Dec9:10_Attendees_List|List of Participants]], [[Dissemination:Workshop_Dec9:10_Summary|Summary]],[[Talk:Dissemination:Workshop_Dec9-10_Boston_Feedback|Attendee Feedback]]
* November 16, 2004. Dissemination Meeting: [[Dissemination:Kickoff_Agenda|Agenda]], [[Dissemination:Kickoff_Summary|Summary]]
* [[Kickoff:Main|October 15, 2004. NA-MIC Kickoff Meeting]]

Miccai 2008 Systems and Architecture Workshop

2008-09-12T20:36:12Z

Dgobbi: /* Presentations Funded Wholly or Partly by NA-MIC */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

'''Software and hardware integration strategy for image guided therapy using Open IGT Link'''. [[media:OpenIGTLink_MICCAI2008_Workshop.ppt|(PowerPoint)]]

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

'''An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images'''. [[media:SynchroGrab_MICCAI2008_Workshop.ppt|(PowerPoint)]]

Jonathan Boisvert (Queen's University), David G. Gobbi (Queen's University), Siddharth Vikal (Queen's University), Robert Rohling (University of British Columbia), Purang Abolmaesumi (Queen’s University)

'''SimITK and SimVTK: ITK and VTK in Simulink'''. [[media:SimITKVTK_MICCAI2008_Workshop.ppt|(PowerPoint)]]

David G. Gobbi, Parvin Mousavi, Karen M. Li, Jing Xiang, Adam Campigotto, Adrien LaPointe, Gabor Fichtinger, Purang Abolmaesumi (Queen's University)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T20:35:30Z

Dgobbi: /* Presentations Funded Wholly or Partly by NA-MIC */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

'''Software and hardware integration strategy for image guided therapy using Open IGT Link'''[[media:OpenIGTLink_MICCAI2008_Workshop.ppt|(PowerPoint)]].

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

'''An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images'''[[media:SynchroGrab_MICCAI2008_Workshop.ppt|(PowerPoint)]].

Jonathan Boisvert (Queen's University), David G. Gobbi (Queen's University), Siddharth Vikal (Queen's University), Robert Rohling (University of British Columbia), Purang Abolmaesumi (Queen’s University)

'''SimITK and SimVTK: ITK and VTK in Simulink'''[[media:SimITKVTK_MICCAI2008_Workshop.ppt|(PowerPoint)]].

David G. Gobbi, Parvin Mousavi, Karen M. Li, Jing Xiang, Adam Campigotto, Adrien LaPointe, Gabor Fichtinger, Purang Abolmaesumi (Queen's University)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

File:SimITKVTK MICCAI2008 Workshop.ppt

2008-09-12T20:30:25Z

Dgobbi: ITK and VTK in Simulink: MICCAI 2008 Workshop

ITK and VTK in Simulink: MICCAI 2008 Workshop

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:34:04Z

Dgobbi: /* Presentations Funded Wholly or Partly by NA-MIC */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

[[media:OpenIGTLink_MICCAI2008_Workshop.ppt|'''Software and hardware integration strategy for image guided therapy using Open IGT Link''']].

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

[[media:SynchroGrab_MICCAI2008_Workshop.ppt|'''An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images''']].

Jonathan Boisvert (Queen's University), David G. Gobbi (Queen's University), Siddharth Vikal (Queen's University), Robert Rohling (University of British Columbia), Purang Abolmaesumi (Queen’s University)

[[media:SimITKVTK_MICCAI2008_Workshop.ppt|'''SimITK and SimVTK: ITK and VTK in Simulink''']].

David G. Gobbi, Parvin Mousavi, Karen M. Li, Jing Xiang, Adam Campigotto, Adrien LaPointe, Gabor Fichtinger, Purang Abolmaesumi (Queen's University)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:30:02Z

Dgobbi:

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

[[media:OpenIGTLink_MICCAI2008_Workshop.ppt|'''Software and hardware integration strategy for image guided therapy using Open IGT Link''']].

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

[[media:SynchroGrab_MICCAI2008_Workshop.ppt|'''An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images''']].

Jonathan Boisvert, David G. Gobbi, Siddharth Vikal, Purang Abolmaesumi (Queen’s University)

[[media:SimITKVTK_MICCAI2008_Workshop.ppt|'''SimITK and SimVTK: ITK and VTK in Simulink''']].

David G. Gobbi, Parvin Mousavi, Karen M. Li, Jing Xiang, Adam Campigotto, Adrien LaPointe, Gabor Fichtinger, Purang Abolmaesumi (Queen's University)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:14:21Z

Dgobbi:

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Presentations Funded Wholly or Partly by NA-MIC ==

'''Software and hardware integration strategy for image guided therapy using Open IGT Link''' ([[media:OpenIGTLink_MICCAI2008_Workshop.ppt|ppt]]).

Junichi Tokuda (Brigham and Women's Hospital and Harvard Medical School), Luis Ibanez (Kitware, Inc.), Csaba Csoma (Johns Hopkins University), Patrick Cheng (Georgetown University), Haiying Liu (Brigham and Women's Hospital), Jack Blevins (Acoustic MedSystems Inc.), Junpei Arata (Nagoya Institute of Technology), Xenophon Papademetris (Yale University) and Nobuhiko Hata (Brigham and Women's Hospital and Harvard Medical School)

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:09:27Z

Dgobbi: /* Systems and Architectures for Computer Assisted Interventions */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:08:32Z

Dgobbi: /* Systems and Architectures for Computer Assisted Interventions */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T18:07:48Z

Dgobbi: /* Systems and Architectures for Computer Assisted Interventions */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
*[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 Official workshop schedule] from [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website]
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:58:12Z

Dgobbi:

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
[http://smarts.lcsr.jhu.edu/CAI-Workshop-2008 The original workshop schedule] is on the [http://smarts.lcsr.jhu.edu/ Johns Hopkins SMARTS Laboratory website].

*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:53:14Z

Dgobbi:

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:52:53Z

Dgobbi: /* Peer Review */

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:52:25Z

Dgobbi: /* Submission Information */

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:51:52Z

Dgobbi: /* NEWS */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Submission Information ==
We are soliciting submissions that describe
''integrated systems for computer-assisted interventions'', regardless of
whether or not they utilize open source software.
Submissions that describe open source software packages for
computer assisted interventions are also appropriate.
All submissions should be made via the [http://www.insight-journal.org Insight Journal].
A special issue has been created for the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 ''Workshop on Systems and Architectures for Computer Assisted Interventions at MICCAI 2008''].
Note that the Insight Journal has a LaTeX style file available
[http://public.kitware.com/pub/itk/InsightJournal/InsightJournalSubmissionTemplate.tgz here].

Key points regarding submission:
* Papers may be up to 8 pages in length. Authors are encouraged to include other files with their submission,particularly videos, code, and data. Extended abstracts will be considered, especially if accompanied by other files.
* Every submission immediately appears on the Insight Journal site in the Special Issue on the MICCAI Workshop. Therefore, every submission is available to any registered member of the Insight Journal (and registration is free).
* Submission requires licensing to the Insight Journal the right to distribute your submission under the Creative Commons' "by-attribution" license. Copyright transfer is not required.
* The Insight Journal is a registered digital library. Therefore, your submission is automatically assigned a unique open-archive "handle" that (unlike URLs) persists on the web and that (unlike other web-based database keys) allows your submission to be indexed by Google and other search engines. Handles also serve as a mechanism whereby submissions can be permanently referenced in publications.

== Peer Review ==
Every submission is available for public peer-review. That is, any
registered member of the Insight Journal (and registration is free) is
able to download, score, and comment on any submission to this
workshop. All reviews are public. Anonymous reviews are discouraged.

The workshop committee
will consider the posted reviews, as well as the intent of the
workshop, to select papers for oral presentation. Those
decisions will be announced on or about July 30, 2008.

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:50:45Z

Dgobbi: /* Final Program */

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== NEWS ==

''Aug 5, 2008''

The final program has been modified to start at 9 AM and end at 6 PM, as requested by MICCAI organizers.

''July 29, 2008''

The [[#Final_Program|workshop program]] has now been posted.

We are still awaiting abstracts and/or papers from some invited speakers. Please send these to pkaz@jhu.edu.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Submission Information ==
We are soliciting submissions that describe
''integrated systems for computer-assisted interventions'', regardless of
whether or not they utilize open source software.
Submissions that describe open source software packages for
computer assisted interventions are also appropriate.
All submissions should be made via the [http://www.insight-journal.org Insight Journal].
A special issue has been created for the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 ''Workshop on Systems and Architectures for Computer Assisted Interventions at MICCAI 2008''].
Note that the Insight Journal has a LaTeX style file available
[http://public.kitware.com/pub/itk/InsightJournal/InsightJournalSubmissionTemplate.tgz here].

Key points regarding submission:
* Papers may be up to 8 pages in length. Authors are encouraged to include other files with their submission,particularly videos, code, and data. Extended abstracts will be considered, especially if accompanied by other files.
* Every submission immediately appears on the Insight Journal site in the Special Issue on the MICCAI Workshop. Therefore, every submission is available to any registered member of the Insight Journal (and registration is free).
* Submission requires licensing to the Insight Journal the right to distribute your submission under the Creative Commons' "by-attribution" license. Copyright transfer is not required.
* The Insight Journal is a registered digital library. Therefore, your submission is automatically assigned a unique open-archive "handle" that (unlike URLs) persists on the web and that (unlike other web-based database keys) allows your submission to be indexed by Google and other search engines. Handles also serve as a mechanism whereby submissions can be permanently referenced in publications.

== Peer Review ==
Every submission is available for public peer-review. That is, any
registered member of the Insight Journal (and registration is free) is
able to download, score, and comment on any submission to this
workshop. All reviews are public. Anonymous reviews are discouraged.

The workshop committee
will consider the posted reviews, as well as the intent of the
workshop, to select papers for oral presentation. Those
decisions will be announced on or about July 30, 2008.

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*Medtronic StealthStation™ StealthLink Research Portal, Leslie Holton, Medtronic
*The daVinci Research Interface, Simon DiMaio, Intuitive Surgical
*Micron Tracker: API and other interfaces, Claudio Gatti, Claron Technology
*VectorVision Link, Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*Open Source Initiative for Surgical Robot Toolkit, Kiyo Chinzei, AIST Japan
*IGSTK: Building High Quality Roads with Open Source Software, Luis Ibanez, Kitware
*The Surgical Assistant Workstation, Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*The ''cisst'' libraries for computer assisted intervention systems, Anton Deguet, Johns Hopkins Univ.
*An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images, Jonathan Boisvert, Queen’s Univ.
*Simulink Libraries for Visual Programming of VTK and ITK, David Gobbi, Queen’s Univ.
*VV: a viewer for the evaluation of 4D image registration, Pierre Seroul, Univ. Lyon
*MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems, Jian Chen, Chinese Academy of Science
*A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool, Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*Integration of Open Source and Commercial Software for a Neurosurgical Robot System, Tian Xia, Tamas Haidegger, JHU
*CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome, Frank Lindseth, SINTEF Norway
*Distributed database framework for real-time image-guidance in robotic surgery, David Kwartowitz, Mayo Clinic
*Software Architecture of a System for Robotic Surgery, Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:46:03Z

Dgobbi:

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|[[Image:miccai-2008-logo.png|left|180px|MICCAI 2008]]
|}
 
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== NEWS ==

''Aug 5, 2008''

The final program has been modified to start at 9 AM and end at 6 PM, as requested by MICCAI organizers.

''July 29, 2008''

The [[#Final_Program|workshop program]] has now been posted.

We are still awaiting abstracts and/or papers from some invited speakers. Please send these to pkaz@jhu.edu.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Submission Information ==
We are soliciting submissions that describe
''integrated systems for computer-assisted interventions'', regardless of
whether or not they utilize open source software.
Submissions that describe open source software packages for
computer assisted interventions are also appropriate.
All submissions should be made via the [http://www.insight-journal.org Insight Journal].
A special issue has been created for the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 ''Workshop on Systems and Architectures for Computer Assisted Interventions at MICCAI 2008''].
Note that the Insight Journal has a LaTeX style file available
[http://public.kitware.com/pub/itk/InsightJournal/InsightJournalSubmissionTemplate.tgz here].

Key points regarding submission:
* Papers may be up to 8 pages in length. Authors are encouraged to include other files with their submission,particularly videos, code, and data. Extended abstracts will be considered, especially if accompanied by other files.
* Every submission immediately appears on the Insight Journal site in the Special Issue on the MICCAI Workshop. Therefore, every submission is available to any registered member of the Insight Journal (and registration is free).
* Submission requires licensing to the Insight Journal the right to distribute your submission under the Creative Commons' "by-attribution" license. Copyright transfer is not required.
* The Insight Journal is a registered digital library. Therefore, your submission is automatically assigned a unique open-archive "handle" that (unlike URLs) persists on the web and that (unlike other web-based database keys) allows your submission to be indexed by Google and other search engines. Handles also serve as a mechanism whereby submissions can be permanently referenced in publications.

== Peer Review ==
Every submission is available for public peer-review. That is, any
registered member of the Insight Journal (and registration is free) is
able to download, score, and comment on any submission to this
workshop. All reviews are public. Anonymous reviews are discouraged.

The workshop committee
will consider the posted reviews, as well as the intent of the
workshop, to select papers for oral presentation. Those
decisions will be announced on or about July 30, 2008.

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*[[StealthLinkAbstract|Medtronic StealthStation™ StealthLink Research Portal]], Leslie Holton, Medtronic
*[http://hdl.handle.net/1926/1464 The daVinci Research Interface], Simon DiMaio, Intuitive Surgical
*[http://www.clarontech.com/API/index.html Micron Tracker: API and other interfaces], Claudio Gatti, Claron Technology
*[[Media:vvlink.pdf|VectorVision Link]], Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*[http://www.intelli-si.org/ Open Source Initiative for Surgical Robot Toolkit], Kiyo Chinzei, AIST Japan
*[http://hdl.handle.net/1926/1470 IGSTK: Building High Quality Roads with Open Source Software], Luis Ibanez, Kitware
*[http://hdl.handle.net/1926/1466 The Surgical Assistant Workstation], Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*[http://hdl.handle.net/1926/1465 The ''cisst'' libraries for computer assisted intervention systems], Anton Deguet, Johns Hopkins Univ.
*[http://hdl.handle.net/1926/1459 An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images], Jonathan Boisvert, Queen’s Univ.
*[http://hdl.handle.net/1926/1461 Simulink Libraries for Visual Programming of VTK and ITK], David Gobbi, Queen’s Univ.
*[http://hdl.handle.net/1926/1458 VV: a viewer for the evaluation of 4D image registration], Pierre Seroul, Univ. Lyon
*[http://hdl.handle.net/1926/1456 MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems], Jian Chen, Chinese Academy of Science
*[http://hdl.handle.net/1926/1455 A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool], Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*[[NeurosurgicalRobotAbstract|Integration of Open Source and Commercial Software for a Neurosurgical Robot System]], Tian Xia, Tamas Haidegger, JHU
*[[CustusAbstract|CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome]], Frank Lindseth, SINTEF Norway
*[http://hdl.handle.net/1926/1462 Distributed database framework for real-time image-guidance in robotic surgery], David Kwartowitz, Mayo Clinic
*[http://hdl.handle.net/1926/1453 Software Architecture of a System for Robotic Surgery], Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Miccai 2008 Systems and Architecture Workshop

2008-09-12T17:42:07Z

Dgobbi: New page: = Systems and Architectures for Computer Assisted Interventions = {|align="right" |{{#imageLink:Logo_miccai2008.png|http://miccai2008.rutgers.edu/}} |} *Location: Kimmel Center, ...

= Systems and Architectures for Computer Assisted Interventions =

{|align="right"
|{{#imageLink:Logo_miccai2008.png|http://miccai2008.rutgers.edu/}}
|}
 
*Location: Kimmel Center, Room 406, New York, NY
*Date: Saturday, September 6, 2008
*Time: 9am - 6pm
 

The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open source community, industry, and researchers in the field. The workshop will include presentations and panel discussions about: 1) existing open source toolkits, 2) open (research) interfaces to medical products, and 3) integrated systems for computer assisted interventions.

One outcome of the workshop will be a technical paper (white paper) that will be
submitted for review to the [http://www.interscience.wiley.com/journal/rcs International Journal of Medical Robotics and Computer Assisted Surgery]. If completed by Oct 2, 2008, the paper will be considered for a special issue on ''New Technologies''.

== NEWS ==

''Aug 5, 2008''

The final program has been modified to start at 9 AM and end at 6 PM, as requested by MICCAI organizers.

''July 29, 2008''

The [[#Final_Program|workshop program]] has now been posted.

We are still awaiting abstracts and/or papers from some invited speakers. Please send these to pkaz@jhu.edu.

== Organizers ==

*Peter Kazanzides, Center for Computer-Integrated Surgical Systems and Technology (CISST ERC), Johns Hopkins University
*Nobuhiko Hata, National Center for Image Guided Therapy (NCIGT), Brigham & Women’s Hospital
*Luis Ibanez, Kitware, Inc.

== Important Dates ==

''Notification of acceptance has been moved to July 29 so that the final program can be announced before the MICCAI early registration deadline. The Insight Journal allows public peer review to be done at any time.''

* July 21, 2008: deadline for paper submissions via the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 Insight Journal]
* July 29, 2008: notification of acceptance for presentation
* September 6, 2008: workshop

== Submission Information ==
We are soliciting submissions that describe
''integrated systems for computer-assisted interventions'', regardless of
whether or not they utilize open source software.
Submissions that describe open source software packages for
computer assisted interventions are also appropriate.
All submissions should be made via the [http://www.insight-journal.org Insight Journal].
A special issue has been created for the [http://www.insight-journal.org/InsightJournalManager/publications.php?journalid=14 ''Workshop on Systems and Architectures for Computer Assisted Interventions at MICCAI 2008''].
Note that the Insight Journal has a LaTeX style file available
[http://public.kitware.com/pub/itk/InsightJournal/InsightJournalSubmissionTemplate.tgz here].

Key points regarding submission:
* Papers may be up to 8 pages in length. Authors are encouraged to include other files with their submission,particularly videos, code, and data. Extended abstracts will be considered, especially if accompanied by other files.
* Every submission immediately appears on the Insight Journal site in the Special Issue on the MICCAI Workshop. Therefore, every submission is available to any registered member of the Insight Journal (and registration is free).
* Submission requires licensing to the Insight Journal the right to distribute your submission under the Creative Commons' "by-attribution" license. Copyright transfer is not required.
* The Insight Journal is a registered digital library. Therefore, your submission is automatically assigned a unique open-archive "handle" that (unlike URLs) persists on the web and that (unlike other web-based database keys) allows your submission to be indexed by Google and other search engines. Handles also serve as a mechanism whereby submissions can be permanently referenced in publications.

== Peer Review ==
Every submission is available for public peer-review. That is, any
registered member of the Insight Journal (and registration is free) is
able to download, score, and comment on any submission to this
workshop. All reviews are public. Anonymous reviews are discouraged.

The workshop committee
will consider the posted reviews, as well as the intent of the
workshop, to select papers for oral presentation. Those
decisions will be announced on or about July 30, 2008.

== Final Program ==

Following is the program for the workshop. The order of talks within a session may be reordered to accommodate speaker requests.

'''09:00 - 09:10 Introduction, Peter Kazanzides, Johns Hopkins University''' 
'''09:10 – 10:10 Industry presentations''' 
*[[StealthLinkAbstract|Medtronic StealthStation™ StealthLink Research Portal]], Leslie Holton, Medtronic
*[http://hdl.handle.net/1926/1464 The daVinci Research Interface], Simon DiMaio, Intuitive Surgical
*[http://www.clarontech.com/API/index.html Micron Tracker: API and other interfaces], Claudio Gatti, Claron Technology
*[[Media:vvlink.pdf|VectorVision Link]], Pratik Patel, BrainLAB
'''10:10 – 10:30 Plenary Session''' 
*Research interfaces for image-guided neurosurgery, Xenophon Papademetris, Yale Univ.
'''10:30 – 10:50 Break''' 
'''10:50 – 11:10 Discussion''' 
*Challenges of open interfaces
'''11:10 – 12:30 CAI Software #1''' 
*[http://www.intelli-si.org/ Open Source Initiative for Surgical Robot Toolkit], Kiyo Chinzei, AIST Japan
*[http://hdl.handle.net/1926/1470 IGSTK: Building High Quality Roads with Open Source Software], Luis Ibanez, Kitware
*[http://hdl.handle.net/1926/1466 The Surgical Assistant Workstation], Russ Taylor, Anton Deguet, Johns Hopkins University, and Simon DiMaio, Intuitive Surgical
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Software and hardware integration strategy for image guided therapy using Open IGT Link], Junichi Tokuda, Brigham & Women’s Hospital
'''12:30 – 13:30 Lunch (on your own)''' 
'''13:30 – 15:30 CAI Software #2''' 
*[http://hdl.handle.net/1926/1465 The ''cisst'' libraries for computer assisted intervention systems], Anton Deguet, Johns Hopkins Univ.
*[http://hdl.handle.net/1926/1459 An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images], Jonathan Boisvert, Queen’s Univ.
*[http://hdl.handle.net/1926/1461 Simulink Libraries for Visual Programming of VTK and ITK], David Gobbi, Queen’s Univ.
*[http://hdl.handle.net/1926/1458 VV: a viewer for the evaluation of 4D image registration], Pierre Seroul, Univ. Lyon
*[http://hdl.handle.net/1926/1456 MITK & 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems], Jian Chen, Chinese Academy of Science
*[http://hdl.handle.net/1926/1455 A XML based component oriented architecture for image guided surgery: illustration for the video based tracking of a surgical tool], Jean-Baptiste Fasquel, IRCAD
'''15:30 – 16:00 Discussion''' 
*Architectures and interoperability
'''16:00 – 16:20 Break''' 
'''16:20 – 17:40 CAI Systems''' 
*[[NeurosurgicalRobotAbstract|Integration of Open Source and Commercial Software for a Neurosurgical Robot System]], Tian Xia, Tamas Haidegger, JHU
*[[CustusAbstract|CustusX: A navigation system and research tool for minimally invasive therapy, improved safety, surgeon confidence and patient outcome]], Frank Lindseth, SINTEF Norway
*[http://hdl.handle.net/1926/1462 Distributed database framework for real-time image-guidance in robotic surgery], David Kwartowitz, Mayo Clinic
*[http://hdl.handle.net/1926/1453 Software Architecture of a System for Robotic Surgery], Hermann Mayer, Technical University of Munich
'''17:40 – 18:20 Discussion and wrap-up''' 
*Successes and unmet needs
*Planning for technical paper (white paper)

Events

2008-09-12T17:24:33Z

Dgobbi: /* 2008 */

__NOTOC__
== Introduction ==

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| NA-MIC organizes a variety of events. The engineering core holds a weekly telephone conference. Workshops address specific research focus areas. Training events aim at training NA-MIC participants and outsiders in NA-MIC technologies. Project weeks are intended for making progress in a variety of projects. The majority of NA-MIC events are hands-on and open to collaborators and interested scientists.
| style="background: #ebeced" colspan="2" align="center"| Example of a Training Event
|-
| style="background: #ebeced"| [[Image:Munich2008-Danielle.jpg|250px]]
| style="background: #ebeced"| The Munich 2008 training workshop in full swing. For more information about the workshop, click [[2008_June_Workshop_Germany|'''here''']].
|}
 

== [[TCON:Main|'''Telephone Conferences''']] ==

== Upcoming Events ==

== 2008 ==
* October 15-16, 2008: '''[[Robarts_Training_Session | NA-MIC kit training event at The University of Western Ontario]]''', London, Ontario, Canada
* December 1, 2008:[[Events:RSNA2008| Tutorial at RSNA]], [http://rsna2008.rsna.org/ RSNA conference website]
* December 8-12, 2008:[[2008_IGT_Project_Week|IGT Hands-on Project Week]], Boston
* Fall Semester 2008 Ibanez and Schroeder teach [http://public.kitware.com/OpenSourceSoftwarePractice/index.php/Main_Page Open Source Software Course] at Rensselaer Polytechnic Institute

== 2009 ==
* '''[[AHM_2009|January 5-9, 2009, AHM,]] [[2009_EAB|EAB,]] [[2009_Winter_Project_Week|Winter Project Week]]'''
* January 8, 2009:[[Events:TutorialContestJan2009| Tutorial Contest:]] announcement of the winners.

== Standing Events ==

* [[TCON:Main|A list of all upcoming and past teleconferences is available here]].
* [[Engineering:Programming_Events|Hands on Project Events]]
* [[Slicer:Developer_Meetings|Slicer developer meetings are here]].

== Past Events ==

=== 2008 ===
* September 10, 2008: '''[[Miccai_2008_Tutorial| Interfacing third-party software with the NA-MIC Kit]]''': Tutorial at MICCAI 2008, New-York City
* September 10, 2008: '''[[Miccai_2008_Prostate_Workshop| Prostate image analysis and computer-assisted intervention]]''': Workshop at MICCAI 2008, New-York City
* September 5, 2008: '''[[Miccai_2008_Systems_and_Architecture_Workshop| Systems & architecture for computer assisted intervention]]''': Workshop at MICCAI 2008, New York City
* September 5, 2008: '''[[OpenIGTLink/Workshop/miccai2008|OpenIGTLink Workshop]]''': Workshop at MICCAI 2008, New York City
* September 3, 2008: '''[[Stanford_2008_Slicer_Workshop| Slicer Training in Stanford]]'''
* September 6, 2008: '''[[Miccai_2008_Segmentation_Workshop| Segmentation in the Clinic Challenge]]''': Workshop at MICCAI 2008, New-York City
* August 21-22, 2008: [[Events:August2008XNATDesktop|Visit by WashU Developers to Boston for Discussions of XND]]
* August 15, 2008: [[Events:NCI_Workshop_August_2008|August 15 2008, NA-MIC Workshop at NCI]]
* August 13-14, 2008: [[Events:August_2008_NCBC_AHM|August 13-14 2008, NCBC all hands meeting]]
* July 30 - August 1, 2008: [[2008_July_RFA_Experiment_Georgetown | RFA Interventional Experiment at Georgetown University]]
* August 1, 2008: [[Events:August2008XNATDesktop| Planning tcon for XNAT Desktop Slicer interface]]
* Steve Pieper presented NA-MIC and Slicer Module development at the [http://www.ipam.ucla.edu/programs/mbi2008/ IPAM MBI] Summer School [[Media:Pieper-UCLA-MBI-2008-07-17.ppt|(Slides)]]
* July 10 or 11, 2008: [[2008 July Slicer Introduction to Princess Margaret Hospital|Slicer Introduction to Princess Margaret Hospital]]
* July 23, 2008: [[2008_July_Slicer_IGT_VV_Link_Session_II|Slicer IGT Integration with Brainlab via VVLink]]
* June 23-27, 2008: '''[[2008_Summer_Project_Week|Summer Project Week]]'''
* June 26, 2008: [[2008_June_IGT_Tumor_Growth_Model_Demo_SPL|June 26, 2008, 4pm, Tumor Growth Model Software Demo at SPL]]
* June 16-17, 2008: '''[[2008 June Workshop Germany |Training Event in Germany]]'''
* May 21, 2008: [[2008_Core_1_UNC_Utah_DTI| Core 1 UNC & Utah Technical Meeting about DTI tool development at Utah]]
* May 22-23, 2008: [[2008_Core_1_Core_3_mtg|Cores 1-3 Technical Meeting at Utah]]
* March - June, 2008: [[3D_Ultrasound_Module_in_Slicer_3|Slicer IGT training for graduate students at SJTU, Shanghai, China (every Thursday 10 am - noon)]]
* May 21, 2008: Kilian Pohl presented on segmentation tools in 3D Slicer at the [http://www.dkfz.de/en/mbi/index.html Division of Medical and Biological Informatics, DKFZ, Germany] ([[media:Pohl_dkfz_08.pdf | Slides]])
* Noon, May 12, 2008: [[Events:May12_2008_FirstMondaySeminar | Brigham and Women's Hospital, First Monday Seminar Talk given by Drs. Ichiro Sakuma and Nassir Navab]]
* May 8, 2008: [[Events:2008_05_08_Collaboration_UWA_Perth|Conference Call to Explore Collaboration with Adam Wittek, UWA Perth]]
*May 2, 2008: [[2008_5_2_Hata_Talk_U_Michigan | Nobuhiko Hata's talk at Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI ]]
* [[Slicer3:Slicer3_Workshop_UNC_Chapel_Hill_2008| April 14, 2008: Full day Slicer 3 Users and Plug-in Workshop]] hosted by UNC-Chapel Hill faculty
* April 7, 2008: [[2008_David_Hawkes|2008 Dr. David Hawkes of UCL's visit to SPL]]
* March 31- Apr 11, 2008: [[2008_Platel_visit_from_TUE|2008 Dr. Platel's, IGT grp leader from Technical University Eindhoven, to SPL]]
* March 24-27, 2008: [[2008_Engineering_review_at_Utah|2008 Engineering review at Utah]]
* [[Events:HST-563-March2008|March 19, 2008: Harvard-MIT Division of Health Sciences and Technology (HST), Lecture on Interventional MRI by Hata, Kikinis, HST 563]]
* March 12, 2008: Steve Pieper presented on the NA-MIC Kit and 3D Slicer at the [http://www.cisst.org/wiki/Seminar_2008_03_12_3D_Slicer Johns Hopkins CISST] ([[media:Pieper-JHU-seminar-2008-03-12.ppt | Slides]])
* March 10-11, 2008: [[IGT:March_2008_IGT_Workshop|IGI Workshop, Rockville, MD]]
* Discussion of NA-MIC Kit for Cardiac EP with [http://www.bidmc.harvard.edu/cmr BIDMC].
* [[Slicer3:Spring-2008-User-Training|February 20th, 2008, Spring 2008 Slicer3 User Training Workshop ]] at the SPL 1249 Boylston St, Boston
* [[Slicer3:MiniRetreat February 5-7, 2008 | February 5-7, 2008, Slicer3 Mini-Retreat, Boston]]
* '''[[AHM_2008|January 7-11, 2008, AHM,]] [[2008_EAB|EAB,]] [[2008_Winter_Project_Week|Winter Project Week]]

=== 2007 ===
*[[2007_December_Slicer_IGT_Programming|December 12-14, 2007, Slicer IGT Programming Event]]
*[http://www.insightsoftwareconsortium.org/wiki/index.php/2007_MICCAI_Open_Workshop Nov 2, 2007: Third Annual Open Source Workshop at MICCAI]
*[[2007_October_Collaboration_Visit_Robert_Israel|October 14-20, 2007, Robert Israel Collaboration Visit to SPL]]
*2007 October 16-17: [http://nbirn.net/about/current/ahm2007.shtm BIRN AHM] Query Atlas and Qdec interfaces in Slicer 3 presented at the BIRN AHM.
** [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Module:QueryAtlas See this page] for links to QueryAtlas slides, movies and example datasets.
** [http://wiki.na-mic.org/Wiki/index.php/Image:Slicer3QDEC_AHM2007.ppt See this page] for links to Qdec slides.
*[[SanteFe.Tractography.Conference | October 1-2, 2007, Contrasting Tractography Methods Conference, Santa Fe]]
*[[Engineering:September 12, 2007 | September 12, 2007, Engineering End of Summer Meeting]]
*[[GPU.Enabled.Tools.Meeting | September 11, 2007, GPU-enabling of NA-MIC Algorithms, Boston]]
* Aug 21, 2007: [[DBP2:UNC:Cortical Thickness Roadmap | UNC DBP Roadmap Tcon]]
* '''[[2007_Programming/Project_Week_MIT|June 25-29, 2007, Summer Programming/Project Week at MIT]]'''
* [[Training:OHBM2007_Training_Workshop|June 9, 2007, OHBM DTI Training Workshop, Chicago]]
*[[2007_Pohl_at_CCB|June 1, 2007, Pohl Talk at CCB: A Hierarchical Segmentation Algorithm for MR Brain Images]]
* '''[[2007_Core_1_Meeting|May 29-31, 2007, Annual Core 1 Workshop, Boston]]'''
* April 24 Steve Pieper presented Slicer3 and the NA-MIC Kit to the [http://gray.mgh.harvard.edu/content/index.php Medical Physics group at MGH] [http://wiki.na-mic.org/Wiki/images/9/9c/Pieper-MGH-medical-physics-2007-04-24.ppt (slides)]
* [[Slicer3:MiniRetreat March 29, 30, 2007| March 29, 30, 2007, Slicer3 Mini-Retreat, Boston]]
* Feb 21-22 Vince Calhoun from MIND is visiting at MIT and MGH [http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1349 Talk announecement]
* Feb 3 and 10, 2007: [http://mri.radiology.uiowa.edu/mediawiki/index.php/ITK_Programming_Short_Course_-_Feb_2007 Iowa ITK Programming Short Course]
* [[Slicer3:MiniRetreat February 7-8, 2007| Feb 7-8, 2007, Slicer3 Mini-Retreat, Boston]]
* Jan 29 2007: [[P41-2007-Joint-Retreat | CFIT NAC P41 2007 Joint Retreat]]
* [[2007-01-16 Core 5, Core 6 Summit]]
* '''[[AHM_2007|Jan 10-11-12, 2007: Third All Hands Meeting, EAB, Project Half Week]]'''

=== 2006 ===

* [[Slicer3:Alpha-release|2006 December 12: Slicer3 retreat at Kitware]]
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]
* [[Slicer3:Usability#Report_from_Usability_Session_with_PNL_at_BWH_11.2F15.2F06|November 15, 2006: Usability session with PNL at BWH ]]
* [[Training:User_Workshop_Fall_HCNR_2006|November 1, 2006: NA-MIC Training Workshop at the Harvard Center for Neurodegeneration and Repair, Boston. ]]
* [[Oct-26-2006-MIND-visit_Visiting_the_MIND_institute|October 26, 2006: New DBP MIND Institute Visit]]
* October 23-26, 2006 [http://www.nbirn.net/press/current/ahm2006.shtm <nowiki>| BIRN All Hands Meeting</nowiki>]
* [[IGT:October_2006_IGT_Workshop|October 19-20 2006, NCIGT and NA-MIC Workshop on Open System Architectures for Image-Guided Therapy]]
* [[Core1-3-meeting-2006|October 17 2006: Coordination meeting]] between Core 1 and Core 3 to plan the specifics for the third and last year of the current DBP's
* [http://www.insightsoftwareconsortium.org/wiki/index.php/2006_MICCAI_Open_Workshop MICCAI_2006 October 1, 2006: Open Source Workshop at MICCAI 2006, Copenhagen]
* [[2006_September_Slicer3_Update|September 19-20, 2006 Slicer 3 Update Meeting in Boston]]
* September 14-15, 2006: We have been invited to participate in [http://usms.nist.gov/workshops/bioimaging.htm NIH Workshop on Standards in Change Measurement]. This workshop will potentially set the stage for additional workshops that focus on Image Guided Interventions and Open Source standards.
* Sept-06-2006, [http://www.ibmisps.org/pdf/InformationparticipantsANGLAIS.pdf 2006 IBMISPS conference:] [[Media:Kikinis-IBMISPS-09-06-2006.ppt|talk]] by [[media:Kikinis-FOSS.ppt|R. Kikinis on FOSS]] ([[2006 FOSS Abstract Kikinis]])
* [[NIH:_2006_All_NCBC_Meeting|July 17-19, 2006, All NCBC All Hands Meeting at NIH]]
* [[Training:NLM_Workshop_2006|July 19, 2006: NA-MIC Training Workshop at NLM]]
* [http://bsp.csie.nctu.edu.tw/lssa06/ July 13-14, 2006: 2nd IEEE-NLM International Life Science Systems and Applications Workshop, Lister Hill Auditorium, NIH, chaired by Stephen Wong, co-sponsored by IEEE, NLM, and NAMIC]
* July 2nd: Ron Kikinis [[Media:NA-MIC-Kit-07-01-2006.ppt| presentation]] (28MB ppt file) at the [http://www.future-cad.org/fcad/Docs/CFP_for_2nd_Int_Sympo_2006_ver3.2.pdf The 2nd International Symposium on Intelligent Assistance in Diagnosis of Multi-Dimensional Medical Images ]
* '''[[2006_Programming/Project_Week_MIT|June 26-30, 2006, Summer Programming/Project Week at MIT]]'''
* [[Georgia_Tech_visit_to_UNC%2C_June_8-9|June 8-9, 2006, Georgia Tech visit to UNC: Shape Analysis Discussion]]
* [[Slicer:Slicer3-June-5-2006-Retreat|June 5, 2006, Slicer 3 Retreat]]
* May 30, 2006 [http://www.cimit.org/forum/forum.html CIMIT Forum] with Steve Pieper and Luis Ibanez ([[Media:CIMIT-BIRN-update-2006-05-30.ppt| Steve's Slides]])([[Media:CIMIT-2006-IGSTK-InsightJournal.ppt| Luis' Slides]])
* [[Training:DTI_Workshop|May 26, 2006 UNC-Chapel Hill NA-MIC DTI Analysis Training Workshop]]
* [[Algorithms:Core1Visit_May06|May 23-24, 2006: NA-MIC Core 1 meeting at UNC]]
* [[DBP:Harvard:Collaboration:GTech#Progress|May 15 2006: Delphine Nain at the PNL]]
* [[Slicer:StevePieper_RonKikinis_VisitToDartmouth_051906|May 19, 2006: Steve Pieper and Ron Kikinis Visit to Dartmouth]]
* [[Training:NIH_Workshop_2006|April 27, 2006: NA-MIC Training Workshop at NIH]]
* April 24, 2006 [http://www.nimh.nih.gov/neuroinformatics/springagenda2006.cfm The Human Brain Project: Linking Within and Beyond] Natcher Conference Center, NIH Campus, Bethesda, Maryland: National Alliance for Medical Image Computing: Science & Technology of One National Center for Biomedical Computing [[Media:NA-MIC_Kit_revised.ppt| (this is a slightly modified version of the presentation)]]
* [[DBP:Harvard:Collaboration:Toronto|April 12-13, 2006: James Kennedy and Aristotle Voineskos at the PNL]]
* [[Training:MIND_Institute_Workshop_Spring_2006|April 10-11, 2006: NA-MIC Training Workshop at MIND Institute, New Mexico]]
* Steve Pieper presented the NA-MIC Kit at [http://www.biomedicalimaging.org ISBI] 2006 on April 7, 2006 ([[Media:NA-MIC-2006-04-07-ISBI.ppt| Slides]], [[Media:Pieper-ISBI-2006-revised.pdf| Paper]]).
* [[Slicer3:_Alpha1_Meeting|April 3-4, 2006: Design Review and Work meeting on Slicer3 (alpha1 release)]]
* [[DBP:Sylvain_Doug_visit_Dartmouth_Feb_22_2006|Feb 22, 2006: Sylvain Bouix to visit Dartmouth]]
* [[Engineering:Slicer3_and_GPU|Feb 22-24, 2006: Meeting at Kitware to discuss Slicer3 (thurs) and GPU programming (fri)]]
* [[IGT:Workshop_Feb_2006|Feb 20-23, 2006: IGT and FUS Workshops]]
* [[Training:User_Workshop_SPL_Winter_HCNR_2005|January 24, 2006: HCNR User Training Workshop at the Surgical Planning Lab in Boston]]
* '''[[AHM_2006:AHM_2006|January 8-13, 2006: The Second All-Hands-Meeting and Programming Event in Salt Lake City, Utah]]'''

=== 2005 ===

* [[DBP:Marek_Kubicki_visit_Dartmouth_December_20_2005|December 20, 2005: Marek Kubicki visit to Dartmouth]]
* [[Collaboration:GT-UCI|December 17, 2005: Jim Fallon from UC Irvine visit to Georgia Tech for work on Rule-Based Segmentation]]
* [[DBP:Andy_Saykin_visit_BWH_December_14_2005|December 14, 2005: Andy Saykin and Group visit to Brigham and Women's Hospital]]
* [[DBP:Dartmouth_Harvard_Slicer_Training_12_01_2005|December 1, 2005 Dartmouth Group Slicer Training Followup at Harvard, 1249 Boylston]]
* [http://rsna2005.rsna.org/rsna2005/V2005/index.cvn November 27-December 2, RSNA 2005, Chicago: Slicer session at the Open source imaging tools workshop ]
* [[DBP:Harvard:Collaboration:GTech#Progress|November 18 2005: Ramsey Al-Hakim at the PNL]]
* [[Collaboration:GT-Kitware|November 17-18, 2005: John Melonakos at Kitware -- Bayesian Classification Filter addition to ITK]]
* [[IGT:2005_Nov_16_IGT_Consortium_Kickoff|November 16, 2005: IGT Consortium Kickoff]]
* [[Collaboration:UNC-UCI|November 16, 2005: Jim Fallon and Martina from UC Irvine visit to UNC on DTI tools and clinical projects]]
* [[Engineering:Slicer3.0_November_15_2005|November 15, 2005, noon-5pm: Slicer 3.0 Meeting at SPL, Boston]]
* [[Dissemination:MICCAI_Workshop_2005|ISC and NA-MIC Workshop on Open Source Toolkits, Applications, and their uses in Medical Image Analysis at MICCAI]]
* October 29, 2005 (Thursday): Informal NA-MIC Lunch at MICCAI, Palm Springs, CA
* [[2005_AHM:_3D_Slicer/Freesurfer_Workshop|October 20, 2005: Slicer Training Workshop, AHM BIRN San Diego, California]]
* [[Dissemination:EPFL_Workshop_2005|October 5-7, 2005, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland: Advanced ITK and Slicer Workshop]]
* [[Collaboration:UNC-PNL|October 7, 2005, UNC visit at the Psychiatry NeuroImaging Laboratory]]
* [[Training:User_Workshop_SPL_Fall_2005|September 30, 2005. User Training Workshop at the SPL on Boylston St, Boston.]]
* [[Engineering:Core_3_Programming_Week#1_Feedback|September 26-27-28, 2005. DBP and Engineering Session on Feedback from Programming Week Projects, and Planning the next 6-months]]
* [[Training:User_Workshop_MGH_Summer_2005|September 16, 2005. User Training Workshop at MGH.]]
* [[Dissemination:CSB2005|August 11 2005 Invited Lecture about NA-MIC.]]
* [[Collaboration:Workshop_July_20_2005|July 20, 2005. UNC visit of Georgia Tech for collaborative work on shape and DTI algorithms.]]
* [[Engineering:Programmers_Week_Summer_2005|June 27-July 1, 2005. Programming Week in Boston]]
* [[Dissemination:NCRR_NIBIB_PI_Meeting_June_22-23_2005|June 22-23, 2005, NCRR/NIBIB PI Meeting]]
* [[Collaboration:Workshop_June_16-19_2005|June 16-19, 2005. Georgia Tech visit of UC-Irvine for collaborative work on anatomically accurate algorithms.]]
* [[Dissemination:Workshop_May_26-27_2005|May 26-27, 2005. User Training and Dissemination Workshop at Dartmouth]]
* [[DBP:Andy_Saykin_visit_BWH_April_21_2005|April 21-22, 2005: Andy Saykin visit to Brigham and Women's Hospital and MIT]]
* March 25, 2005. University of Utah visit of Harvard VA for collaborative work on DTMRI.
* [[FBIRN:retreat2005|March 21-23,2005: fBIRN Retreat in Irvine with User Tutorials for Slicer, Brains2 Wednesday on March 23]]
* [[AHM_2005:Main|February 20-22, 2005 AHM in SLC]]
* [[Dissemination:Workshop_Feb17-18_2005|February 17-18, 2005 Dissemination Workshop at UCSD]]
* January 26, 2005. Slicer User Workshop at BWH: [[Slicer:User_Workshop_Jan26|Information for Atendees]]
* January 24-25, 2005. Dissemination Workshop at [[Dissemination:Workshop_Jan24-25_Boston|Agenda]], [[Dissemination:Workshop_Jan2005_Interested_Attendee_List|List of Participants]], [[Talk:Dissemination:Workshop_Jan24-25_Boston_Feedback|Attendee Feedback]]
* January 17-18, 2005. [http://www.imaginggenetics.uci.edu First International Imaging Genetics Conference] at the Beckman Center of the National Academy of Sciences in Irvine, CA.

=== 2004 ===

* December 9-10, 2004. Dissemination Workshop at SPL, BWH:[[Dissemination:Workshop_Dec9-10_Boston|Agenda]], [[Dissemination:Workshop_Dec9-10_Boston_Presentations|Presentations]], [[Dissemination:Workshop_Dec9:10_Attendees_List|List of Participants]], [[Dissemination:Workshop_Dec9:10_Summary|Summary]],[[Talk:Dissemination:Workshop_Dec9-10_Boston_Feedback|Attendee Feedback]]
* November 16, 2004. Dissemination Meeting: [[Dissemination:Kickoff_Agenda|Agenda]], [[Dissemination:Kickoff_Summary|Summary]]
* [[Kickoff:Main|October 15, 2004. NA-MIC Kickoff Meeting]]

DBP2:Queens:Roadmap

2008-09-05T15:00:55Z

Dgobbi: /* Schedule */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3. The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (David) --- REMOVED (use automatic segmentation instead) ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- DONE ---

09/19/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

09/12/2008 Integrate optical encoders with our Slicer module (David)

09/19/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

09/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

10/17/2008 Workflow validation (Siddharth)

10/31/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

11/07/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-19T12:23:08Z

Dgobbi: /* Schedule */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3. The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- ON HOLD ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:56:53Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3. The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:56:28Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>
The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:56:18Z

Dgobbi:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:55:16Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images.

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:50:36Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
{|
|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

File:TRProstateBiopsyRobot.jpg

2008-08-12T20:48:13Z

Dgobbi: View of the transrectal prostate biopsy robot.

View of the transrectal prostate biopsy robot.

DBP2:Queens:Roadmap

2008-08-12T20:47:42Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}

{|
[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:47:08Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
{|
[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:46:43Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

<center>
[[Image:TRProstateBiopsyRobot.jpg|thumb|320px|The transrectal prostate robot.]]
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:37:47Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Fiducial calibration of interventional robot]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:37:20Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|320px|Calibration of interventional robot with fiducials]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

File:TRProstateTargeting.jpg

2008-08-12T20:36:55Z

Dgobbi: TRProstateBiopsyModule targeting step.

TRProstateBiopsyModule targeting step.

File:TRProstateCalibration.jpg

2008-08-12T20:36:10Z

Dgobbi: Calibration step for TRProstateBiopsy module.

Calibration step for TRProstateBiopsy module.

DBP2:Queens:Roadmap

2008-08-12T20:35:07Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|270px|Calibration of interventional robot with fiducials]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|270px|Trajectory calculation from target locations]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]

DBP2:Queens:Roadmap

2008-08-12T20:34:36Z

Dgobbi: /* Slicer Transrectal Prostate Biopsy Module */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:JHU|JHU DBP 2]]
__NOTOC__
== Objective ==

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

*Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
*Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
*Prostate Measurement: Measure volume of all segmented structures
*Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
*Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

== Roadmap ==

We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

=== Current Status of System Components ===

*Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
*Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
*Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
*Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
*Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

=== Slicer Transrectal Prostate Biopsy Module ===

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3.

<center>
{|
|[[Image:TRProstateCalibration.jpg|thumb|170px|Calibration of interventional robot with fiducials]]
|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|170px|Trajectory calculation from target locations]]
|}
</center>

=== Schedule ===

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Csaba, Gabor) --- DONE ---

10/22/2007 Create GUI templates for the workflow steps (David) --- DONE ---

Device Modeling:

12/15/2007 Conversion of engineering data into VTK-viewable objects (David) -- DONE --

Data Display:

12/15/2007 Provide display logic for targets and prostate outlines (David) --- DONE ---

Measurement Tools:

07/01/2008 Semi-automatic identification of fiducials via thresholding & centroids (Csaba) --- DONE ---

07/01/2008 Logic for robot registration with fiducials (Csaba) --- DONE ---

08/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David) --- IN PROCESS ---

Biopsy Planning:

07/01/2008 Calculations for robot trajectory based on target position (Csaba) --- DONE ---

08/08/2008 Implement planning tools (display, logic) in Slicer3 (David) --- MOSTLY DONE ---

08/15/2008 Verification against pre-existing software and data (David, Siddharth)

Robot positioning:

08/22/2008 Integrate optical encoders with our Slicer module (David)

08/22/2008 GUI targeting readouts for optical encoders (David, Siddharth)

Integration of contour-based prostate display into Slicer3:

08/29/2008 2D Contour outline display of 3D models in Slicer (David)

Verification and testing of integrated system

09/12/2008 Workflow validation (Siddharth, David)

09/12/2008 Complete testing, performance characterization (Siddharth)

Tutorial and Documentation

Continuous unit documentation (David)

09/26/2008 Complete tutorial with example data

=== Team and Institutes ===

*PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
*Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
*Software Engineer Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
*Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
*JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University, csoma at jhu.edu
*NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital, hayes at bwh.harvard.edu
*NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech, tannenba at ece.gatech.edu
*Host Institutes: Queen's University & Johns Hopkins University

[[Category: Segmentation]] [[Category: Registration]] [[Category: Slicer]] [[Category: Prostate]]