NAMIC Wiki - User contributions [en]

2017 Winter Project Week/ROS Surface Scan

2016-12-08T14:20:20Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank (Institute of Mechatronic Systems, Leibniz University of Hannover, Germany)
*Junichi Tokuda (SPL, Boston)
*Longquan Chen (SPL, Boston)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Tracking of 3D print model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting after registration of the robot to slicer(ROS).

|

* For objective 1
** Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
* For objective 2
** A 3D printed organ will be used for surface scan, and 3d model of the organ is also available.
** Perform real time particle filter registration on the surface scan data and the 3d organ model.
* For objective 3
** Registration of the robot and Slicer(or ROS) could be done by manually by matching the points from surface scan and a 3D robot model. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
** Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week/ROS Surface Scan

2016-12-08T14:17:09Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank (Institute of Mechatronic Systems, Leibniz University of Hannover, Germany)
*Junichi Tokuda (SPL, Boston)
*Longquan Chen (SPL, Boston)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Registration of segmented model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting based on the registration.

|

*
** Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
*
** A 3D printed organ will be used for surface scan, and 3d model of the organ is also available.
** Perform ICP registration on the surface scan data and the 3d organ model, (corse-to-fine registration maybe be needed)
*
** Registration of the robot and Slicer could be done by manually by matching the points from surface scan and a 3D robot model. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
** Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week/ROS Surface Scan

2016-12-08T14:16:08Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank (Institute of Mechatronic Systems, Leibniz University of Hannover, Germany)
*Junichi Tokuda (SPL, Boston)
*Longquan Chen (SPL, Boston)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Registration of segmented model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting based on the registration.

|

*
** Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
*
** A 3D printed organ will be used for surface scan, and 3d model of the organ is also available.
** Perform ICP registration on the surface scan data and the 3d organ model, (corse-to-fine registration maybe be needed)
*
** Registration of the robot and Slicer could be done by manually by matching the points from surface scan and a 3D robot model. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
** Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week/ROS Surface Scan

2016-12-07T23:21:59Z

Lchen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank (Institute of Mechatronic Systems, Leibniz University of Hannover, Germany)
*Junichi Tokuda (SPL, Boston)
*Longquan Chen (SPL, Boston)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Registration of segmented model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting based on the registration.

|

* Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
* A 3D printed organ will be used for surface scan, and 3d model of the organ is also available. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
* Registration of the robot and Slicer could be done by manually by matching the points from surface scan and a 3D robot model.
* Perform ICP registration on the surface scan data and the 3d organ model, (corse-to-fine registration maybe be needed)
* Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week/ROS Surface Scan

2016-12-07T23:21:47Z

Lchen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank (
Institute of Mechatronic Systems, Leibniz University of Hannover, Germany)
*Junichi Tokuda (SPL, Boston)
*Longquan Chen (SPL, Boston)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Registration of segmented model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting based on the registration.

|

* Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
* A 3D printed organ will be used for surface scan, and 3d model of the organ is also available. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
* Registration of the robot and Slicer could be done by manually by matching the points from surface scan and a 3D robot model.
* Perform ICP registration on the surface scan data and the 3d organ model, (corse-to-fine registration maybe be needed)
* Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week/ROS Surface Scan

2016-12-07T22:39:24Z

Lchen: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

*Tobias Frank
*Junichi Tokuda
*Longquan Chen

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Transmission of poly data ( from surface scan ) between ROS environment and Slicer via ROS-OpenIGTLink-bridge
* Registration of segmented model data with the real time surface scan data.
* Ask a 2 DOF Lego robot to perform targeting based on the registration.

|

* Transmission of the poly data could be directly using the PolydataMessage, or compress the data first and send via VideoMessage.
* A 3D printed organ will be used for surface scan, and 3d model of the organ is also available. Under the 3d model, a 2D flat desktop model is attached. This 2D flat desktop model is the working space of the robot
* Registration of the robot and Slicer could be done by manually by matching the points from surface scan and a 3D robot model.
* Perform ICP registration on the surface scan data and the 3d organ model, (corse-to-fine registration maybe be needed)
* Targets are selected from the desk model in Slicer. The robot is asked to perform targeting on the these targets.
|

*
|}

==Background and References==

2017 Winter Project Week

2016-12-07T22:11:44Z

Lchen: /* IGT */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

'''Welcome to the web page for the 24th Project Week!'''
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 <br>
Access code: 7327389 <br>

[[media:TollFree.png|International conference call numbers]] <br>
Access code: 7327389 <br>

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day <br> (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==

'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)

== Infrastructure ==
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)

== DICOM ==

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].

File:AudioSimulator.zip

2016-06-27T10:04:36Z

Lchen: Lchen uploaded a new version of File:AudioSimulator.zip

This is a simple simulator for audio test
Only for unix-based system as the lo library has build issue on Window system

2016 Summer Project Week/Auditory Display

2016-06-27T09:56:45Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS
* Tamas Ungi
* Rocio Lopez
* Elvis Chen
*Julian Hettig

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [http://www.na-mic.org/Wiki/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)
*coverage of needle in US

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* common sound synthesis software: [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider] DOWNLOAD PUREDATA EXTENDED>>> [https://puredata.info/downloads/pd-extended here]
* Test program for Puredata to listen for incoming OSC messages: [http://wiki.na-mic.org/Wiki/images/8/81/Test_incoming_OSC.zip link]
* libraries for OpenSoundControl include C++: [http://liblo.sourceforge.net/ liblo], Python: [http://das.nasophon.de/pyliblo/ PyLiblo]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]
* Tried out iplementing liblo library for OSC messages, this workson Mac but not well on Windows.
* Switched to python-based library, which works well. Rocio tried this out but not enough time to integrate with their existing apps.
* Friendly contact between groups who are interested in working together (Rocio, Tamas, Elvis, Longquan)

*[[Code from Jay Jagadeesan for OgenIGTLink]], [http://www.na-mic.org/Wiki/images/3/3d/ReceiveClient.cxx.zip here as zip.]
*Only for Linux and Mac system, as the "lo" library has some build issue with visual studio. For windows user, it is recommended to use the python version of lo [http://das.nasophon.de/pyliblo/ Python library for lo]
*[http://www.na-mic.org/Wiki/index.php/File:AudioSimulator.zip A small lo simulator from Longquan Chen]
** This simulator use the lo library, sends note to the local/remote server running PD-Extended.
** Instructions about how to build and test the program is written in the readme.txt file
</div>
</div>

2016 Summer Project Week/Auditory Display

2016-06-27T09:54:57Z

Lchen: /* Project Description */

2016 Summer Project Week/Auditory Display

2016-06-27T09:52:33Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS
* Tamas Ungi
* Rocio Lopez
* Elvis Chen
*Julian Hettig

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [http://www.na-mic.org/Wiki/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)
*coverage of needle in US

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* common sound synthesis software: [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider] DOWNLOAD PUREDATA EXTENDED>>> [https://puredata.info/downloads/pd-extended here]
* Test program for Puredata to listen for incoming OSC messages: [http://wiki.na-mic.org/Wiki/images/8/81/Test_incoming_OSC.zip link]
* libraries for OpenSoundControl include C++: [http://liblo.sourceforge.net/ liblo], Python: [http://das.nasophon.de/pyliblo/ PyLiblo]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]
* Tried out iplementing liblo library for OSC messages, this workson Mac but not well on Windows.
* Switched to python-based library, which works well. Rocio tried this out but not enough time to integrate with their existing apps.
* Friendly contact between groups who are interested in working together (Rocio, Tamas, Elvis, Longquan)

[[Code from Jay Jagadeesan for OgenIGTLink]], [http://www.na-mic.org/Wiki/images/3/3d/ReceiveClient.cxx.zip here as zip.]
Only for Linux and Mac system, as the "lo" library has some build issue with visual studio. For windows user, it is recommended to use the python version of lo [http://das.nasophon.de/pyliblo/ Python library for lo]
[http://www.na-mic.org/Wiki/index.php/File:AudioSimulator.zip Simplified version from Longquan Chen]
</div>
</div>

2016 Summer Project Week/Auditory Display

2016-06-27T09:51:22Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS
* Tamas Ungi
* Rocio Lopez
* Elvis Chen
*Julian Hettig

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [http://www.na-mic.org/Wiki/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)
*coverage of needle in US

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* common sound synthesis software: [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider] DOWNLOAD PUREDATA EXTENDED>>> [https://puredata.info/downloads/pd-extended here]
* Test program for Puredata to listen for incoming OSC messages: [http://wiki.na-mic.org/Wiki/images/8/81/Test_incoming_OSC.zip link]
* libraries for OpenSoundControl include C++: [http://liblo.sourceforge.net/ liblo], Python: [http://das.nasophon.de/pyliblo/ PyLiblo]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]
* Tried out iplementing liblo library for OSC messages, this workson Mac but not well on Windows.
* Switched to python-based library, which works well. Rocio tried this out but not enough time to integrate with their existing apps.
* Friendly contact between groups who are interested in working together (Rocio, Tamas, Elvis, Longquan)

[[Code from Jay Jagadeesan for OgenIGTLink]], [http://www.na-mic.org/Wiki/images/3/3d/ReceiveClient.cxx.zip here as zip.]
Only for Linux and Mac system, as the "lo" library has some build issue with visual studio. For windows user, it is recommended to use the python version of lo [http://das.nasophon.de/pyliblo/]
[http://www.na-mic.org/Wiki/index.php/File:AudioSimulator.zip Simplified version from Longquan Chen]
</div>
</div>

File:AudioSimulator.zip

2016-06-27T09:50:02Z

Lchen: This is a simple simulator for audio test Only for unix-based system as the lo library has build issue on Window system

This is a simple simulator for audio test
Only for unix-based system as the lo library has build issue on Window system

2016 Summer Project Week/Auditory Display

2016-06-22T14:09:08Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [http://www.na-mic.org/Wiki/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Connect OpenIGTLink to OpenSoundcontrol for use in common sound synthesis software such as [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider]
* libraries for OpenSoundControl include [http://liblo.sourceforge.net/ liblo], [http://das.nasophon.de/pyliblo/ PyLiblo]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]

[[Code from Jay Jagadeesan for OgenIGTLink]], [http://www.na-mic.org/Wiki/images/3/3d/ReceiveClient.cxx.zip here as zip.]
http://www.na-mic.org/Wiki/images/9/98/ReceiveClient.txt
</div>
</div>

File:ReceiveClient.txt

2016-06-22T14:07:17Z

Lchen: Simple example to send audio data]

Simple example to send audio data]

2016 Summer Project Week

2016-06-22T14:02:22Z

Lchen: /* Augmented Reality */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9am-10am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''Background'''=
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world and is led by [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD]. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

An introduction and summary of all previous Project Events is available [[Project_Events|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Guidelets | Guidelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Mónica García, Javier Pascau)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells, Christian Hansen)
* [[2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs | Intraoperative Imaging in Hybrid ORs]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)

=== Infrastructure ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

=== Augmented Reality ===
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

=== Informatics ===
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine, Andrey Fedorov)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso)

=== Atlas construction ===
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI]] (Fernando Pérez García)

=== Tutorial===
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS (Mon)
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Jorge Onieva, BWH/HMS, Boston

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/Auditory Display

2016-06-22T14:00:02Z

Lchen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [http://www.na-mic.org/Wiki/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Connect OpenIGTLink to OpenSoundcontrol for use in common sound synthesis software such as [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider]
* libraries for OpenSoundControl include [http://liblo.sourceforge.net/ liblo], [http://das.nasophon.de/pyliblo/ PyLiblo]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]

[[Code from Jay Jagadeesan for OgenIGTLink]], [http://www.na-mic.org/Wiki/images/3/3d/ReceiveClient.cxx.zip here as zip.]

</div>
</div>

2016 Summer Project Week

2016-06-20T10:57:58Z

Lchen: Undo revision 93071 by Christian.askeland (talk)

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9am-10am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''Background'''=
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world and is led by [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD]. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

An introduction and summary of all previous Project Events is available [[Project_Events|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Guidelets | Guildelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Mónica García, Javier Pascau)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells, Christian Hansen)
* [[2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs | Intraoperative Imaging in Hybrid ORs]] (Sarah Frisken, Anna Roethe, Prashin Unadkat, Christian Hansen)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials]] (Thomas Vaughan)

=== Infrastructure ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

=== Augmented Reality ===
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen)

=== Informatics ===
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso)

=== Atlas construction ===
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI]] (Fernando Pérez García)

=== Tutorial===
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices

2016-06-13T11:43:52Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Scheherazade Kraß
* Longquan Chen

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Obtaining a better understanding of OpenIGTLink:
# How to use and integrate it in different robotic devices using:
## MeVisLab applications
## Slicer

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

<h5>PLUS Platform</h5>
*Plus is an open-source software toolkit for data acquisition, pre-processing, and calibration for navigated image-guided interventions. OpenIGTLink is integrated inside for communication.
#Website: https://app.assembla.com/spaces/plus/wiki
#OpenIGTLInk is only a communication protocal, the control of the medical devices is achieved by PLUS
#Kuka LBR is supported

<h5>Robotic Devices</h5>
*Defining different workflows for communication between robotic device and MeVislab applications, including sending/receiving strings, image sets and control commands for:
#The Kuka LBR robot used in a MeVislab based research project.
#The MRI compatible Manipulator, a 5 DoF robot for performing transrectal prostate biopsies.
*Defined Scenarios:
**Workflow01:
***Ask for the status of the robotic device
***Get the current position of the device tip
***Send commands to the robot (simulator) to get to the new target position
***Set /ask/ retrieve time stamps

<h5>MLab Interface</h5>
*Design and implement a generic interface for using OpenIGT commands in MeVislab network layer.
#OpenIGTLinkIO is a slicer independent library to use OpenIGTLink, could be used as good example (https://github.com/IGSIO/OpenIGTLinkIO)
**Create Client /Server
***Host name(IP), port, show status, connection time out, start/stop, connect/disconnect
**Create Thread for realtime (?)
**Define Datatypes: Vector position, Status, etc..
**Communication: Send and recieve and save:
***Massages and nr. of massages
***Data-sets
***Images
**Sending control commands
**loggs: showing, saving
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* to be defined in the project week.
</div>
</div>

2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices

2016-06-13T11:33:38Z

Lchen: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Scheherazade Kraß
* Longquan Chen

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Obtaining a better understanding of OpenIGTLink:
# How to use and integrate it in different robotic devices using:
## MeVisLab applications
## Slicer

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
<h5>Robotic Devices</h5>
*Defining different workflows for communication between robotic device and MeVislab applications, including sending/receiving strings, image sets and control commands for:
#The Kuka LBR robot used in a MeVislab based research project.
#The MRI compatible Manipulator, a 5 DoF robot for performing transrectal prostate biopsies.
*Defined Scenarios:
**Workflow01:
***Ask for the status of the robotic device
***Get the current position of the device tip
***Send commands to the robot (simulator) to get to the new target position
***Set /ask/ retrieve time stamps

<h5>MLab Interface</h5>
*Design and implement a generic interface for using OpenIGT commands in MeVislab network layer.
OpenIGTLinkIO is a slicer independent library to use OpenIGTLink, could be used as good example (https://github.com/IGSIO/OpenIGTLinkIO)
**Create Client /Server
***Host name(IP), port, show status, connection time out, start/stop, connect/disconnect
**Create Thread for realtime (?)
**Define Datatypes: Vector position, Status, etc..
**Communication: Send and recieve and save:
***Massages and nr. of massages
***Data-sets
***Images
**Sending control commands
**loggs: showing, saving
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* to be defined in the project week.
</div>
</div>

2016 Summer Project Week

2016-05-31T13:28:39Z

Lchen: /* IGT */

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-05-31T13:27:22Z

Lchen:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in CustusX, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
** Coordinate efforts with others systems doing the same job (Slicer, MITK, IBIS)
* Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
** Semi-automatic gui-based configuration on the CX side.
** Modify PLUS if necessary.
** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
* Replace in-house US-streaming solutions by the new standards.
** Try to use PLUS as backend for the Ultrasonix scanner.
** Write a lightweight OpenIGTLink server for proprietary scanners.
** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week

2016-05-17T17:55:13Z

Lchen: /* Registrants */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.

==Agenda==
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''Background''' ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

==Equipment==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

#[[2016_VRPN_Integration | VRPN Integration]]
#Needle Segmentation from MRI (Tina Kapur, Andre Mastmeyer, Guillaume Pernelle)
#Guided Ultrasound Calibration (Elvis Chen, Robarts Research) http://link.springer.com/article/10.1007/s11548-016-1390-7
#[[2016_MRI_Manipulator | Integrating/Using OpenIGTLink for the communications of Robotics devices.]] (Scheherazade Kraß, MIC of university of Bremen, Germany)

= '''Registrants''' =

'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html and then add your name to this list. DKFZ members who will only be attending Monday should only add their name to this list.

#Tina Kapur, BWH/HMS, Boston, USA
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
# Steve Pieper, Isomics, Inc., USA
# Nicole Aucoin, Brigham and Women's Hospital
# Simon Drouin, Montreal Neurological Institute
# Thomas Kirchner, German Cancer Research Center
# Elvis Chen, Robarts Research Institute, Canada
# Christian Askeland, SINTEF, Norway
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA

2016 Summer Project Week/MRI Manipulator

2016-05-17T17:53:55Z

Lchen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Scheherazade Kraß
* Longquan Chen

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integrating/Using OpenIGTLink for the communications of robotic devices:
# The <b>MRI_Manipulator</b>, a 5 DoF robot for performing transrectal prostate biopsies.
# The Kuka LBR robot in <b>MITIGATE</b>, a MeVislab based research project.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
#<b>MRI_Manipulator</b>: The system is based on MeVisLab, the robot is controlled with a pneumatic motor via PLC controller, the movement commands are transferred through an Emulator. The goal is making this system working with OpenIGTLink (in Simulation).
#<b>MITIGATE</b>: The overall objective of the EU-project MITIGATE is to develop and validate an integrated closed-loop process to effectively treat metastatic gastrointestinal stromal tumour (GIST) patients resistant to the currently available class of medication. We are involved in WP7 "Minimally Invasive Therapy" and will develop a control software for robot-assisted minimally invasive interventions. There we have to deal with DynaCT images from an interventional Artis Zeego External Link and steer a Kuka LBR External Link robot that holds the interventional device. The gola is to define workflows for robot communications and implement this via OpenIGTLink. See: https://www.youtube.com/watch?v=8BeerXldDq0
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* to be started in the project week.
</div>
</div>