NAMIC Wiki - User contributions [en]

2016 Summer Project Week

2016-06-24T16:05:39Z

Jpascau: /* IGT Other */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>

<font color="red" size="30">Please fill in the survey about project weeks today!</font>

<font size="28">
[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]
</font>

=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].

='''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"|'''9:00am-10:00am'''
|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 (all day)]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|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"| 10:30am-12pm: 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"|
|-
|}

='''Projects'''=

* Note: Please use this [[2016_Summer_Project_Week_Template | template]] to create project pages

=== Worldwide Ultrasound Navigation ===
Over the last several PWs, an international group has emerged for collaborative specification and development of ultrasound-based navigation for surgical and interventional radiology applications. This group represents the leadership of ultrasound navigation technology from Queens University (PLUS library: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinter), Montreal Neurologic Institute (Simon Drouin), Brigham and Women's Hospital/HMS (William Wells, Steve Pieper, Sarah Frisken), Robarts University (Adam Rankin), Trondheim University and SINTEF (CustusX: Christian Askeland, Frank Lindseth).

* [[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)

=== Simplified Human-Computer Interactions for Intra-Operative Usage===
This theme focuses on infrastructure for simplified human-computer interactions for intra-operative usage. This includes Guidelets, simplified graphical user interfaces that can access the same backend as 3D Slicer; as well as interfaces for virtual reality/augmented reality devices from the consumer market that are that are improving by leaps and bounds and show promise for surgical use.

* [[2016 Summer Project Week/Guidelets | Guidelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[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)

===Machine Learning for IGT===
This theme applies concepts from machine learning to image-guided therapy, including the application of convolutional neural networks for segmentation of mechanically implanted devices during surgery, and the use of Gaussian processes for estimation of uncertainty in image-fusion.

* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Tina Kapur)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, Christian Hansen, William Wells)

===IGT Other===
* [[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/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI to aid Deep Brain Stimulation]] (Fernando Pérez García)
* [[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/Intraoperative Imaging workflow in Hybrid ORs | Intraoperative Imaging in Hybrid ORs]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)

=== Informatics ===
This theme deals with creating data formats to enable medical image informatics. Led by the [http://qiicr.org/about.html QIICR project], the results will be made available in the DICOM for Quantitative Imaging (DCMQI) Library for sharing quantitative image-processing results in a standardized way.

* [[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, Marco Nolden, Christian Herz)

=== Infrastructure ===
Improvements to the core functionality of widely used open source tools is an on-going theme.

* [[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/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi, Steve Pieper)

=== Tutorial===
Creation of tutorials and documentation is an on-going theme.

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

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
==Location==
*'''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.

=='''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'''

= '''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
# Caspar Goch, German Cancer Research Center (Mon)

'''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/Sacral Neuromodulation

2016-06-24T15:38:55Z

Jpascau: /* Project Description */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Gallery==
<gallery>
Sacral_Navigation.jpeg|Navigation
3D_printed_Models.jpeg|3D printed models adapted to EM sensors
</gallery>

==Background==

Sacral Neuromodulation is a surgical procedure performed for the treatment of pathologies, such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.

Nowadays, this intervention is only validated through intraoperative x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation of the nerve.

We propose a new 3D Slicer module to guide the needle intervention using an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
* Collaboration with David Black for including his Auditory Display functionality into current module.
</div>
</div>

File:DiagramWithChessboard.PNG

2016-06-24T15:14:00Z

Jpascau: Jpascau uploaded a new version of File:DiagramWithChessboard.PNG

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-24T15:10:01Z

Jpascau: /* Project Description */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Simon Drouin (Montreal Neurological Institute, Canada)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
SlicerModule.png|Slicer Module
DiagramWithChessboard.PNG |New System Diagram
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objectives</h3>
* To combine tablet camera view with Slicer virtual models.
* To include guidelets.
* Improvement of existing Slicer module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.
* Able to receive tablet camera images in Slicer using PLUS.
* Calibration procedure based on chessboard.
* Able to improve slicer module visualization using Slicelets.
</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-24T15:05:26Z

Jpascau: /* Gallery */

File:DiagramWithChessboard.PNG

2016-06-24T15:04:43Z

Jpascau:

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-24T14:50:35Z

Jpascau: /* Gallery */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Simon Drouin (Montreal Neurological Institute, Canada)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
SlicerModule.png|Slicer Module
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objectives</h3>
* To combine tablet camera view with Slicer virtual models.
* To include guidelets.
* Improvement of existing Slicer module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-24T14:48:15Z

Jpascau: /* Gallery */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Simon Drouin (Montreal Neurological Institute, Canada)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
SlicerModule.PNG|Slicer Module
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objectives</h3>
* To combine tablet camera view with Slicer virtual models.
* To include guidelets.
* Improvement of existing Slicer module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

File:SlicerModule.png

2016-06-24T14:45:02Z

Jpascau:

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-24T09:10:40Z

Jpascau: /* Key Investigators */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Simon Drouin (Montreal Neurological Institute, Canada)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objectives</h3>
* To combine tablet camera view with Slicer virtual models.
* To include guidelets.
* Improvement of existing Slicer module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T08:35:03Z

Jpascau: Add participants

= Introduction =

Several groups have developed ultrasound-guided intervention systems in the last two decades but until recently these groups have worked mostly in parallel, independently from each other. The Image Guided Systems Inter-Operability (IGSIO) group was founded in 2016 January after lengthy discussions regarding the standardization of tracked ultrasound communication to work towards improving the interoperability between industrial products and research software platforms. See more information about this effort at http://igsio.github.io/.

The goal of this workshop is to promote the concept and practice of a shared software platform for ultrasound-guided interventions. Participants will learn, in practice, to build clinical applications using software platform tools.

= Tentative agenda (keep checking this page for more details) =

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** Plus/SlicerIGT/3DSlicer (Andras Lasso)
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

No registration is required, just add your name to the participant list below or send an email to Andras Lasso (lasso@queensu.ca).

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* Longquan Chen
* Simon Drouin
* Jon Eiesland
* Thomas Kirchner
* Adam Rankin
* Ole Vegard Solberg
* Junichi Tokuda
* Sarah Frisken
* Bojan Kocev
* Ines Machado
* Tamas Ungi
* David Black
* Lauren O'Donnell
* Yannick Suter
* Hans Meine
* David García-Mato
* Javier Pascau
* Rocío Lopez-Velazco
* Mónica García-Sevilla
* Verónica García-Vazquez

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T08:34:27Z

Jpascau: /* Participants */

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-20T11:20:22Z

Jpascau: /* Project Description */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objectives</h3>
* To combine tablet camera view with Slicer virtual models.
* To include guidelets.
* Improvement of existing Slicer module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-20T11:18:17Z

Jpascau: /* Key Investigators */

==Key Investigators==
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week

2016-06-20T10:21:49Z

Jpascau: /* IGT */

__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)
* [[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)

=== 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)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== 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)

=== Infrastructure ===
* [[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)

=== 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

2016-06-20T10:21:26Z

Jpascau: /* IGT */

__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)
* [[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)

=== 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)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== 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)

=== Infrastructure ===
* [[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)

=== 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

2016-06-20T10:19:45Z

Jpascau: /* 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
**'''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)
* [[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)
* [[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 ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Javier Pascau, Mónica García)
* [[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)

=== 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)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== 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)

=== Infrastructure ===
* [[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)

=== 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/Sacral Neuromodulation

2016-06-17T13:46:22Z

Jpascau: /* Gallery */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Gallery==
<gallery>
Sacral_Navigation.jpeg|Navigation
3D_printed_Models.jpeg|3D printed models adapted to EM sensors
</gallery>

==Background==

Sacral Neuromodulation is a surgical procedure performed for the treatment of pathologies, such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.

Nowadays, this intervention is only validated through intraoperative x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation of the nerve.

We propose a new 3D Slicer module to guide the needle intervention using an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

File:3D printed Models.jpeg

2016-06-17T13:43:41Z

Jpascau:

2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data

2016-06-17T13:43:15Z

Jpascau:

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Slicer module for needle tip localization combining the information of an electromagnetic tracking system and a surface scanner.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for electromagnetic tracker data acquisition and to obtain tip's position.
* Use a surface scanner to obtain the surface.
* Use a rigid body with color markers (3D printed), visible for both systems.
* Register one space to the other in order to view it altogether.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer module partially implemented.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-17T13:42:24Z

Jpascau: /* Gallery */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Gallery==
<gallery>
Sacral_Navigation.jpeg|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==

Sacral Neuromodulation is a surgical procedure performed for the treatment of pathologies, such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.

Nowadays, this intervention is only validated through intraoperative x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation of the nerve.

We propose a new 3D Slicer module to guide the needle intervention using an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-17T13:41:39Z

Jpascau: /* Key Investigators */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Gallery==
<gallery>
Sacral_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==

Sacral Neuromodulation is a surgical procedure performed for the treatment of pathologies, such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.

Nowadays, this intervention is only validated through intraoperative x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation of the nerve.

We propose a new 3D Slicer module to guide the needle intervention using an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

File:Sacral Navigation.jpeg

2016-06-17T13:37:37Z

Jpascau:

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:32:57Z

Jpascau: /* Gallery */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Navigation
NavigationSystem_Diagram.PNG|System Diagram
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:29:44Z

Jpascau: /* Gallery */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Gallery==
<gallery>
Tablet_Phantom_Navigation.JPG|Caption1
NavigationSystem_Diagram.PNG|Caption2
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

File:NavigationSystem Diagram.PNG

2016-06-16T08:29:03Z

Jpascau: By David García-Mato

By David García-Mato

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:27:56Z

Jpascau: /* Key Investigators */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Gallery==
<gallery>
Tablet Phantom Navigation.JPG|Caption1
Example.jpg|Caption2
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

File:Tablet Phantom Navigation.JPG

2016-06-16T08:26:29Z

Jpascau:

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:21:39Z

Jpascau: /* Key Investigators */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

<gallery>
Example.jpg|Caption1
Example.jpg|Caption2
</gallery>

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:19:37Z

Jpascau: /* Project Description */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module already implemented.

</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-16T08:10:52Z

Jpascau: Approach

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* To include guidelets.
* To combine tablet camera view with Slicer virtual models.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Tablet-based AR Navigation System using a tablet movable display and a multi-camera optical tracking system.
* Steps:
** Generation of virtual anatomical models from preoperative image.
** Registration between virtual and real space.
** Tablet viewpoint calibration.
** Navigation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Basic Slicer module
**
**
*
**
**
</div>
</div>

2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data

2016-06-15T15:10:37Z

Jpascau: Added project description

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Slicer module for needle tip localization combining the information of an electromagnetic tracking system and a surface scanner.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for electromagnetic tracker data acquisition and to obtain tip's position.
* Use a surface scanner to obtain the surface.
* Use a rigid body with color markers, visible for both systems.
* Register one space to the other in order to view it altogether.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer module partially implemented.
</div>
</div>

2016 Summer Project Week

2016-06-15T09:06:08Z

Jpascau: Added a project to the list

__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
*** 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
!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"|'''9am-10am'''
|bgcolor="#ffffff"| [[Breakout Session/Ultrasound Data Collection during Neurosurgery]] (Sarah Frisken)
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]] (Andras Lasso)
|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"| [[Breakout Session/Slicer Extensions]]
|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"|
|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. 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)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]]

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

=== IGT ===
* [[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, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[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/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/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[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/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Javier Pascau, Mónica García)

=== Infrastructure ===
* [[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)

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

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== 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)

=== 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)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[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)
#Gabor Fichtinger, Queen's University, Canada
# 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/Sacral Neuromodulation

2016-06-01T10:55:23Z

Jpascau: /* Background */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Background==

Sacral Neuromodulation is a surgical procedure performed for the treatment of pathologies, such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.

Nowadays, this intervention is only validated through intraoperative x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation of the nerve.

We propose a new 3D Slicer module to guide the needle intervention using an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-01T10:49:58Z

Jpascau: /* Key Investigators */

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

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* Rocío López (Universidad Carlos III de Madrid, Spain)
* David García (Universidad Carlos III de Madrid, Spain)
* Tamas Ungi (Queen's University, Canada)

==Background==

Sacral Neuromodulation intervention is a surgery performed in pathologies such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.
Nowadays this process is only validated through x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation.

We propose a new module in the Software 3D Slicer, to guide the needle intervention using as navigation system an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-01T10:45:56Z

Jpascau: /* Background */

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

==Key Investigators==
* Javier Pascau (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Rocío López (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* David Garía (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Tamas Ungi (Queen's University)

==Background==

Sacral Neuromodulation intervention is a surgery performed in pathologies such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.
Nowadays this process is only validated through x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation.

We propose a new module in the Software 3D Slicer, to guide the needle intervention using as navigation system an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-01T10:43:14Z

Jpascau:

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

==Key Investigators==
* Javier Pascau (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Rocío López (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* David Garía (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Tamas Ungi (Queen's University)

==Background==

Sacral Neuromodulation surgery is a surgery performed in pathologies such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.
Nowadays this process is only validated through x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation.

We propose a new module in the Software 3D Slicer, to guide the needle intervention using as navigation system an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.

* The GUI for the guidance: Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/Sacral Neuromodulation

2016-06-01T10:40:00Z

Jpascau:

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

==Key Investigators==
* Javier Pascau (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Rocío López (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* David Garía (Medical Imaging Lab in Gregorio Marañon Hospital, Madrid)
* Tamas Ungi (Queen's University)

==Background==

Sacral Neuromodulation surgery is a surgery performed in pathologies such as urinary and fecal incontinence, urinary retention and constipation. An electrode is inserted through a needle in a sacral root which controls the bladder and the intestine to stimulate the efferent and afferent vias.
Nowadays this process is only validated through x-ray fluoroscopy while the insertion of the needle is being performed. The main challenge of the doctor in the surgery is the placement of the needle in the correct position for proper stimulation.

We propose a new module in the Software 3D Slicer, to guide the needle intervention using as navigation system an electromagnetic tracking system.

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for tracking the needle in a Sacral Neuromodulation intervention.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (electromagnetic tracker transforms) acquisition.
*
*
** The GUI for the guidance
*** Is guidelet only useful with ultrasound? We have used their properties to create our GUI, hiding ultrasound properties, which is not very smart.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:27:37Z

Jpascau: /* Project Description */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* Include guidelets.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
**
**
*
**
**
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
**
**
*
**
**
</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:26:53Z

Jpascau: /* Project Description */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improvement of Slicer module.
* Include guidelets.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:23:54Z

Jpascau: /* Background */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* A slicer module/GUI for US calibration
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Use PLUS library for data (US image and tracker transforms) acquisition
* port existing C++/VTK code into the slicer environment
* There are 2 parts to the development:
** The GUI for the calibration
*** use python for GUI development?
** TRE prediction
*** use numpy for the math. HOWEVER, we need multi-threading
*** alternatively, we can write a CLI module for the computation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Slicer development has been properly set up.
</div>
</div>

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:23:06Z

Jpascau: /* Background */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. A new AR navigation system based on a movable tablet display and a multi-camera optical tracking system has been implemented using Slicer. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient.

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:20:35Z

Jpascau: /* Key Investigators */

==Key Investigators==
* Javier Pascau (Universidad Carlos III de Madrid, Spain)
* David García-Mato (Universidad Carlos III de Madrid, Spain)
* Mónica García-Sevilla (Universidad Carlos III de Madrid, Spain)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. In this paper, we present a new AR navigation system based on a movable tablet display and a multi-camera optical tracking system. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient. The system performance was assessed by a group of experts in the field of image-guided surgery and surgeons. The proposed AR systems was concluded to be really useful in a wide range of surgical procedures, allowing an accurate intraoperative planning of the intervention.

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:18:30Z

Jpascau: /* Background */

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)
* Tamas Ungi (Queen's University)

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. In this paper, we present a new AR navigation system based on a movable tablet display and a multi-camera optical tracking system. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient. The system performance was assessed by a group of experts in the field of image-guided surgery and surgeons. The proposed AR systems was concluded to be really useful in a wide range of surgical procedures, allowing an accurate intraoperative planning of the intervention.

2016 Summer Project Week/AR with a tablet device in the surgical room

2016-06-01T10:15:33Z

Jpascau: /* Background */

==Background==
The navigation information during image-guided surgeries is usually displayed in external screens which force surgeons to switch views between the surgical field and the screen during surgery. Augmented reality (AR) technology has been applied to surgeries in order to improve the navigation workflow. However, the existing AR systems are really complex and expensive, and they present important drawbacks. In this paper, we present a new AR navigation system based on a movable tablet display and a multi-camera optical tracking system. Firstly, the movable tablet device allows to show the navigation information within the actual surgical field, thanks to a wireless connection with the computer. Moreover, another available functionality of this system is the possibility of showing the anatomical structures of interest from the tablet viewpoint, as looking through a window into the internal anatomy of the patient. The system performance was assessed by a group of experts in the field of image-guided surgery and surgeons. The proposed AR systems was concluded to be really useful in a wide range of surgical procedures, allowing an accurate intraoperative planning of the intervention.

2016 Summer Project Week/Sacral Neuromodulation

2016-06-01T10:04:25Z

Jpascau: /* Key Investigators */

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)
* Tamas Ungi (Queen's University)

2016 Summer Project Week

2016-05-31T21:34:59Z

Jpascau: /* Augmented Reality */

2016 Summer Project Week

2016-05-31T21:31:59Z

Jpascau: /* IGT */

2016 Summer Project Week

2016-05-31T13:10:45Z

Jpascau: /* Registrants */

2015 Multimodal Guidance for Breast Cancer Surgery

2015-06-24T15:20:38Z

Jpascau:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:Mikael-Capture2.PNG|Fig 1. 'Stage 1'
Image:Mikael-Capture3.PNG|Fig 2. 'Stage 2'
Image:Mikael-Capture4.PNG|Fig 3. Hitachi US
Image:Mikael-Capture5.PNG|Fig 4. Philips US
Image:Mikael-Capture1.PNG|Fig 5. 3D Slicer
</gallery>

==Key Investigators==
* Mikael Brudfors, Universidad Carlos III de Madrid (UC3M) --- formerly KTH & UBC, next UCL
* David García, UC3M
* Javier Pascau, UC3M
* Tamas Ungi, Andras Lasso (Queen's University, Kingsotn, ON, Canada)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Development of an intraoperative guidance system for breast cancer surgery that would allow for guidance, tumor detection and localization.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Possibilities of combining multiple imaging modalities (3D Scanner Surface data, US, MR) and visualizing these in 3D Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Acquire tracked US using the PLUS toolkit (DONE)
* Record surface data using an Artec 3D scanner and visualize it in 3D Slicer (DONE)
* Communicate with the 3D Scanner through 3D slicer module (WORK IN PROGRESS)
* Define an acquisition protocol. Tamas Ungi showed their protocol and Slicer module that includes needle tracking and a possible collaboration was identified (WORK IN PROGRESS)
</div>
</div>