2016 Summer Project Week

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Welcome to the web page for the 23rd Project Week!

• Fill out the survey about this project weeks today!
• Hold January 9-13, 2017 for 24th Project Week at MIT.
• Hold June 26-30, 2017 for 25th Project Week in Europe.
• Add photos from this week here.

Summary

The 23rd Project Week open source hackathon was held in conjunction with the 30th International Conference on Computer Assisted Radiology and Surgery (CARS) and the IPCAI 2016 conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact Tina Kapur, PhD.

A summary of all past Project Events.

Agenda

Please note that on Tuesday there is no organized Project Week activity due to IPCAI @ CARS

Time	Monday, June 20 DKFZ	Tuesday, June 21 IPCAI	Wednesday, June 22 Congress Hall of CARS, Room Trübnersaal	Thursday, June 23 Congress Hall of CARS, Room Trübnersaal	Friday, June 24 Congress Hall of CARS, Room Trübnersaal	Saturday, June 25 Congress Hall of CARS, Room Trübnersaal
9:00am-10:00am			Workshop: Ultrasound-guided interventions software platform (all day)
10:00am-10:30am	Coffee Break		Coffee Break	Coffee Break	Coffee Break	Coffee Break
10:30-12pm						10:30am-12pm: Progress Review
12:00pm-1:00pm	Lunch		Lunch	Lunch	Lunch	Lunch and adjourn
1:00pm-3:00pm	Welcome! Project Introductions
3:00pm-3:30pm	Coffee Break		Coffee Break	Coffee Break	Coffee Break
3:30pm-5:00pm	What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)		Breakout Session: Slicer Extensions (JC, Steve)

Projects

• Note: Please use this 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 (PERK Lab, PLUS: 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 Research Institute, Western University (Terry Peters, Adam Rankin), Trondheim University and SINTEF (CustusX: Christian Askeland, Frank Lindseth).

• Tracked Ultrasound Standardization II: The Implementering (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland)
• Guided Ultrasound Calibration (Elvis Chen, Inês Prata, Tamas Ungi)
• 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.

• Guidelets (Slicelets for IGT) (Tamas Ungi, Andras Lasso, Thomas Vaughan)
• Slicelet for Ultrasound Acquisition (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
• OpenVR Integration (Adam Rankin, Andras Lasso)
• AR with a Tablet Device in the Surgical Room (David García, Javier Pascau)
• 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.

• Needle Segmentation from MRI (Guillaume Pernelle, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Tina Kapur)
• Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation (Bojan Kocev, Sarah Frisken, Christian Hansen, William Wells)

IGT Other

• SliceTracker for Data Collection and Prostate Biopsy Support (Christian Herz, Peter Behringer, Andrey Fedorov)
• Prostate Motion Characterization (Peter Behringer, Christian Herz, Andrey Fedorov)
• Structural - Functional Relationship Measurements of Tractography Data with fMRI (Yannick Suter, Lauren J. O'Donnell)
• Sacral Neuromodulation (Rocío López, Javier Pascau, Tamas Ungi)
• Tool for the construction of an integrated brain atlas based on histology and MRI to aid Deep Brain Stimulation (Fernando Pérez García, Sara Fernandez Vidal, Sonia Pujol, Steve Pieper, Csaba Pinter, Andras Lasso)
• Integrating/Using OpenIGTLink for the Communications of Robotics Devices (Scheherazade Kraß, Longquan Chen)
• Intraoperative Functional Guidance Workflows in Neurosurgery (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)

Informatics

This theme deals with creating data formats to enable medical image informatics. Led by the 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.

• DICOM for Quantitative Imaging (dcmqi) Library (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
• Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
• Support Reading and Writing DICOM Tags for SEG Properties (Hans Meine, Andrey Fedorov, Christian Herz, Steve Pieper)
• 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.

• Medical Imaging WebApp Software (Steve Pieper, Marco Nolden, Hans Meine)
• Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
• Integration of Segmentations Infrastructure and Related Modules to Slicer Core (Csaba Pinter, Andras Lasso)
• Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project (Lauren O'Donnell, Isaiah Norton, Michael Onken)
• 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)
• CommonGL: GPU Rendering and Computation (Steve Pieper, Christian Askeland, Andra Lasso, Simon Drouin, Fernando Pérez García)

Tutorial

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

• Tutorials and Documentation in SlicerDMRI (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
• Create the basics of a university course about medical image computing (Attila Nagy)
• 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 the local transportation services VRN. If you are up early there is also a nice 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 (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. (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

• Specialized equipment people are going to bring (Please add to this list if you are bringing anything)
• 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 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.

1. Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA :: tkapur@bwh.harvard.edu (Mon)
2. Ron Kikinis, BWH/HMS, Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany :: kikinis@bwh.harvard.edu (Mon)
3. Dženan Zukić, Kitware, USA :: dzenan.zukic@kitware.com
4. Ines Prata Machado, MIT Portugal Program, Lisbon, Portugal :: ines7_prata@hotmail.com (Mon)
5. Sonia Pujol, BWH/HMS, Boston :: spujol@bwh.harvard.edu (Mon)
6. Scheherazade Kraß, PhD Student, University of Bremen, Medical Image Computing group, Germany :: shery@uni-bremen.de (Mon)
7. Maria Francesca Spadea ImagEngLab, Italy :: mfspadea@unicz.it (Mon)
8. Paolo Zaffino ImagEngLab, Italy :: p.zaffino@unicz.it (Mon)
9. Salvatore Scaramuzzino ImagEngLab, Italy :: salvatorescaramuzzino@gmail.com (Mon)
10. Steve Pieper, Isomics, Inc., USA :: pieper@isomics.com (Mon)
11. Nicole Aucoin, BWH/HMS, Boston :: nicole@bwh.harvard.edu (Mon)
12. Simon Drouin, Montreal Neurological Institute :: simon.drouin@mail.mcgill.ca (Mon)
13. Thomas Kirchner, German Cancer Research Center :: t.kirchner@dkfz.de (Mon)
14. Elvis Chen, Robarts Research Institute, Canada :: chene@imaging.robarts.ca (Mon)
15. Adam Rankin, Robarts Research Institute, Canada :: arankin@robarts.ca (Mon)
16. Christian Askeland, SINTEF, Norway :: christian.askeland@gmail.com (Mon)
17. Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany :: hans.meine@mevis.fraunhofer.de (Mon)
18. Longquan Chen, BWH/HMS, Boston, USA :: lchen@bwh.harvard.edu (Mon)
19. Davide Punzo, Kapteyn Astronomical Institute, Netherlands :: punzodavide@hotmail.it (Mon)
20. Lauren O'Donnell, BWH/HMS :: odonnell@bwh.harvard.edu (Mon)
21. Yannick Suter, BWH/HMS :: yannicksuter@bluewin.ch (Mon)
22. Junichi Tokuda, BWH/HMS :: tokuda@bwh.harvard.edu (Mon)
23. Sarah Frisken, BWH/HMS :: sfrisken@bwh.harvard.edu (Mon)
24. Prashin Unadkat, BWH/HMS :: punadkat@partners.org
25. Anna Roethe, Charite, Berlin
26. Michael Onken, Open Connections, Germany :: onken@open-connections.de (Mon)
27. Jan Schlamelcher, Open Connections/OFFIS, Germany
28. Janne Beate Bakeng, SINTEF, Norway :: janne.beate.bakeng@sintef.no
29. Ole Vegard Solberg, SINTEF, Norway :: OleVegard.Solberg@sintef.no
30. Jon Eiesland, SINTEF, Norway
31. Tamas Ungi, Queen's University, Canada :: ungi@queensu.ca (Mon)
32. Andras Lasso, Queen's University, Canada :: lasso@queensu.ca (Mon)
33. Csaba Pinter, Queen's University, Canada :: pinter@cs.queensu.ca (Mon)
34. Thomas Vaughan, Queen's University, Canada :: vaughan.thomas.a@gmail.com (Mon)
35. Javier Pascau, Universidad Carlos III de Madrid, Spain :: jpascau@hggm.es (Mon)
36. Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain :: vgarcia@hggm.es (Mon)
37. Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain :: mgsevilla@hggm.es (Mon)
38. David García-Mato, Universidad Carlos III de Madrid, Spain :: dgmato@hggm.es (Mon)
39. Rocío López-Velazco, Universidad Carlos III de Madrid, Spain :: rlopez@hggm.es (Mon)
40. Raúl San José, BWH/HMS, Boston :: rsanjose@bwh.harvard.edu
41. Pietro Nardelii, BWH/HMS, Boston :: pietro@bwh.harvard.edu
42. Andrey Fedorov, BWH/HMS, Boston :: fedorov@bwh.harvard.edu (Mon, Wed, Thu)
43. Christian Herz, BWH/HMS, Boston :: cherz1@partners.org (Mon)
44. Frank Lindseth, NTNU/SINTEF, Norway :: Frank.Lindseth at sintef.no
45. Peter Behringer, Basler AG, Germany :: peterbehringer@gmx.de
46. Santhirarajah Mathimugan, Basler AG, Germany :: Santhirarajah.Mathimugan@baslerweb.com
47. Koji Kobayashi, Vocsis Corporation, Japan
48. David Black, University of Bremen / Fraunhofer MEVIS, Germany :: david.black@mevis.fraunhofer.de (Mon)
49. William Wells, BWH/HMS :: sw@bwh.harvard.edu (Mon)
50. Attila Nagy, University of Szeged, Hungary :: attila@orl.szote.u-szeged.hu (Mon)
51. Bojan Kocev, University of Bremen, Medical Image Computinggroup, Germany :: bkocev@uni-bremen.de (Mon)
52. Sara Fernández Vidal, Institute of the Brain and Spine, France :: sara.fernandez_vidal@upmc.fr (Mon)
53. Fernando Pérez García, Institute of the Brain and Spine, France (Mon)
54. Marco Nolden, Medical and Biological Informatics, German Cancer Research Center (Mon)
55. Christian Hansen, University of Magdeburg, Germany :: hansen@isg.cs.uni-magdeburg.de (Mon)
56. Julian Hettig, University of Magdeburg, Germany :: Julian.Hettig@ovgu.de (Mon)
57. Jorge Onieva, BWH/HMS, Boston :: jonieva@bwh.harvard.edu
58. Caspar Goch, German Cancer Research Center (Mon)

Please make sure that you are on the NA-MIC Project Week mailing list.