2016 Summer Project Week

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

The 23rd Project Week open source hackathon is being 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.

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 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
  • 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.

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
9am-10am			Workshop: Ultrasound-guided interventions software platform			Progress Review
10:00am-10:30am	Coffee Break		Coffee Break	Coffee Break	Coffee Break	Coffee Break
10:30-12pm						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)
6:00pm

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 NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and 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.

Project Week is a semi-annual event which draws researchers from around the world and is led by 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 NAC, NCIGT, QIICR, OCAIRO, and NCI Funded Image-Guided Fellowship Program.

An introduction and summary of all previous Project Events is available here.

This project week is an event endorsed by the MICCAI society.

The 23rd Project Week is being held in conjunction with the 30th International Conference on Computer Assisted Radiology and Surgery (CARS).

Please make sure that you are on the na-mic-project-week mailing list.

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

Projects

• Use this template for project pages

IGT

• Guildelets (Slicelets for IGT) (Tamas Ungi, Andras Lasso, Thomas Vaughan)
• Tracked Ultrasound Standardization II: The Implementering (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
• 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)
• Slicelet for Ultrasound Acquisition (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
• Structural - Functional Relationship Measurements of Tractography Data with fMRI (Lauren J. O'Donnell, Yannick Suter)
• SliceTracker for Data Collection and Prostate Biopsy Support (Christian Herz, Peter Behringer, Andrey Fedorov)
• Prostate Motion Characterization (Peter Behringer, Christian Herz, Andrey Fedorov)
• Sacral Neuromodulation (Rocío López, Javier Pascau, Tamas Ungi)
• Fusion of Electromagnetic and Surface Scanner Data (Mónica García, Javier Pascau)
• Integrating/Using OpenIGTLink for the Communications of Robotics Devices (Scheherazade Kraß, Longquan Chen)
• Needle Segmentation from MRI (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
• Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation (Bojan Kocev, Sarah Frisken, William Wells, Christian Hansen)
• Intraoperative Imaging in Hybrid ORs (Sarah Frisken, Anna Roethe, Prashin Unadkat, Christian Hansen)
• Curve and Surface Creation from Fiducials (Thomas Vaughan, Junichi Tokuda)

Infrastructure

• 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)
• Measuring the Impact of Project Weeks (Tina Kapur)
• 2016 Summer Project WEB and 3D DICOM viewer to the rest of us (Koji Kobayashi)

Augmented Reality

• OpenVR Integration (Adam Rankin, Andras Lasso)
• VRPN Integration (Dženan Zukić)
• AR with a Tablet Device in the Surgical Room (David García, Javier Pascau)
• Auditory Display Integration (David Black, Sarah Frisken, Christian Hansen)

Informatics

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

Atlas construction

• Tool for the construction of an integrated brain atlas based on histology and MRI (Fernando Pérez García)

Tutorial

• Tutorials and Documentations in SlicerDMRI (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
• How to use Basler Cameras for Medical Applications (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
• 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 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 (Mon)
2. Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
3. Dženan Zukić, Kitware, USA
4. Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
5. Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
6. Scheherazade Kraß, PhD Student, University of Bremen, Medical Image Computinggroup, Germany (Mon)
7. Maria Francesca Spadea ImagEngLab, Italy (Mon)
8. Paolo Zaffino ImagEngLab, Italy (Mon)
9. Salvatore Scaramuzzino ImagEngLab, Italy (Mon)
10. Steve Pieper, Isomics, Inc., USA (Mon)
11. Nicole Aucoin, Brigham and Women's Hospital (Mon)
12. Simon Drouin, Montreal Neurological Institute (Mon)
13. Thomas Kirchner, German Cancer Research Center (Mon)
14. Elvis Chen, Robarts Research Institute, Canada (Mon)
15. Adam Rankin, Robarts Research Institute, Canada (Mon)
16. Christian Askeland, SINTEF, Norway (Mon)
17. Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
18. Longquan Chen, BWH/HMS, Boston, USA (Mon)
19. Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
20. Lauren O'Donnell, BWH/HMS
21. Yannick Suter, BWH/HMS (Mon)
22. Junichi Tokuda, BWH/HMS (Mon)
23. Sarah Frisken, BWH/HMS (Mon)
24. Prashin Unadkat, BWH/HMS
25. Anna Roethe, Charite, Berlin
26. Michael Onken, Open Connections, Germany (Mon)
27. Jan Schlamelcher, Open Connections/OFFIS, Germany
28. Janne Beate Bakeng, SINTEF, Norway
29. Ole Vegard Solberg, SINTEF, Norway
30. Jon Eiesland, SINTEF, Norway
31. Tamas Ungi, Queen's University, Canada (Mon)
32. Andras Lasso, Queen's University, Canada (Mon)
33. Csaba Pinter, Queen's University, Canada (Mon)
34. Thomas Vaughan, Queen's University, Canada (Mon)
35. Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
36. Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
37. Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
38. David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
39. Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
40. Raúl San José, BWH/HMS, Boston
41. Pietro Nardeli, BWH/HMS, Boston
42. Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
43. Christian Herz, BWH/HMS, Boston (Mon)
44. Frank Lindseth, NTNU/SINTEF, Norway
45. Peter Behringer, Basler AG, Germany
46. Santhirarajah Mathimugan, Basler AG, Germany
47. Koji Kobayashi, Vocsis Corporation, Japan
48. David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
49. William Wells, BWH/HMS (Mon)
50. Attila Nagy, University of Szeged, Hungary (Mon)
51. Bojan Kocev, University of Bremen, Medical Image Computinggroup, Germany (Mon)
52. Sara Fernández Vidal, Institute of the Brain and Spine, France (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 (Mon)
56. Julian Hettig, University of Magdeburg, Germany

Please don't forget to add yourself to the na-mic-project-week mailing list.