2015 Summer Project Week

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A summary of all past Project Events.

Welcome to the web page for the 21st Project Week!

Summary

The 21st PROJECT EVENT was held on June 21-24, 2015 in Barcelona, Spain, in conjunction with the CARS conference (http://www.cars-int.org/). It recorded 55 registered attendees, who worked on 39 projects. These attendees represented 20 academic sites (Boston Children’s Hospital, Brigham and Women’s Hospital, Charité University Hospital Berlin (Germany), École de Technologie Supérieure, (Canada), École supérieure d'informatique (Belgium), Fraunhofer (Germany), Leibniz University, Hannover (Germany), Magna Graecia University (Italy),Massachusetts General Hospital, Queen’s University (Canada), Robarts Research Institute (Canada), Semmelweis Medical University (Hungary), Universidad Autonoma del Estado de Mexico, Universidad Carlos III de Madrid, University of Groningen (Netherlands), Universidad de la Republica (Uruguay), Universidad Rey Juan Carlos (Madrid), Universidad Politécnica de Madrid, University of Strasbourg (France), University of Utah, and 7 companies (Kitware, Isomics Inc,Open Connections, Galgo Medical, BK Medical ApS, ICM, Perk Lab).

Logistics

• Dates: June 21-24, 2015.
• Location: NH Collection Constanza Hotel, Barcelona, Spain
• REGISTRATION: Please register by adding your name to the list at the end of this page
• Registration Fee: None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
• Hotel: You are welcome to book a room using the CARS 2015 conference services (Click here for form)
• To attend the CARS meeting, please visit http://www.cars-int.org/
• Premium Network at Berlin Room:
  • username: EVENT/CARS2015
  • Password=CARS

• Please get a badge for CARS, even if you did not register for the CARS conference. Otherwise you will not be able to come in tomorrow.

Agenda

Time	Sunday, June 21	Monday, June 22 Room Berlin	Tuesday, June 23 Room Berlin	Wednesday, June 24 Room Berlin
9:00am-3:00pm:	6pm Meeting with All Participants in Hotel Constanza Lobby	10:00-11am: Rapid Introduction of all Projects and Teams 11am-3pm Work	10:00am-11am: Breakout Session: - Ask expert physicians (Ron Kikinis, Clare Tempany) 11am-3pm Work	Work
1:00pm-3:00pm		Lunch Places to Eat	Lunch Places to Eat	Lunch Places to Eat
4:00-7:00pm		Work	5:00-7:00pm: Breakout Session: Open Software Stack (Steve Pieper) 4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges.	4:00-5:00pm: Work 4:30-6pm: Report Progress
7:00pm		Adjourn for the day Places to Eat	Adjourn for the day Sant Joan Festival	6:00pm Adjourn Project Week and relocate to CARS Opening 7:30pm CARS Welcome Reception

• Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
• Here is a list of locally recommended places to eat in the vicinity of the conference hotel. All participants are responsible for their own meals.

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. 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.

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

The 21st Project Week is being held on conjunction with the CARS conference.

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

Projects

• Template for project pages

Equipment

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

Image-Guided Therapy

• SlicerIGT tutorials for use cases (Tamas, Andras, Jay, Steve, Alvaro, Javier, Adam, Caroline, Noby, Tina)
• Refinement of RegistrationModule (Peter Behringer, Andrey Fedorov)
• Create base classes for IGT slicelet (Andras Lasso, Andrey Fedorov, Adam Rankin)
• BRAINSFit registration in SimpleITK (Peter Behringer, Andrey Fedorov, Dženan Zukić)
• Multi atlas based prostate segmentation (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
• Multimodal Guidance for Breast Cancer Surgery (Mikael Brudfors, David García, Javier Pascau)
• Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)
• Linear Feature Registration (Matthew Holden)
• Integration of a KUKA robot using OpenIGTLink (Sebastian Tauscher, Junichi Tokuda)
• Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer (Frank Preiswerk, Laurent Chauvin)
• Orthognathic Surgery (Dženan Zukić, Kitware)
• SlicerTAVI (Adam Rankin)
• pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)
• Open-source MRI-TRUS Fusion for Prostate biopsy (Andrey Fedorov, Andras Lasso, Clare Tempany)
• Trackerless MRI - US Registration (Utsav Pardasani)
• Sordina LINAC Guidance (Eugenio Marinetto)
• US Reconstruction (Steve Pieper, Tamas Ungi,Mikael Brudfors)

Feature Based Image Analysis

• LungCAD (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells, Clara Meinzer, Raúl San José Estepar, Jorge Onieva)
• Texture Analysis for Prostate Imaging (Tobias Penzkofer, Jay Jagadeesan, Matthew Toews, Tina Kapur)
• Big Data Medical Image Analysis using Local Features (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
• Automatic Cephalometric Analysis (J. Jesus Montufar, Marcelo Romero)

Chest Imaging Platform

• Slicer CIP: advanced features and deployment (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
• PAA Ratio Module (Jorge Onieva,Raúl San José)
• Planning for tracheal stents (Raúl San José, Jorge Onieva, George Cheng)
• Volumetric Quantification of Atelectasis (Ángel Torrado-Carvajal, Carolina Romero, Norberto Malpica)

QIICR

• Dynamic Susceptibility Contrast (DSC) MRI for brain (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
• T1 mapping for Dynamic Contrast Enhanced (DCE) MRI (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
• Integration and testing of new DCMTK with Slicer (Michael Onken, Andrey Fedorov, Steve Pieper)

Infrastructure

• Return fiducials from CLIs (Nicole Aucoin,Hans Meine)
• Integrated Virtual Reality Viewer (Franklin King, Utsav Pardasani)
• Use new Segmentation node in Editor (Andras Lasso, Steve Pieper)
• Integrate Conda Python in Slicer (Jorge Onieva, Raúl San José, Utsav Pardasani, Steve Pieper)

Web

• Dicom parsing with DCMJS (Nicolas Rannou, Yves Martelli, Michael Onken, Steve Pieper)
• Volume Rendering with DCMJS and THREEJS (Nicolas Rannou, Steve Pieper)
• CTK for the web and touch devices (Nicolas Rannou, Yves Martelli, Steve Pieper)
• Slicer for mobile-based vr goggles (Utsav Pardasani, Adam Rankin)
• Python developer tutorial (Adam Rankin)

Astronomy

• Visualization of HI in galaxies (Davide Punzo)

Registrants

Please add your name to the list. This is the registration mechanism for this project week.

1. Nicole Aucoin :: Brigham and Women's Hospital
2. Peter Behringer :: Brigham and Women's Hospital
3. Mikael Brudfors :: Charles III University of Madrid
4. Laurent Chauvin :: Brigham and Women's Hospital
5. Xiao Da :: Massachusetts General Hospital
6. Arnaud de Bruecker :: Ecole supérieure d'informatique
7. Caroline Essert :: University of Strasbourg
8. Andriy Fedorov :: Brigham and Women's Hospital
9. Sara Fernandez Vidal :: ICM
10. David García :: Charles III University of Madrid
11. Jorge García :: Technical University of Madrid
12. Guido Gerig :: University of Utah
13. Alvaro Gomez :: University of the Republic of Uruguay
14. Ali Gottschal :: Ecole supérieure d'informatique
15. Nobuhiko Hata :: Brigham and Women's Hospital
16. Alfredo Higueras :: Galgo Medical
17. Matthew Holden :: Queen's University
18. Jayender Jagadeesan :: Brigham and Women's Hospital
19. Laszlo Kanyasi :: Queen's University
20. Tina Kapur :: Brigham and Women's Hospital
21. Ron Kikinis :: Brigham and Women's Hospital
22. Franklin King :: Queen's University
23. Andras Lasso :: Queen's University
24. Eugenio Marinetto :: Charles III University of Madrid
25. Yves Martelli :: Galgo Medical
26. Clara Meinzer :: Semmelweis University
27. J. Jesus Montufar :: Universidad Autonoma del Estado de Mexico
28. Jorge Onieva :: Brigham and Women's Hospital
29. Michael Onken :: Open Connections
30. Robert H. Owen :: BK Medical ApS
31. Utsav Pardasani :: Robarts Research Institute
32. Javier Pascau :: Charles III University of Madrid
33. Tobias Penzkofer :: Charité Berlin Germany
34. Steve Pieper :: Isomics, Inc.
35. Giampaolo Pileggi :: Magna Graecia University
36. Frank Preiswerk :: Brigham and Women's Hospital
37. Sonia Pujol :: Brigham and Women's Hospital
38. Davide Punzo :: University of Groningen
39. Adam Rankin :: Robarts Research Institute
40. Nicolas Rannou :: Boston Children's Hospital
41. Marcelo Romero :: Universidad Autonoma del Estado de Mexico
42. Raul San Jose Estepar :: Brigham and Women's Hospital
43. Laura Sanz :: Charles III University of Madrid
44. Salvatore Scaramuzzino :: Magna Graecia University
45. Tsotne Shonia :: Ecole supérieure d'informatique
46. Sebastian Tauscher :: Leibniz Universität Hannover
47. Christophe Teixeira Pereira :: Ecole supérieure d'informatique
48. Clare Tempany :: Brigham and Women's Hospital
49. Matthew Toews :: Ecole de Technologie Superieure
50. Angel Torrado-Carvajal :: King Juan Carlos University
51. Tamas Ungi :: Queen's University
52. Sandy Wells :: Brigham and Women's Hospital
53. Paolo Zaffino :: Magna Græcia University of Catanzaro
54. Yulong Zhao :: University of Rennes
55. Dženan Zukić :: Kitware, Inc.