1. Seamless Medical Image Processing on the Grid on the Example of Segmentation and Partition of the Airspaces Andrzej Rutkowski 1, Michał Chlebiej 1, Marcelina Borcz 2, Rafał Kluszczyński 2, Krzysztof Benedyczak 2 Piotr Bała 2 bala@icm.edu.pl 1 WMiI, Nicolaus Copernicus University, Toruń, PL 2 ICM, University of Warsaw, Warsaw, PL

2. Outline  Motivation  PL-Grid infrastructure resources middleware  Segmentation and Partition of the AirspacesSolution  Details of the solution  Conclusions eTELEMED 2015Piotr Bała 2

3. Motivation  Analysis of the medical images is important part of the medical doctor activities  Growing need for use of CPU intensive applications providing better analysis  Distributed resources available  Requirement for seamless access  Web portal as preferred access method  Existing web portals are complicated, difficult to install and maintain  Requirement for strong security processing of medical images eTELEMED 2015Piotr Bała 3

4. PL-Grid  National Grid Initiative  Partners: Polish supercomputer centers: Cyfronet, ICM, PCSS, WCSS, TASK  Project aims: Build and operate Polish National Grid Provide training and user’s support Provide support for application deployment on the grid  ICM role in PL-GRID Operate UNICORE infrastructure Domain applications: health, materials Piotr Bała 4 eTELEMED 2015

5. UNICORE 7 Architecture Piotr Bała 5 Computational Resources Data Storages Databases Client Layer Target System Interface Target System Files Execution Manager UNICORE 6 Hosting Environment SECURITY WSRF Container User DB Policies Gateway HTTPS Registry Atomic Services Other Services HTTPS / HTTP eTELEMED 2015

6. UNICORE Client framework  Eclipse-based rich client  Eclipse based workflow editor  Command line client  Web client  UNICORE Portal Piotr Bała 6 eTELEMED 2015

7. UNICORE portal – Generic gridbean Piotr Bała 7 eTELEMED 2015

8. UNITY IDP  Authentication who is who wide range of mechanisms & security levels  Federations where do they come from?  Authorization levels The relying system must be able to decide easily who has an access granted  Privacy from none to paranoid  Identity management as a service Could be used for grids and clouds eTELEMED 2015Piotr Bała 8

9. UNICORE – UNITY Integration eTELEMED 2015Piotr Bała 9

10. CT image segmentation eTELEMED 2015Piotr Bała 10

11. Segmentation process  CT image set (DICOM-Dir) is used as starting point  CT data is selected  Affine registration  Free Form Deformation parametrized by B-splines.  The resulting deformation field is segmented  Volumetric tuning of every segment boundary using patients original data. segmentation proces depends on the image library eTELEMED 2015Piotr Bała 11

12. Deformation eTELEMED 2015Piotr Bała 12

13. Deformation eTELEMED 2015Piotr Bała 13

14. UNICORE Portal – job preparation eTELEMED 2015Piotr Bała 14

15. UNICORE Portal – job execution eTELEMED 2015Piotr Bała 15

16. UNICORE Portal – Job output eTELEMED 2015Piotr Bała 16

17. UNICORE Portal – Job output eTELEMED 2015Piotr Bała 17

18. Conclusions  Grid technology became mature enough to offer reliable, high quality services designed to suit requirements of different scientific communities.  UNICORE Portal offers web interface and automation of the processing of selected applications  The medical doctors can focus on diagnosis instead of writing complicated scripts, transferring the files and mastering complicated IT infrastructure.  With the UNICORE Portal creation of the application and domain specific solution become simple and straightforward.  The software stack necessary to build full featured gateway is now small and easy to handle. eTELEMED 2015Piotr Bała 18

19. Acknowledgmens  This research was supported in part by the PL-Grid Infrastructure.  The authors thank prof. A. Kukwa from Faculty of Medical Sciences, University of Warmia and Mazury for providing inspiration and medical data for tests. eTELEMED 2015Piotr Bała 19