Johan Montagnat Lyon, April 28, 2006 NA4 biomed EGEE-II quick-off meeting Work organisation in medical imaging Johan Montagnat Lyon, April 28, 2006

Applications deployed in EGEE-I CDSS UPV (University Polytechnic of Valencia) Pharmacokinetics GATE LPC (CNRS – Clermont Ferrand) SiMRI3D CREATIS (CNRS - Lyon) gPTM3D LRI-LAL-LIMSI (CNRS - Orsay) Bronze Standard I3S (CNRS – Sophia), INRIA EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

CDSS: Clinical Decision Support System Scientific objectives Extract clinically relevant knowledge from a large set of information with the objective of guiding the practitioners in their clinical practice. Similar (but non computer-based) systems exist since the 1950s. Example: “what are the genetic factors that can be involved in schizophrenia”? CDSS does reinforce human decision by improving factors such as sensitivity, sensibility, and working conditions. Method Starting from trained databases such as classification of tumours soft tissues or classification of thalassemia and other anemia. Use classifier engines and compare to annotated databases to classify data. EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Pharmacokinetic:s contrast agent diffusion Scientific objectives The study of Contrast Agent Diffusion can characterize tumour tissues without requiring biopsy. The process requires obtaining a sequence of MRI volumetric images. Before analyzing the variation of each voxel, images must be co-registered to minimize deformation due to different breath holds. Method The co-registration in the abdomen requires deformable registration methods. The Sequence of Images is co-registered with respect to the first volume. Voxel X,Y in all images must refer to the same body location. Co-registration is compute intensive, especially when dealing with many input images. EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

GATE: radiotherapy planning Scientific objectives Radiotherapy planning for improving the treatment of cancer by ionizing radiations of the tumours. Therapy planning is computed from pre-treatment MR scans by accurately locating tumours in 3D and computing radiation doses applied to the patients. Method GEANT4 base software to model physics of nuclear medicine. Use Monte Carlo simulation to improve accuracy of computations (as compared to the deterministic classical approach) EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

SiMRI3D: MRI simulator Scientific objectives Better understand MR physics. Study MR sequences in-silico. Study MR artefacts. Validate MR Image processing algorithms on synthetic yet realistic images. Method Simulate Bloch's electromagnetism equations. Paralle (MPI)l implementation to speed- up computations. EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

gPTM3D: radiology analysis Scientific objectives Interactive volume reconstruction on large radiological data. PTM3D is an interactive tool for performing computer-assisted 3D segmentation and volume reconstruction and measurement (RSNA 2004) Reconstruction of complex organs (e.g. lung) or entire body from modern CT-scans is involved in augmented reality use case e.g. therapy planning. Method Starting from an hand-made rough Initialization,a snake-based algorithm segments each slice of a medical volume. 3D reconstruction is achieved in parallel by triangulating contours from consecutive slices. EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Bronze Standard: assessment Scientific objectives Evaluate medical image registration algorithms in the absence of reference gold standard. Method Through the MOTEUR workflow engine, the computation of a bronze standard takes a couple of hours only. It enables systematic assessment procedures for medical image registration algorithms. The application should be extended to integrate more algorithms. It should deploy an open portal to allow developers to integrate their own algorithm in the workflow. EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

First task: identification of requirements CDSS Fast turn over of short jobs, data confidentiality GATE Data parallel problem, data confidentiality Pharmacokinetics Data parallel problem + code parallelism SiMRI3D MPI compute intensive code, web portal gPTM3D Interactivity, fast turn over of very short jobs, data confidentiality Bronze Standard Workflow computing, data sets federation, data confidentiality EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Requirements in EGEE-I Challenging set of requirements for a grid infrastructure! PTF (Project Technical Forum) detailed analysis Savannah PTF project: http://savannah.cern.ch/support/?group=egeeptf Reqs #100564 to #100459 for biomed in particular TCG services-wise approach TCG twiki: https://uimon.cern.ch/twiki/bin/view/EGEE/PriorityList Service-requirement matrices produced More to do, at an application level Data access control policies User roles ... EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Application level services Medical Data Manager Grid storage interface to DICOM databases Represented in a TCG Working Group Trencadis developed at UPV? Data protection Encryption (storage/network protection) Access control (privacy protection) Two existing systems: Hydra key store integrated in gLiteIO (JRA1) Perroquet (Parrot based, IBCP) Data parallel workflows Data intensive service composition-based applications EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Hospital Medical Data Manager DICOM server File Catalog AMGA Metadata Storage Element Trigger file registration Encryption Key store User Interface Worker Node SRM-DICOM interface Hospital DICOM GET DICOM PUSH DICOM server EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Medical Data Manager Medical Data Management library and medical imaging frontend SRM DICOM storage manager Built-in encryption of the file before releasing to the grid Storing the encryption keys in the Hydra keystore Registration of the file in the Fireman catalog Registration of DICOM metadata in AMGA catalog gLite I/O with encryption/decryption capability Standard glite I/O client interaction Hydra keystore key lookup Client-side decryption AMGA Metadata Catalog Storage of Metadata for DICOM images EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Workflow management MOTEUR http://www.i3s.unice.fr/~gla tard/ Service-based approach Legacy code service wrapper Grid submission interfaces EGEE Grid5000 Transparent parallelism exploitation Data parallelism Code parallelism EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Future services? More data protection Role-based access control Considering multiple actors involved in clinical procedures (patient, doctor, surgeon, radiologist, nurse, anesthesist...) Data semantics Metadata associated to data (AMGA metadata catalog) Ontologies Content-based data identification, indexing, mining... User interfaces Integrated in end-users environments Often specific to application EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

EGEE-I achievements Requirements analysis Applications deployment 6 applications to medical imaging (12 in the biomed activity) Regular infrastructure usage for production ~25 Kjobs per month Not so compute intensive, large scale computations in Drug Discovery area for molecular docking (Data Challenges) First data management tools Data protection, Medical Data Manager Deployment not achieved, more to do in this area Recognized pilot area EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Challenges in front of us Get out of the usecases implementation / deployment phase More production More scientific results in the medical area Touch the real end-users (physicians, clinicians) Grid adoption, uncontested security Adapted interfaces / portal More specific services Interconnect hospital data networks to the grid Find a killer application New scientific results, for which grid infrastructure was mandatory EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006

Plan of work Consolidate requirements Probably little to do in this area Porting / evolving applications The real challenge is to find relevant applications Validation of the EGEE infrastructure Through scientific production New services developments and sharing Which ones? Fostering application communities EGEE bodies VO management, OAG, TCG... EGEE-II NA4/biomed kickoff meeting, J. Montagnat, Lyon, April 28, 2006