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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. Requirements in EGEE-I
Challenging set of requirements for a grid infrastructure!
PTF (Project Technical Forum) detailed analysis
Savannah PTF project:
Reqs # to # for biomed in particular
TCG services-wise approach
TCG twiki:
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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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