derek hill kcl, imperial, oxford ixi.uk
DESCRIPTION
Derek Hill KCL, Imperial, Oxford http://www.ixi.org.uk. Team. Derek Hill, Kelvin Leung, Bea Sneller, Jinsong Ren, Julia Schnabel, Jason Harris KCL Jo Hajnal, Daniel Rueckert, Michael Burns, Andrew Rowland, Rolf Heckerman, Carlos Thomaz, Imperial Steve Smith, John Vickers, Oxford. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/1.jpg)
Derek HillKCL, Imperial, Oxfordhttp://www.ixi.org.uk
![Page 2: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/2.jpg)
Team
• Derek Hill, Kelvin Leung, Bea Sneller, Jinsong Ren, Julia Schnabel, Jason Harris KCL
• Jo Hajnal, Daniel Rueckert, Michael Burns, Andrew Rowland, Rolf Heckerman, Carlos Thomaz, Imperial
• Steve Smith, John Vickers, Oxford
![Page 3: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/3.jpg)
Information eXtraction from Images (IXI)
• 3 year UK e-science project funded by core programme– Additional support from GSK, Philips
Medical Systems, Dunhill Charitable Trust
• Uses grid-enabled image registration and segmentation for drug discovery, medical research, and decision support in healthcare.
![Page 4: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/4.jpg)
Image registration
Reference image(example slice)
Database subject image(example slice)
![Page 5: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/5.jpg)
Brain image segmentation
![Page 6: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/6.jpg)
Application to large cohorts
Example slicesFrom MRI Volumeimages
![Page 7: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/7.jpg)
Research activities
• Image acquisition and analysis– Between all sites have about 100 full
time image analysis researchers (students and post-docs)
– We distribute various image analysis s/w, including image-registration.com (KCL) and FSL (from Oxford)
![Page 8: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/8.jpg)
![Page 9: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/9.jpg)
Why IXI?
• We call this project Information eXtraction from Images to emphasize the key concept which is using image analysis to generate image metadata – information about the images – and the generic applicability of this technology.
![Page 10: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/10.jpg)
Why the grid?• Data grid
– Sharing distributed image databases– Enables collaborative working
• Compute grid– “on demand” computing provided by distributed
infrastructure– Users can access high performance computing when they
need it– Algorithms presented as grid services that can be combined
with workflow tools– Provenance tools (eg: Chimera) to provide “electronic paper
trail” – evolving link with Wilde/Foster Argonne National Lab
• People in “virtual organizations”– Researchers can work together more effectively– New ways for industry and academia to collaborate
![Page 11: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/11.jpg)
Technical aims
• Scalability – To show that the grid can scale medical image analysis
to huge cohorts, using condor between sites
• Ability to share data across sites– Interoperable databases– Secure file transfer to trusted machines
• Grid services for image analysis– Wrap image analysis algorithms to create grid service
• Provenance– Keep track of how all results were obtained
• Information Extraction methodology– New algorithm that take advantage of the grid
![Page 12: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/12.jpg)
Exemplars
• Developmental neuroimaging– Neonates from Hammersmith– Children/teens from Institute of Psychiatry
• Drug discovery– Pre-clinical brain and joint imaging
• Decision support in healthcare– Normative reference data in “dynamic brain
atlas”
• Cardiac MRI dynamic image analysis
![Page 13: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/13.jpg)
Normative MRI reference data
• 600 normal subjects, approximately uniformly distributed between 18 and 80
• T1 volumes, multislice spin echo, [angio and DTI on sub-cohort]
• medical history questionnaire• 1.5T and 3T scanners, different vendors• Ethics approval for sharing on grid
![Page 14: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/14.jpg)
Achievements
• Wrapping of image registration algorithms from within our consortium and also from a group at INRIA in France for demonstration of grid-enabled cross-validation of algorithms (demonstration at HealthGrid 2004,Clermont- Ferrand)
• Testbed based on XML workflow schema providing web access to grid services
• Use of IXI components to delineate talus and calcaneus from wrist to quantify disease progression in model of rheumatoid arthritis (collaboration with GSK) – Paper presented at IEEE ISBI conference, April, USA
![Page 15: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/15.jpg)
Images onlocal client Globus
Web-based portal
Imperial Condor Cluster
Local client
INRIA MPICluster
Architecture for intraoperatible image registration (health grid demo)
![Page 16: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/16.jpg)
![Page 17: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/17.jpg)
![Page 18: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/18.jpg)
![Page 19: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/19.jpg)
![Page 20: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/20.jpg)
IXI testbed
• Resources– 400 node sun grid engine cluster, London e-
science centre– 200 node condor installation, Imperial
College– 45 node condor installation, KCL– Distributed image database, 3 sites (MySQL
based, directly connected to MR scanners for data acquisition at 2 sites)
– globus installed at each site
![Page 21: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/21.jpg)
IXI test bed system design
• xml schema language to describe existing image analysis applications– Defines common types, parameters, i/o of
each component, relationships between input and output
– Defines categorisation information for application discovery
– Used to construct image analysis workflows
![Page 22: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/22.jpg)
IXI testbed Workflow Service
• OGSI compliant GT3 service, executes workflow based on xml schema
• Maps workflow to RSL specification or grid service invocation
• Handles dependencies between each workflow stage
• Tries to execute as much of workflow in parallel as possible.
![Page 23: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/23.jpg)
IXI testbed service discovery
• OGSI based registry deployed at each site
• Users can register applications that they wish to make available to the project
• Registries aggregated to project-wide registry, which can be queried by user
![Page 24: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/24.jpg)
IXI testbed Example Application
• demonstrator– Database can be queried for head scans (one
selected as reference) which are accessed by the workflow engine using grid-ftp
– Each head passed through workflow to extract brain
– All images aligned with reference– Atlas of variability produced– Accessible via a web server for users without
globus installed– Aim to demonstrate easy of analysis for non-
expert users.
![Page 25: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/25.jpg)
Drug discovery with provenance
• Pharmaceutical industry in investing massively in imaging (eg: £70+m investment at Imperial announced last month)
• For drug discovery, keeping track of exactly how result were obtained is critical
• We use the Virtual Data Systems Chimera system within a web interface to do this
![Page 26: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/26.jpg)
Application - drug discovery
• Disease model of Rheumatoid Arthritis (RA)
• Injected with disease inducing agent• MR images were acquired• Interested in talus and calcaneus• Identify them from the MR images
and study them, e.g. calculate volume to measure any erosion
![Page 27: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/27.jpg)
Reference (atlas)image
Target image
Rigid + non-rigidregistration
Displacement field
Manual segmentation
Apply displacement field
Computed boundary of calcaneus
Segmentation Propagation
calcaneus
![Page 28: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/28.jpg)
IXI provenance system
• Web interface wrapped around VDS, Globus Toolkit 2.4 and Condor
• Tomcat (https), VDS, Globus client, Condor on my machine– Web portal
• Globus gatekeeper, GridFTP server, Globus RLS, Condor on another machine– Storage site and execution site
• Not yet integrated with IXI testbed
![Page 29: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/29.jpg)
My systemservices
![Page 30: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/30.jpg)
My system
Service to delineate the calcaneus and talus from the target image
target reference_image
rigid registration
cal_seg
calcaneus cal_dof
segmentation propagation
segmentation propagation
aregdof
talus_seg
talus tal_dof
![Page 31: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/31.jpg)
My system
![Page 32: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/32.jpg)
My system
Jobs generated
![Page 33: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/33.jpg)
My systemJob status in Condor
![Page 34: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/34.jpg)
My systemClick to download files and view in vtkview
![Page 35: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/35.jpg)
Result – intra-subject registration
Day +3
Overlay images with the computed boundaries of calcaneus highlighted
![Page 36: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/36.jpg)
Result – inter-subject registration
Overlay images with the computed boundaries of calcaneus highlighted
Day -12
![Page 37: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/37.jpg)
My systemService to render the surfaces of the bones
![Page 38: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/38.jpg)
My systemJob submitted
Job status
![Page 39: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/39.jpg)
My system
![Page 40: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/40.jpg)
My systemBrowse all the executed services
and click on a file to view the history
![Page 41: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/41.jpg)
My system
![Page 42: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/42.jpg)
Provenance requirements
• Access control and security– We have some unusual
provenance requirements– Provenance information needs
access control so not everyone can see provenance of data
– We have started a collaboration with Mike Wilde and Ian Foster using our application as a use case for VDS.
![Page 43: Derek Hill KCL, Imperial, Oxford ixi.uk](https://reader030.vdocuments.us/reader030/viewer/2022020717/56812de5550346895d933e32/html5/thumbnails/43.jpg)
Conclusions
• Medical image analysis has some characteristics that make it well suited to grid computing– Algorithms have increasing computational
complexity (> moores law)– There is a need to deal with larger data
volumes– Latency is not critical– Collaboration is essential– Regulatory environment requires good
curation and provenance