Biobanking

Mass spectrometry

Microarray technology

Nanoscopy and imaging

Next generation sequencing

NMR Spectroscopy


Generic infrastructure

Medical Imaging

MDI

Medical imaging enables non-invasive observation of living tissue and it is widely used for clinical care and research. A variety of acquisition modalities (CT, MRI, etc) generate images that are increasingly detailed, large and complex. The challenges for data management and analysis are also increasingly large, and distributed infrastructures such as grids and clouds have been adopted to address them. In the Netherlands the first attempts to run for medical image analysis on the Dutch Grid were done by the Medical Imaging and Diagnosis program of the Virtual Laboratory for e-Science project (VL-e). Currently these efforts continue in various academic hospitals and universities.

e-BioGrid is open to take more Medical Imaging dedicated projects on board. Contact us if you are involved in Medical Imaging and you need support in software or hardware infrastructure.


Projects in this technology area

Medical Imaging on the e-BioInfra platform *
description:The e-infrastructure for bioscience research, e-bioinfra, is routinely used by researchers at the AMC to perform medical image analysis on the Dutch Grid. The image analysis pipelines are implemented as workflows that are executed on the grid in an automated fashion. Various neuroimaging applications have been ported to this platform and made available for researchers from the Radiology, Psychiatry and other clinical departments at the AMC. The web interface of the e-bioinfra gateway provides easy access to novice users to applications such as FreeSurfer (brain surface segmentation) and DTI atlas construction. The goal of the project is to enable and enhance medical imaging research via advanced tools for data analysis. This is achieved in close collaboration with medical imaging researchers.
applicant:Silvia Olabarriaga, on behalf of the VLEMED VO, Amsterdam Medical Centre / University of Amsterdam
results:Users of the e-BioInfra Gateway, the web interface to the e-BioInfra platform for non-expert users, can now analyse their medical imaging data with the FSL BEDPOSTX on the BiG Grid resources. e-BioInfra Gateway is now equipped with four medical imaging and three sequencing data analysis applications that are utilized by the AMC researchers. For more information please refer to the gateway documentations.

S.D. Olabarriaga, T. Glatard, P.T. de Boer, "A Virtual Laboratory for Medical Image Analysis", IEEE Transactions on Information Technology In Biomedicine (TITB), 2010 Apr 5.
M.W.A. Caan, F.M. Vos, L.J. van Vliet, A.H.C. van Kampen, S.D. Olabarriaga. "Gridifying a Diffusion Tensor Imaging Analysis Pipeline". Proceedings of the 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid 2010) Melbourne, VIC, Australia, May 17-May 20. IEEE Computer Society. pp.733-738, 2010.
T. Glatard, R. S. Soleman, D. J. Veltman, A.J. Nederveen, S. D. Olabarriaga. Large scale functional MRI study on a production grid, Future Generation Computer Systems vol. 26, no. 4, pp. 685-692, 2010
status:ongoing
team:Matthan Caan, Silvia Olabarriaga, Antoine van Kampen, Mark Santcroos, Jan Just Keijser, Shayan Shahand, Vladimir Korkhov, Souley Madougou
type:This is a main project.
Testing the feasibility of Massive MRI data analysis
description:Magnetic resonance Imagery is a modern technique for recording brain activity. The analysis of this data, both functional and anatomical, will undoubtedly bring new insights in the neural basis of cognitive functioning. Up to now the complexity of analysis has been determined by the available computational power and certain types of approaches have been avoided in typical analytical approaches. In this project we want to evaluate whether is it feasible to use computational heavy approaches to noise reduction, and anatomical and functional connectivity methods, for the normal experiments that are being conducted at the Spinoza Center for NeuroImaging.
applicant:Steven Scholte, University of Amsterdam
results:anticipated results: Matlab module to serve standard fMRI preprocessing tool for all brain and cognition researchers, and a DTI analysis tool for new type of connectivity analysis
status:ongoing
team:Steven Scholte, Sennay Ghebreab, Lourens Waldorp, Caan Matthan
type:This is a dedicated project.


* This is the main project in this technology area

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