Johan Montagnat

Flexible and Efficient Workflow Deployment of Data-Intensive Applications On Grids With MOTEUR

Workflows offer a powerful way to describe and deploy applications on grid infrastructures. Many workflow management systems have been proposed but there is still a lack of a system that would allow both a simple description of the dataflow of the application and an efficient execution on a grid platform. In this paper, we study the requirements of such a system, underlining the need for well-defined data composition strategies on the one hand and for a fully parallel execution on the other. As combining those features is not straightforward, we then propose algorithms to do so and we describe the design and implementation of MOTEUR, a workflow engine that fulfills those requirements. Performance results and overhead quantification are shown to evaluate MOTEUR with respect to existing comparable workflow systems on a production grid.

4D deformable models with temporal constraints: application to 4D cardiac image segmentation

Segmentation of time series of 3D cardiac images is clinically used for the assessment of the mechanical function of the left ventricle. To take into account the 4D (3D+T) nature of those images, we propose to extend the deformable surface framework by introducing time-dependent constraints. Thus, in addition to computing an internal force for enforcing the regularity of the deformable model, prior motion knowledge is introduced in the deformation process through either temporal smoothing or trajectory constraints. In this paper, deformable surfaces are represented as simplex meshes owing to their generality and their ability to compute mean curvature at each vertex. The segmentation accuracy of this 4D deformable model is estimated on synthetic SPECT image sequences for which a ground truth about the LV volume is known. Segmentation of non-synthetic SPECT and other modalities 4D images is also discussed.

Texture based medical image indexing and retrieval: application to cardiac imaging

Although digital images indexing and querying techniques have extensively been studied for the last years, few systems are dedicated to medical images today while the need for content-based analysis and retrieval tools increases with the growth of digital medical image databases. We analyze medical image properties and we evaluate Gabor-filter based features extraction for medical images indexing and classification. The goal is to perform clinically relevant queries on large image databases that do not require user supervision. We demonstrate on the concrete case of cardiac imaging that these techniques can be used for indexing, retrieval by similarity queries, and to some extent, extracting clinically relevant information out of the images

Globally constrained deformable models for 3D object reconstruction

Abstract To achieve geometric reconstruction from 3D datasets two complementary approaches have been widely used. On one hand, the deformable model framework locally applies forces to fit the data. On the other hand, the non-rigid registration framework computes a global transformation minimizing the distance between a template and the data. We first show that applying a global transformation on a surface template, is equivalent to applying certain global forces on a deformable model. Second, we propose a scheme which combines the registration and free-form deformation. This globally constrained deformation model allows us to control the amount of deformation from the reference shape with a single parameter. Finally, we propose a general algorithm for performing model-based reconstruction in a robust and accurate manner. Examples on both range data and medical images are used to illustrate and validate the globally constrained deformation framework.

Medical Images Simulation, Storage, and Processing on the European DataGrid Testbed

The European 1ST DataGrid project was a pioneer in identifying the medical imaging field as an application domain that can benefit from Grid technologies. This paper describes how and for which purposes medical imaging applications can be Grid-enabled. Applications that have been deployed on the DataGrid testbed and middleware are described. They relate to medical image manipulation, including image production, secured image storage, and image processing. Results show that Grid technologies are still in their youth to address all issues related to complex medical imaging applications. If the benefit of Grid enabling for some medical applications is clear, there remain opened research and technical issues to develop and integrate all necessary services.

A data-driven workflow language for grids based on array programming principles

Different scientific workflow languages have been developed to help programmers in designing complex data analysis procedures. However, little effort has been invested in comparing and finding a common root for existing approaches. This work is motivated by the search for a scientific workflow language which coherently integrates different aspects of distributed computing. The language proposed is data-driven for easing the expression of parallel flows. It leverages array programming principles to ease data-intensive applications design. It provides a rich set of control structures and iteration strategies while avoiding unnecessary programming constructs. It allows programmers to express a wide set of applications in a compact framework.

A Service-Oriented Architecture enabling dynamic service grouping for optimizing distributed workflow execution

In this paper, we describe a Service-Oriented Architecture allowing the optimization of the execution of service workflows. We discuss the advantages of the service-oriented approach with regard to the enactment of scientific applications on a grid infrastructure. Based on the development of a generic Web-Services wrapper, we show how the flexibility of our architecture enables dynamic service grouping for optimizing the application execution time. We demonstrate performance results on a real medical imaging application. On a production grid infrastructure, the optimization proposed introduces a significant speed-up (from 1.2 to 2.9) when compared to a traditional execution.

Using grid technologies to face medical image analysis challenges

The availability of digital imagers inside hospitals and their ever growing inspection capabilities have established digital medical images as a key component of many pathologies diagnosis, follow-up and treatment. To face the growing image analysis requirements, automated medical image processing algorithms have been developed over the two past decades. In parallel, medical image databases have been set up in health centers. Some attempts have been made to cross data coming from different origins for studies involving large databases. Grid technologies appear to be a promising tool to face the raising challenges of computational medicine. They offer wide area access to distributed databases in a secured environment and they bring the computational power needed to complete some large scale statistical studies involving image processing. In this paper, we review grid-related requirements of medical application that we illustrate through two real examples.

Reliability Support in Virtual Infrastructures

Through the recent emergence of joint resource and network virtualization, dynamic composition and provisioning of time-limited and isolated virtual infrastructures is now possible. One other benefit of infrastructure virtualization is the capability of transparent reliability provisioning (reliability becomes a service provided by the infrastructure). In this context, we discuss the motivations and gains of introducing customizable reliability of virtual infrastructures when executing large-scale distributed applications, and present a framework to specify, allocate and deploy virtualized infrastructure with reliability capabilities. An approach to efficiently specify and control the reliability at runtime is proposed. We illustrate these ideas by analyzing the introduction of reliability at the virtual-infrastructure level on a real application. Experimental results, obtained with an actual medical-imaging application running in virtual infrastructures provisioned in the experimental large-scale Grid’5000 platform, show the benefits of the virtualization of reliability.

A Secure Grid Medical Data Manager Interfaced to the gLite Middleware

The medical community is producing and manipulating a tremendous volume of digital data for which computerized archiving, processing and analysis is needed. Grid infrastructures are promising for dealing with challenges arising in computerized medicine but the manipulation of medical data on such infrastructures faces both the problem of interconnecting medical information systems to Grid middlewares and of preserving patients’ privacy in a wide and distributed multi-user system. These constraints are often limiting the use of Grids for manipulating sensitive medical data. This paper describes our design of a medical data management system taking advantage of the advanced gLite data management services, developed in the context of the EGEE project, to fulfill the stringent needs of the medical community. It ensures medical data protection through strict data access control, anonymization and encryption. The multi-level access control provides the flexibility needed for implementing complex medical use-cases. Data anonymization prevents the exposure of most sensitive data to unauthorized users, and data encryption guarantees data protection even when it is stored at remote sites. Moreover, the developed prototype provides a Grid storage resource manager (SRM) interface to standard medical DICOM servers thereby enabling transparent access to medical data without interfering with medical practice.