In recent years, various terms the Virtual Physiological Human (VPH), Integrative Biology, Physiome Research have been used to describe the trend in biomedical research towards the consideration of systemic processes. These phenomena are commonly observed in living organisms but cannot be explained within a single sub-system but reflect, rather, systemic outcomes that result from the interaction of multiple sub-systems. Traditionally, when confronted by the complexity exhibited in biomedical problems, researchers have been forced to focus purely on individual sub-systems; the most common boundary separating these has been spatiotemporal scale.
The current interest in VPH is demanding greater concentration on the study and simulation of biological systems at multiple scales, and multiscale data collection and multiscale modelling have recently become synonymous with integrative research. The many VPH projects that will start to demand multiscale visualisation in the coming years suggests that this area should receive urgent attention. The Multiscale Spatiotemporal Visualisation (MSV) project aims, by international cooperation between the European @neurIST and VPHOP integrated projects, the US National Alliance for Medical Imaging Computing (NA-MIC), and the New Zealand-based IUPS Physiome initiative:
- to define an interactive visualisation paradigm for biomedical multiscale data,
- to validate it on the large collections produced by the VPH projects
- to develop a concrete implementation as an open-source extension to the Visualisation Took Kit (VTK), ready to be incorporated by virtually any biomedical modelling software project.
MSV Project is partially funded by the European Commission under the Information Communication Technologies Programme.
The project partners are the following:
- SCS SRL, Italy
- UNIVERSITAT POMPEU FABRA, Spain
- UNIVERSITY OF BEDFORDSHIRE, United Kingdom
- KITWARE INC., United States of America
- THE UNIVERSITY OF AUCKLAND, New Zealand
Description of target users and groups
Users of the MSV project results are most of all developers of biomedical and computer-aided applications, but also bioengineers and clinical reserachers who have to design an application to support diagnosis and treatment having to support multiscale data navigation and visualisation.
Description of the way to implement the initiativeThe global objectives of the MSV project have been four:
- Shared vision: to develop a white paper on biomedical multiscale visualisation to capture the shared vision.
- Exemplary problems: to create a collection of exemplary problems that the multiscale visualisation paradigm should solve effectively and to be used to validate the concrete implementation.
- Best practice: to define, on the basis of the shared vision, the essential characteristics that any biomedical multiscale visualisation application should have and the criteria that programmers should use to guide their development.
- Shared implementation: to develop a concrete software implementation, based on best practice, as an extension to the popular VTK visualisation library.
The Multiscale Visualisation ToolKit (MSVTK) born and it is being developed to solve the specific challenges of multiscale visualisation and interaction with biomedical data. MSVTK is a C++ open-source software library based on VTK, which allows to easily add to your computer-aided medicine applications support to the interactive visualisation of multiscale data.Technology choice: Proprietary technology
Main results, benefits and impactsTHe project is producing a number of results which are here listed and which are available in the project-related websites.
- Shared vision. The consortium had put together a “White paper” on biomedical multiscale visualisation to capture the state of the art in multiscale visualisation also outside the biomedical domain, to summarise the main MSV concepts, and to formalise it into a taxonomy for multiscale visualisation.
- Exemplary problems. The consortium has collected a set of exemplary problems from different biomedical domains that the multiscale visualisation paradigm should solve effectively; these examples have been used to define the MSV challenges and priorities to be addressed in the implementation phase and they will be used to validate the concrete implementation.
- Moreover the consortium has used the data collection to identify the multiscale visualisation problem challanges.
- Best practice. A survey has been undertaken on the different forms that multiscale data may take, the common problems that need to be addressed and the techniques that may be applied to deal with them. For the purposes of the MSV project, the report defines, on the basis of the shared vision, the essential characteristics that any biomedical multiscale visualisation application should have and the criteria that programmers should use to guide their development.
- Collaborative tools: The consortium has reviewed the tools available for an efficient joint implementation of an open source. This allows MSV partners to deploy a state of the art collaborative environment for the development phase. This activity has been associated to the important decision on the licence model for the MSV library: to encourage a large adoption by the community a BSD-like licence will be associated to the MSV software releases.
- The last but not least achievement is the open-source library development, which is made available world-wide under an open-source licence.
This field will be completed by the submitter when the lessons learnt have been identified and understood.Scope: International