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Multiscale visualisation: Exemplary problems collection and assessment

by Debora Testi last modified 2011-02-15 13:46

The EU has funded 5 institutions to investigate and address challenges associated with multiscale spatiotemporal visualization (MSV) as an international cooperation starting from the VPHOP project. The ultimate goal of this effort is to produce open-source extensions to VTK that support MSV and that can be incorporated into Slicer (http://www.slicer.org/), OpenMAF (http://www.openmaf.org), GIMIAS (http://www.gimias.org), CTK (www.commontk.org), and other open-source biomedical applications. The project is now collecting from the biomedical community input on exemplary problems that could be effectively solved by an MSV approach.

The MSV project will, 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:

  1. define an interactive visualisation paradigm for biomedical multiscale data,
  2. validate it on the large collections produced by the VPH projects, and
  3. develop a concrete implementation as an open-source extension to the Visualisation Toolkit (VTK), ready to be incorporated by virtually any biomedical modelling software project.

  

This global objective will be pursued in four steps:

  • Shared vision. The consortium will develop a white paper on biomedical multiscale visualisation to capture the shared vision and will update it regularly over the course of the project.
  • Exemplary problems. The consortium will create a collection of exemplary problems from different VPH-I projects that the multiscale visualisation paradigm should solve effectively; these will be used to validate the concrete implementation.
  • Best practice. The Best Practice report will 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. A concrete software implementation, based on best practice, will be developed as an extension to the popular VTK visualisation library and will be made available to the worldwide research community under an open source licence.

 

The consortium partners have started contacting representative from many VPH-I projects to get input both for the exemplary problems identification and collection and for the approach to be followed.

In this context we invite anyone with a project with MSV components or with suggestions on challenges or solutions regarding MSV, to get in contact with us. Any form of contribution is welcome, but it would be particularly helpful if you could provide the following:

 

  • a short description of the problem being addressed, including the range of scales involved;
  • the sources/types of data as input;
  • existing visualizations and models being used;
  • the expected outcome (e.g., data to be produced or hypothesis to be tested); and
  • references to websites and/or publications that provide more information.

 

Furthermore, we welcome references to or the contribution of exemplary data that we and others can use in the development and testing of MSV solutions.

We understand that it can be difficult to find time to answer surveys such as this one, but by contributing at this early stage you can help guide our efforts to produce solutions that fit your needs.   

The results of the assessment on the exemplary problems will be shared in the next months together with a draft of the "Shared vision" document to the all biomedical community. 

 

We thank in advance all who will contribute to this effort.

Debora Testi (SCS Srl, Italy)

Nacho Larrabide (Universitat Pompeu Fabra, Spain)

Stephen Aylward (Kitware)