GIMIAS: An open source framework for efficient development of research tools and clinical prototypes Ignacio Larrabide a;b;∗, Pedro Omedas b;a, Yves Martelli b;a, Xavier Planes b;a, Maarten Nieber b;a, Juan A. Moya b;a, Constantine Butakoff b;a, Rafael Sebasti´an b;a, Oscar Camara b;a, Mathieu De Craene b;a, Bart H. Bijnens c;b;a, and Alejandro F. Frangi b;a;c Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB) aNetworking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain bUniversitat Pompeu Fabra, Barcelona, Spain cInstituci´oCatalana de Recerca i Estudis Avan¸cats(ICREA), Barcelona, Spain ignacio.larrabide,pedro.omedas,[email protected] Abstract. GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computa- tional models, which is extensible through the development of application- specific plug-ins. In addition, GIMIAS provides an open source frame- work for efficient development of research and clinical software proto- types integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and com- mercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart. Key words: Biomedical imaging, cardiovascular modeling, Virtual Phys- iological Human, personalized simulations, open source software 1 Introduction The integrative multi-scale and multi-disciplinar community that tries to under- stand the human patho-physiology is internationally known as \IUPS Physiome Project" [1,2] or, in the European context as \Virtual Physiological Human" (VPH) [3]. Besides the strategic character that it has regarding the priorities of the 7th Framework Programme of the EU, the VPH is of great relevance in the current context given its integrative vision of the physiological and compu- tational knowledge. In this perspective, a key challenge in the development of integrative and predictive models for the human physiology is the creation of 2 GIMIAS: Graphical Interface for Medical Image Analysis and Simulation computational tools that enable the collaborative work between scientists, in- dustry and health care to bridge the gap between scientific discovery and clinical treatment. An essential condition for the success of the VPH is the development of software tools that ensure methodology integration. As examples we can site all multi-scale integration, access and exploitation of large repositories and databases, processing of data with state-of-the-art algorithms, creation of personalized mod- els, data fusion and visualization. In this paper we present GIMIAS (Graphical Interface for Medical Image Analysis and Simulation), a workflow-oriented environment that has been spe- cially tailored for fast development of biomedical imaging and modeling software prototypes. GIMIAS provides an open source framework for the development of research tools and clinical prototypes, allowing the integration of contributions from the Physiome community while allowing business-friendly technology trans- fer. 2 Related work Current tools (see Table 1) have their own strengths and weaknesses, mainly linked to the core skills of the research group behind it. However, there is not currently, a single application that fulfills all the requirements of all possible VPH applications. For this reason, the VPH community is steadily progressing towards establishing data, modeling and communication standards that ensure interoperability between different tools rather than creating a single application that accounts for all possible needs. Furthermore, there is also a need for a Free Open Source Software platform that allows efficient development of prototypes, that requires minimal training time or prior knowledge to get started. What GIMIAS brings to the community is a common framework to help on data manipulation and visualization in which processing algorithms can be easily integrated. In this environment new algorithms and models (developed by the user or provided by an existing library) can be easily integrated in more complex processing workflows. Furthermore, GIMIAS and all the libraries on which it relies are Free Open Source Software. In this way, different teams using the platform, either from academia or industry, can interact and share modules easily. The main goal of this platform is to transfer novel technologies into clinical environment by the fast development of prototypes. 3 Specifications Taking into account all the requirements for the platform, GIMIAS architecture has been designed to accomplish the following specifications. The following non- functional requirements, i.e., criteria usable to judge the system other than its functionalities, should be addressed by GIMIAS: { Modularity: its functionalities should be modular allowing flexibility in the way that they are combined to facilitate exchangeability and reuse. Graphical Interface for Medical Image Analysis and Simulation 3 { Simplicity: to allow technologists and scientists to easily integrate their al- gorithms in the platform in with small amount of time and effort. { Flexibility: to support the development of research and clinical prototypes with different degrees of complexity. Also, binary (compiled) and/or inter- preted (script-based) plug-in development should be possible requiring an even smaller amount of prior knowledge to integrate new features. { Interoperability: to cope with the increasing amount of image processing and modeling tools available and to ensure maximum reuse, it is of crucial importance that this software is capable of inter-operating with others. Name Distribution license Brief list of features BrainVISA Open source software. CeCILL Li- - scientific visualization cense. - signal and image processing CMGUI Open source software. Mozilla - scientific visualization Public License. - scripting capabilities - model personalization - signal and image processing MedINRIA Free for non-commercial use. - scientific visualization - model personalization - signal and image processing MeVisLab Basic version free for non- - scientific visualization commercial use. SDK version - scripting capabilities requires a commercial license. - plug-in architecture - image processing OpenMAF Open source software. BSD-style - generic application framework License. - scientific visualization - model personalization - image processing ParaView Open source software. BSD-style - scientific visualization License. - scripting capabilities - plug-in architecture Slicer 3D Open source software. BSD-style - scientific visualization License. - plug-in architecture - image processing Table 1. Summarized list of current software development projects focused on medical image processing and end-user software for model personalization. The brief feature list is based on the description provided by their distributors. The following list contains the corresponding websites for the tools described above where further details can be found: www.brainvisa.info, www.cmiss.org/cmgui, www- sop.inria.fr/asclepios/software/MedINRIA, www.mevislab.de/, www.openmaf.org/, www.paraview.org, www.slicer.org. In order to illustrate how GIMIAS can be used for the implementation of a particular workflow, let us use as an example an application for cardiac model- ing. On this regard, the treatment of biomedical data often involves (sometimes large) work-flows that require different data processing tools. This is particularly important in the case of cardiac modeling, where the use of computational tools 4 GIMIAS: Graphical Interface for Medical Image Analysis and Simulation Fig. 1. Left: Schematic overview of the plug-in based architecture of GIMIAS. General infrastructure services are used by the different plug-ins according to the specific application. Plug-ins can be changed to create new workflows. Right: Classes to be developed, and their associated complexity and interaction, for the creation of a new plug-in. For the classes Widget and DataView the developer can choose either implementing them or using the standard implementation provided by the framework. for image and signal processing, surface and volume mesh editing, creation of numerical models and data visualization is required. GIMIAS framework users GIMIAS, as a fast prototyping open source framework, has been developed think- ing in two different user profiles: 1. Researchers who want to test methodologies and easily create prototypes for validating the practical feasibility of research concepts. Using the proposed framework, they can create new plug-ins that incorporate their methods and algorithms, allowing potential end-users (e.g., medical doctors, clinical scientists, among others) to assess them. 2. Scientific developers (from academic or industrial environment) that need to create fast and cheap prototypes for research tools and/or clinical products. Moreover, by having a BSD licence, GIMIAS is appropriate for promoting interaction between industrial and academic software development teams. GIMIAS provides a simple Application Programming Interface (API) that permits, with minimal effort, to trial methodologies and algorithms in the form of end-user applications. Also, prototypes developed within/for GIMIAS can be tested by end users in real scenarios and with real