Research Article: Using the CustusX toolkit to create an image guided bronchoscopy application: Fraxinus

Date Published: February 8, 2019

Publisher: Public Library of Science

Author(s): Janne Beate Lervik Bakeng, Erlend Fagertun Hofstad, Ole Vegard Solberg, Jon Eiesland, Geir Arne Tangen, Tore Amundsen, Thomas Langø, Ingerid Reinertsen, Tormod Selbekk, Håkon Olav Leira, Ron Kikinis.


The aim of this paper is to show how a specialized planning and guidance application called Fraxinus, can be built on top of the CustusX platform (, which is an open source image-guided intervention software platform. Fraxinus has been customized to meet the clinical needs in navigated bronchoscopy.

The application requirements for Fraxinus were defined in close collaboration between research scientists, software developers and clinicians (pulmonologists), and built on top of CustusX. Its superbuild system downloads specific versions of the required libraries and builds them for the application in question, including the selected plugins. New functionality is easily added through the plugin framework. The build process enables the creation of specialized applications, adding additional documentation and custom configurations. The toolkit’s libraries offer building blocks for image-guided applications. An iterative development process was applied, where the clinicians would test and provide feedback during the entire process.

Fraxinus has been developed and is released as an open source planning and guidance application built on top of CustusX. It is highly specialized for bronchoscopy. The proposed workflow is adapted to the different steps in this procedure. The user interface of CustusX has been modified to enhance information, quality assurance and user friendliness with the intention to increase the overall yield for the patient. As the workflow of the procedure is relatively constant, some actions are predicted and automatically performed by the application, according to the requirements from the clinicians.

The CustusX platform facilitates development of new and specialized applications. The toolkit supports the process and makes important extension and injection points available for customization.

Partial Text

Bronchoscopy is the endobronchial procedure for inspection and diagnostic sampling in the airways, e.g. to diagnose lung cancer. Navigating the flexible video bronchoscope in the lungs is difficult due to the numerous divisions in the tree structure of the airways. Another challenge is the lack of direct visibility of smaller peripheral lesions located outside the airways. This makes it difficult to hit the target for the diagnostic sampling using biopsy or fine needle aspiration. Even with fluoroscopy guidance, the diagnostic success rate for bronchoscopically non-visible tumors is as low as 15% compared to 80% for visible tumors, dependent on tumor size, the doctors experience and the method used for sampling [1–3].

The application specifications were defined over many years through an iterative process involving both technical and clinical personnel. In order to design a system that meets the clinical requirements, it is critically important for technical personnel to understand the tasks and challenges faced by the clinicians before and during the procedure. To gain first-hand experience with the procedure, the software developers therefore attended bronchoscopy procedures in the bronchoscopy suite where CustusX was used [7, 8]. The system specifications were then further refined through numerous discussions and demonstrations of early versions of the software where all team members contributed to the process. This resulted in the specification of the required features and the workflow.

The CustusX platform uses the plugin-centered architecture from CTK (The Common Toolkit) [11] making it a flexible platform for building new applications. The CTK plugin framework is based on OSGi (Open Services Gateway initiative) [12]. Plugins can be used to extend or alter the core system behaviour through extension point services. Developers can use the libraries of the platform as building blocks for assembling their own customized application. The graphical user interface can be customized to fit the applications needs. As CustusX is not specialized towards any particular procedure, the amount of options available might become distracting to a specialized user. Additionally, the generic workflow might not sufficiently cover the clinical procedure at hand.

Information on how to aquire Fraxinus can be found on the Fraxinus website ( There is a short introduction video presenting the application, links to downloadable binaries, datasets which can be used for testing, and also links to the source code.

Fraxinus is not the only application developed on top of CustusX.

We have presented an open source software application, Fraxinus, which uses CustusX toolkit features to build a planning and guiding system for bronchoscopy. We have shown that it is possible to create a specialized application for this specific clinical procedure using CustusX.

Fraxinus is a specialized image-guided planning application built on top of the open source image-guided intervention software platform, CustusX. The CustusX toolkit facilitated the development by offering extension points into many of the important steps of the software development process. Fraxinus is customized to the particular clinical needs in bronchoscopy. Addressing these needs have resulted in a tool which can offer free assistance to clinicians performing these procedures, currently within a research environment. The application is an example of an open source solution targeting a specific clinical need, that is freely available for further development and research. The software has the potential to become a useful tool for the future patient treatment.




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