National, inter-institutional, graduate modules – blended learning approaches for PhD education in Ireland

This paper is a case study that describes the design and delivery of national PhD lectures with 40 PhD candidates in Digital Arts and Humanities in Ireland simultaneously to four remote locations, in Trinity College Dublin, in University College Cork, in NUI Maynooth and NUI Galway. Blended learning approaches were utilized to augment traditional teaching practices combining: face-to-face engagement, video-conferencing to multiple sites, social media lecture delivery support – a live blog and micro blogging, shared, open student web presence online. Techniques for creating an effective, active learning environment were discerned via a range of learning options offered to students through student surveys after semester one. Students rejected the traditional lecture format, even through the novel delivery method via video link to a number of national academic institutions was employed. Students also rejected the use of a moderated forum as a means of creating engagement across the various institutions involved. Students preferred a mix of approaches for this online national engagement. The paper discusses successful methods used to promote interactive teaching and learning. These included Peer to peer learning, Workshop style delivery, Social media. The lecture became a national, synchronous workshop. The paper describes how allowing students to have a voice in the virtual classroom they become animated and engaged in an open culture of shared experience and scholarship, create networks beyond their institutions, and across disciplinary boundaries. We offer an analysis of our experiences to assist other educators in their course design, with a particular emphasis on social media engagement.

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance.