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.

A palaeobiologist's guide to 'virtual' micro-CT preparation

This paper provides a brief but comprehensive guide to creating, preparing and dissecting a 'virtual' fossil, using a worked example to demonstrate some standard data processing techniques. Computed tomography (CT) is a 3D imaging modality for producing 'virtual' models of an object on a computer. In the last decade, CT technology has greatly improved, allowing bigger and denser objects to be scanned increasingly rapidly. The technique has now reached a stage where systems can facilitate large-scale, non-destructive comparative studies of extinct fossils and their living relatives. Consequently the main limiting factor in CT-based analyses is no longer scanning, but the hurdles of data processing (see disclaimer). The latter comprises the techniques required to convert a 3D CT volume (stack of digital slices) into a virtual image of the fossil that can be prepared (separated) from the matrix and 'dissected' into its anatomical parts. This technique can be applied to specimens or part of specimens embedded in the rock matrix that until now have been otherwise impossible to visualise. This paper presents a suggested workflow explaining the steps required, using as example a fossil tooth of Sphenacanthus hybodoides (Egerton), a shark from the Late Carboniferous of England. The original NHMUK copyrighted CT slice stack can be downloaded for practice of the described techniques, which include segmentation, rendering, movie animation, stereo-anaglyphy, data storage and dissemination. Fragile, rare specimens and type materials in university and museum collections can therefore be virtually processed for a variety of purposes, including virtual loans, website illustrations, publications and digital collections. Micro-CT and other 3D imaging techniques are increasingly utilized to facilitate data sharing among scientists and on education and outreach projects. Hence there is the potential to usher in a new era of global scientific collaboration and public communication using specimens in museum collections.

De la ontología de la imagen-cine a la ética del primer plano

Este texto propone un análisis ontológico y ético de la imagen-cine como simulacro. Se consideran tres posturas diferentes: la platónica, la bergsoniana y la deleuziana. El cine de Ingmar Bergman utiliza los elementos de la nueva imagen-cine y resalta el primer plano por expresar el devenir subjetivo y las relaciones interpersonales.

Evanescent

Exhibition of original artworks created in 2013. Evanescent is a new series produced in 2013 which premiered at the Castlemaine State Festival 15-24 March 2013. The series revisits a childhood delight and fascination with the projected image and the natural world. For me then, as it is now, a magnifying glass was a wonder; its simple optics twisted light into abstract comas and sci-fi aberrations; able to compact a whole view into a luminous, paradoxically inverted phantom that could fit literally into the palm of my hand. By curling fingers and thumb around the lens and cupping both hands around the elusive rays, and by peering into the space in which I had trapped them, I fancied that I had entered into the secret workings of the eye. Chrysalis, for example, appears as a scenic projection from a hand-held lens and simultaneously as the litter of the forest floor. It is produced with a makeshift camera-obscura. The nebulous silhouettes of trees, some blurred under the passing clouds of a summer wind resolve here and there into crisp lines curled across the surface of a fallen leaf on which a moth chrysalis adheres. The leaf assumes Brobdingnagian proportions and thickness as the evanescent image shrinks and is foreshortened then dissolves in the enlarged dust and grit. It manifests the unique sight anchored at this fixed point, to reveal what we might see if we were to become vegetable or mineral. Near and far, large and small, superimpose, trigonometrically exact in their adjacency and spatial relations, presenting us with a located point of view.Why? I want to understand more intimately the interior of the natural landscape, rather than any ‘scene’ of human presence, or the context of any cultural landmark. In the steep, bush locations in which I am making these images, my means are necessarily makeshift; my camera and an old manual-aperture lens able to be carried in a backpack with a black T-shirt as a 'dark-tent'. The project is not systematic but intuitive and responsive to prevailing conditions and the effect on the projection caused by sun, shade, weather and situation. I am guided by the response of objects, textures and surfaces to the projected image and how they modulate and map it. This is landscape, but not from a human point of view.

Desenvolvimento de uma metodologia para elaboração de modelos de predição dos níveis de ruído do campo acústico de usinas hidrelétricas

Pós-graduação em Engenharia Mecânica - FEIS

Crime, Mass Media and the General Public in Lithuania

The project investigated the presentation of crime in the Lithuanian media and its possible impact on the general public's understanding of crime-related problems in society. Dobryninas concentrated on three main aspects of this problem: the development of the image of crime in the Lithuanian press and television, journalists' principles in presenting crime-related information, and the public attitude to the presentation of crime in the media. A content analysis of national newspapers from the period of 1992-1997 showed not only increasing interest in crime problems, but also the distorted nature of the image of crime in the media. In-depth interviews with Lithuanian journalists demonstrated that they understood their role in presenting crime-related information firstly as providing information oriented to high public demand, although at the same time they did not deny the commercial and entertainment aspects of crime reporting. Readership and audience research illustrated the clear influence of the media on the public understanding of crime problems in society. However, the virtual image of crime did not greatly affect the system of values and beliefs of Lithuanians, nor did it challenge their insistence that problems of crime could and should be managed within the framework of a civil and open society.

Using hybrid knowledge engineering and image processing in color virtual restoration of ancient murals

IEEE Transactions on Knowledge and Data Engineering, vol. 15, no. 5, pp. 1338-1343, 2003.

Exploring the effects of image persistence in low frame rate virtual environments

© 2015 IEEE.In virtual reality applications, there is an aim to provide real time graphics which run at high refresh rates. However, there are many situations in which this is not possible due to simulation or rendering issues. When running at low frame rates, several aspects of the user experience are affected. For example, each frame is displayed for an extended period of time, causing a high persistence image artifact. The effect of this artifact is that movement may lose continuity, and the image jumps from one frame to another. In this paper, we discuss our initial exploration of the effects of high persistence frames caused by low refresh rates and compare it to high frame rates and to a technique we developed to mitigate the effects of low frame rates. In this technique, the low frame rate simulation images are displayed with low persistence by blanking out the display during the extra time such image would be displayed. In order to isolate the visual effects, we constructed a simulator for low and high persistence displays that does not affect input latency. A controlled user study comparing the three conditions for the tasks of 3D selection and navigation was conducted. Results indicate that the low persistence display technique may not negatively impact user experience or performance as compared to the high persistence case. Directions for future work on the use of low persistence displays for low frame rate situations are discussed.

Male body image in real and virtual environments

My research investigated the relevance of men’s online avatars to their body image concerns in real life. The results revealed that the size and muscle of avatars are of clinical significance for certain men, particularly those who value and identify with the aesthetic properties of their avatars.

The application of distributed virtual machines for enterprise computer management: A two-tier network file system for image provisioning and management

In order to simplify computer management, several system administrators are adopting advanced techniques to manage software configuration of enterprise computer networks, but the tight coupling between hardware and software makes every PC an individual managed entity, lowering the scalability and increasing the costs to manage hundreds or thousands of PCs. Virtualization is an established technology, however its use is been more focused on server consolidation and virtual desktop infrastructure, not for managing distributed computers over a network. This paper discusses the feasibility of the Distributed Virtual Machine Environment, a new approach for enterprise computer management that combines virtualization and distributed system architecture as the basis of the management architecture. © 2008 IEEE.

Digitisation and Presentation of Historical Materials in a Virtual Exhibition ‘The Image of India in Bulgaria: from the late 19th to the late 20th Century’

The main contribution of this project is the study of collections of valuable documents related to the image of India in Bulgaria. Digital repositories of selected samples are constructed using modern information technologies. The results are presented in a virtual exhibition ‘The Image of India in Bulgaria: from the late 19th to the late 20th century’.

Studying collaborative design in high bandwidth virtual environments

In today’s global design world, architectural and other related design firms design across time zones and geographically distant locations. High bandwidth virtual environments have the potential to make a major impact on these global design teams. However, there is insufficient evidence about the way designers collaborate in their normal working environments using traditional and/or digital media. This paper presents a method to study the impact of communication and information technologies on collaborative design practice by comparing design tasks done in a normal working environment with design tasks done in a virtual environment. Before introducing high bandwidth collaboration technology to the work environment, a baseline study is conducted to observe and analyze the existing collaborative process. Designers currently rely on phone, fax, email, and image files for communication and collaboration. Describing the current context is important for comparison with the following phases. We developed the coding scheme that will be used in analyzing three stages of the collaborative design activity. The results will establish the basis for measures of collaborative design activity when a new technology is introduced later to the same work environment – for example, designers using electronic whiteboards, 3D virtual worlds, webcams, and internet phone. The results of this work will form the basis of guidelines for the introduction of technology into global design offices

Improved image contrast of the bone-muscle interface with 3T MRI compared to 1.5T MRI [Abstract]

Virtual 3D models of long bones are increasingly being used for implant design and research applications. The current gold standard for the acquisition of such data is Computed Tomography (CT) scanning. Due to radiation exposure, CT is generally limited to the imaging of clinical cases and cadaver specimens. Magnetic Resonance Imaging (MRI) does not involve ionising radiation and therefore can be used to image selected healthy human volunteers for research purposes. The feasibility of MRI as alternative to CT for the acquisition of morphological bone data of the lower extremity has been demonstrated in recent studies [1, 2]. Some of the current limitations of MRI are long scanning times and difficulties with image segmentation in certain anatomical regions due to poor contrast between bone and surrounding muscle tissues. Higher field strength scanners promise to offer faster imaging times or better image quality. In this study image quality at 1.5T is quantitatively compared to images acquired at 3T. --------- The femora of five human volunteers were scanned using 1.5T and 3T MRI scanners from the same manufacturer (Siemens) with similar imaging protocols. A 3D flash sequence was used with TE = 4.66 ms, flip angle = 15° and voxel size = 0.5 × 0.5 × 1 mm. PA-Matrix and body matrix coils were used to cover the lower limb and pelvis respectively. Signal to noise ratio (SNR) [3] and contrast to noise ratio (CNR) [3] of the axial images from the proximal, shaft and distal regions were used to assess the quality of images from the 1.5T and 3T scanners. The SNR was calculated for the muscle and bone-marrow in the axial images. The CNR was calculated for the muscle to cortex and cortex to bone marrow interfaces, respectively. --------- Preliminary results (one volunteer) show that the SNR of muscle for the shaft and distal regions was higher in 3T images (11.65 and 17.60) than 1.5T images (8.12 and 8.11). For the proximal region the SNR of muscles was higher in 1.5T images (7.52) than 3T images (6.78). The SNR of bone marrow was slightly higher in 1.5T images for both proximal and shaft regions, while it was lower in the distal region compared to 3T images. The CNR between muscle and bone of all three regions was higher in 3T images (4.14, 6.55 and 12.99) than in 1.5T images (2.49, 3.25 and 9.89). The CNR between bone-marrow and bone was slightly higher in 1.5T images (4.87, 12.89 and 10.07) compared to 3T images (3.74, 10.83 and 10.15). These results show that the 3T images generated higher contrast between bone and the muscle tissue than the 1.5T images. It is expected that this improvement of image contrast will significantly reduce the time required for the mainly manual segmentation of the MR images. Future work will focus on optimizing the 3T imaging protocol for reducing chemical shift and susceptibility artifacts.

Typical accuracy and quality control of a process for creating CT-Based virtual bone models

A pragmatic method for assessing the accuracy and precision of a given processing pipeline required for converting computed tomography (CT) image data of bones into representative three dimensional (3D) models of bone shapes is proposed. The method is based on coprocessing a control object with known geometry which enables the assessment of the quality of resulting 3D models. At three stages of the conversion process, distance measurements were obtained and statistically evaluated. For this study, 31 CT datasets were processed. The final 3D model of the control object contained an average deviation from reference values of −1.07±0.52 mm standard deviation (SD) for edge distances and −0.647±0.43 mm SD for parallel side distances of the control object. Coprocessing a reference object enables the assessment of the accuracy and precision of a given processing pipeline for creating CTbased 3D bone models and is suitable for detecting most systematic or human errors when processing a CT-scan. Typical errors have about the same size as the scan resolution.