A method for viewing and interacting with medical volumes in virtual reality

The medical field has long benefited from advancements in diagnostic imaging technology. Medical images created through methods such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) are used by medical professionals to non-intrusively peer into the body to make decisions about surgeries. Over time, the viewing medium of medical images has evolved from X-ray film negatives to stereoscopic 3D displays, with each new development enhancing the viewer’s ability to discern detail or decreasing the time needed to produce and render a body scan. Though doctors and surgeons are trained to view medical images in 2D, some are choosing to view body scans in 3D through volume rendering. While traditional 2D displays can be used to display 3D data, a viewing method that incorporates depth would convey more information to the viewer. One device that has shown promise in medical image viewing applications is the Virtual Reality Head Mounted Display (VR HMD). VR HMDs have recently increased in popularity, with several commodity devices being released within the last few years. The Oculus Rift, HTC Vive, and Windows Mixed Reality HMDs like the Samsung Odyssey offer higher resolution screens, more accurate motion tracking, and lower prices than earlier HMDs. They also include motion-tracked handheld controllers meant for navigation and interaction in video games. Because of their popularity and low cost, medical volume viewing software that is compatible with these headsets would be accessible to a wide audience. However, the introduction of VR to medical volume rendering presents difficulties in implementing consistent user interactions and ensuring performance. Though all three headsets require unique driver software, they are compatible with OpenVR, a middleware that standardizes communication between the HMD, the HMD’s controllers, and VR software. However, the controllers included with the HMDs each has a slightly different control layout. Furthermore, buttons, triggers, touchpads, and joysticks that share the same hand position between devices do not report values to OpenVR in the same way. Implementing volume rendering functions like clipping and tissue density windowing on VR controllers could improve the user’s experience over mouse-and-keyboard schemes through the use of tracked hand and finger movements. To create a control scheme that is compatible with multiple HMD’s A way of mapping controls differently depending on the device was developed. Additionally, volume rendering is a computationally intensive process, and even more so when rendering for an HMD. By using techniques like GPU raytracing with modern GPUs, real-time framerates are achievable on desktop computers with traditional displays. However, the importance of achieving high framerates is even greater when viewing with a VR HMD due to its higher level of immersion. Because the 3D scene occupies most of the user’s field of view, low or choppy framerates contribute to feelings of motion sickness. This was mitigated through a decrease in volume rendering quality in situations where the framerate drops below acceptable levels. The volume rendering and VR interaction methods described in this thesis were demonstrated in an application developed for immersive viewing of medical volumes. This application places the user and a medical volume in a 3D VR environment, allowing the user to manually place clipping planes, adjust the tissue density window, and move the volume to achieve different viewing angles with handheld motion tracked controllers. The result shows that GPU raytraced medical volumes can be viewed and interacted with in VR using commodity hardware, and that a control scheme can be mapped to allow the same functions on different HMD controllers despite differences in layout

Calibration Methods for Head-Tracked 3D Displays

Head-tracked 3D displays can provide a compelling 3D effect, but even small inaccuracies in the calibration of the participant’s viewpoint to the display can disrupt the 3D illusion. We propose a novel interactive procedure for a participant to easily and accurately calibrate a head-tracked display by visually aligning patterns across a multi-screen display. Head-tracker measurements are then calibrated to these known viewpoints. We conducted a user study to evaluate the effectiveness of different visual patterns and different display shapes. We found that the easiest to align shape was the spherical display and the best calibration pattern was the combination of circles and lines. We performed a quantitative camera-based calibration of a cubic display and found visual calibration outperformed manual tuning and generated viewpoint calibrations accurate to within a degree. Our work removes the usual, burdensome step of manual calibration when using head-tracked displays and paves the way for wider adoption of this inexpensive and effective 3D display technology

Holoscopic 3D image depth estimation and segmentation techniques

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonToday’s 3D imaging techniques offer significant benefits over conventional 2D imaging techniques. The presence of natural depth information in the scene affords the observer an overall improved sense of reality and naturalness. A variety of systems attempting to reach this goal have been designed by many independent research groups, such as stereoscopic and auto-stereoscopic systems. Though the images displayed by such systems tend to cause eye strain, fatigue and headaches after prolonged viewing as users are required to focus on the screen plane/accommodation to converge their eyes to a point in space in a different plane/convergence. Holoscopy is a 3D technology that targets overcoming the above limitations of current 3D technology and was recently developed at Brunel University. This work is part W4.1 of the 3D VIVANT project that is funded by the EU under the ICT program and coordinated by Dr. Aman Aggoun at Brunel University, West London, UK. The objective of the work described in this thesis is to develop estimation and segmentation techniques that are capable of estimating precise 3D depth, and are applicable for holoscopic 3D imaging system. Particular emphasis is given to the task of automatic techniques i.e. favours algorithms with broad generalisation abilities, as no constraints are placed on the setting. Algorithms that provide invariance to most appearance based variation of objects in the scene (e.g. viewpoint changes, deformable objects, presence of noise and changes in lighting). Moreover, have the ability to estimate depth information from both types of holoscopic 3D images i.e. Unidirectional and Omni-directional which gives horizontal parallax and full parallax (vertical and horizontal), respectively. The main aim of this research is to develop 3D depth estimation and 3D image segmentation techniques with great precision. In particular, emphasis on automation of thresholding techniques and cues identifications for development of robust algorithms. A method for depth-through-disparity feature analysis has been built based on the existing correlation between the pixels at a one micro-lens pitch which has been exploited to extract the viewpoint images (VPIs). The corresponding displacement among the VPIs has been exploited to estimate the depth information map via setting and extracting reliable sets of local features. ii Feature-based-point and feature-based-edge are two novel automatic thresholding techniques for detecting and extracting features that have been used in this approach. These techniques offer a solution to the problem of setting and extracting reliable features automatically to improve the performance of the depth estimation related to the generalizations, speed and quality. Due to the resolution limitation of the extracted VPIs, obtaining an accurate 3D depth map is challenging. Therefore, sub-pixel shift and integration is a novel interpolation technique that has been used in this approach to generate super-resolution VPIs. By shift and integration of a set of up-sampled low resolution VPIs, the new information contained in each viewpoint is exploited to obtain a super resolution VPI. This produces a high resolution perspective VPI with wide Field Of View (FOV). This means that the holoscopic 3D image system can be converted into a multi-view 3D image pixel format. Both depth accuracy and a fast execution time have been achieved that improved the 3D depth map. For a 3D object to be recognized the related foreground regions and depth information map needs to be identified. Two novel unsupervised segmentation methods that generate interactive depth maps from single viewpoint segmentation were developed. Both techniques offer new improvements over the existing methods due to their simple use and being fully automatic; therefore, producing the 3D depth interactive map without human interaction. The final contribution is a performance evaluation, to provide an equitable measurement for the extent of the success of the proposed techniques for foreground object segmentation, 3D depth interactive map creation and the generation of 2D super-resolution viewpoint techniques. The no-reference image quality assessment metrics and their correlation with the human perception of quality are used with the help of human participants in a subjective manner

Satellite based synthetic aperture radar and optical spatial-temporal information as aid for operational and environmental mine monitoring

A sustainable society is a society that satisfies its resource requirements without endangering the sustainability of these resources. The mineral endowment on the African continent is estimated to be the first or second largest of world reserves. Therefore, it is recognised that the African continent still heavily depends on mineral exports as a key contributor to the gross domestic product (GDP) of various countries. These mining activities, however, do introduce primary and secondary environmental degradation factors. They attract communities to these mining areas, light and heavy industrial establishments occur, giving rise to artisanal activities. This study focussed on satellite RS products as an aid to a mine’s operations and the monitoring of its environment. Effective operational mine management and control ensures a more sustainable and profitable lifecycle for mines. Satellite based RS holds the potential to observe the mine and its surrounding areas at high temporal intervals, different spectral wavelengths and spatial resolutions. The combination of SAR and optical information creates a spatial platform to observe and measure the mine’s operations and the behaviour of specific land cover and land use classes over time and contributes to a better understanding of the mining activities and their influence on the environment within a specific geographical area. This study will introduce an integrated methodology to collect, process and analyse spatial information over a specific targeted mine. This methodology utilises a medium resolution land cover base map, derived from Landsat 8, to understand the predominant land cover types of the surrounding area. Using very high resolution mono- and stereoscopic satellite imagery provides a finer scale analysis and identifies changes in features at a smaller scale. Combining these technologies with the synthetic aperture radar (SAR) applications for precise measurement of surface subsidence or upliftment becomes a spatial toolbox for mine management. This study examines a combination of satellite remote sensing products guided by a systematic workflow methodology to integrate spatial results as an aid for mining operations and environmental monitoring. Some of the results that can be highlighted is the successful land cover classification using the Landsat 8 satellite. The land cover that dominated the Kolomela mine area was the “SHRUBLAND/GRASS” class with a 94% coverage and “MINE” class of 2.6%. Sishen mine had a similar dominated land cover characteristic with a “SHRUBLAND/GRASS” class of 90% and “MINE” class of 4.8%. The Pléiades time-series classification analysis was done using three scenes each acquired at a different time interval. The Sishen and Kolomela mine showed especially changes from the bare soil class to the asphalt or mine class. The Pléiades stereoscopic analysis provided volumetric change detection over small, medium, large and recessed areas. Both the Sishen and Kolomela mines demonstrated height profile changes in each selected category. The last category of results focused on the SAR technology to measure within millimetre accuracy the subsidence and upliftment behaviour of surface areas over time. The Royal Bafokeng Platinum tailings pond area was measured using 74 TerraSAR-X scenes. The tailings wall area was confirmed as stable with natural subsidence that occurred in its surrounding area due to seasonal changes of the soil during rainy and dry periods. The Chuquicamata mine as a large open pit copper mine area was analysed using 52 TerraSAR-X scenes. The analysis demonstrated significant vertical surface movement over some of the dumping sites. It is the wish of the researcher that this dissertation and future research scholars will continue to contribute in this scientific field. These contributions can only assist the mining sector to continuously improve its mining operations as well as its monitoring of the primary as well as the secondary environmental impacts to ensure improved sustainability for the next generation.Environmental SciencesM. Sc. (Environmental Science

Frame localisation optical projection tomography

Funder: EPSRC IPESAbstract: We present a tomographic reconstruction algorithm (flOPT), which is applied to Optical Projection Tomography (OPT) images, that is robust to mechanical jitter and systematic angular and spatial drift. OPT relies on precise mechanical rotation and is less mechanically stable than large-scale computer tomography (CT) scanning systems, leading to reconstruction artefacts. The algorithm uses multiple (5+) tracked fiducial beads to recover the sample pose and the image rays are then back-projected at each orientation. The quality of the image reconstruction using the proposed algorithm shows an improvement when compared to the Radon transform. Moreover, when adding a systematic spatial and angular mechanical drift, the reconstruction shows a significant improvement over the Radon transform

Data extraction in holographic particle image velocimetry

Holographic Particle Image Velocimetry (HPIV) is potentially the best technique to obtain instantaneous, three-dimensional, flow field information. Several researchers have presented their experimental results to demonstrate the power of HPIV technique. However, the challenge to find an economical and automatic means to extract and process the immense amount of data from the holograms still remains. This thesis reports on the development of complex amplitude correlation as a means of data extraction. At the same time, three-dimensional quantitative measurements for a micro scale flow is of increasing importance in the design of microfluidic devices. This thesis also reports the investigation of HPIV in micro-scale fluid flow. The author has re-examined complex amplitude correlation using a formulation of scalar diffraction in three-dimensional vector space. [Continues.

Development of an augmented reality guided computer assisted orthopaedic surgery system

Previously held under moratorium from 1st December 2016 until 1st December 2021.This body of work documents the developed of a proof of concept augmented reality guided computer assisted orthopaedic surgery system – ARgCAOS. After initial investigation a visible-spectrum single camera tool-mounted tracking system based upon fiducial planar markers was implemented. The use of visible-spectrum cameras, as opposed to the infra-red cameras typically used by surgical tracking systems, allowed the captured image to be streamed to a display in an intelligible fashion. The tracking information defined the location of physical objects relative to the camera. Therefore, this information allowed virtual models to be overlaid onto the camera image. This produced a convincing augmented experience, whereby the virtual objects appeared to be within the physical world, moving with both the camera and markers as expected of physical objects. Analysis of the first generation system identified both accuracy and graphical inadequacies, prompting the development of a second generation system. This too was based upon a tool-mounted fiducial marker system, and improved performance to near-millimetre probing accuracy. A resection system was incorporated into the system, and utilising the tracking information controlled resection was performed, producing sub-millimetre accuracies. Several complications resulted from the tool-mounted approach. Therefore, a third generation system was developed. This final generation deployed a stereoscopic visible-spectrum camera system affixed to a head-mounted display worn by the user. The system allowed the augmentation of the natural view of the user, providing convincing and immersive three dimensional augmented guidance, with probing and resection accuracies of 0.55±0.04 and 0.34±0.04 mm, respectively.This body of work documents the developed of a proof of concept augmented reality guided computer assisted orthopaedic surgery system – ARgCAOS. After initial investigation a visible-spectrum single camera tool-mounted tracking system based upon fiducial planar markers was implemented. The use of visible-spectrum cameras, as opposed to the infra-red cameras typically used by surgical tracking systems, allowed the captured image to be streamed to a display in an intelligible fashion. The tracking information defined the location of physical objects relative to the camera. Therefore, this information allowed virtual models to be overlaid onto the camera image. This produced a convincing augmented experience, whereby the virtual objects appeared to be within the physical world, moving with both the camera and markers as expected of physical objects. Analysis of the first generation system identified both accuracy and graphical inadequacies, prompting the development of a second generation system. This too was based upon a tool-mounted fiducial marker system, and improved performance to near-millimetre probing accuracy. A resection system was incorporated into the system, and utilising the tracking information controlled resection was performed, producing sub-millimetre accuracies. Several complications resulted from the tool-mounted approach. Therefore, a third generation system was developed. This final generation deployed a stereoscopic visible-spectrum camera system affixed to a head-mounted display worn by the user. The system allowed the augmentation of the natural view of the user, providing convincing and immersive three dimensional augmented guidance, with probing and resection accuracies of 0.55±0.04 and 0.34±0.04 mm, respectively

A family of stereoscopic image compression algorithms using wavelet transforms

With the standardization of JPEG-2000, wavelet-based image and video compression technologies are gradually replacing the popular DCT-based methods. In parallel to this, recent developments in autostereoscopic display technology is now threatening to revolutionize the way in which consumers are used to enjoying the traditional 2D display based electronic media such as television, computer and movies. However, due to the two-fold bandwidth/storage space requirement of stereoscopic imaging, an essential requirement of a stereo imaging system is efficient data compression. In this thesis, seven wavelet-based stereo image compression algorithms are proposed, to take advantage of the higher data compaction capability and better flexibility of wavelets. In the proposed CODEC I, block-based disparity estimation/compensation (DE/DC) is performed in pixel domain. However, this results in an inefficiency when DWT is applied on the whole predictive error image that results from the DE process. This is because of the existence of artificial block boundaries between error blocks in the predictive error image. To overcome this problem, in the remaining proposed CODECs, DE/DC is performed in the wavelet domain. Due to the multiresolution nature of the wavelet domain, two methods of disparity estimation and compensation have been proposed. The first method is performing DEJDC in each subband of the lowest/coarsest resolution level and then propagating the disparity vectors obtained to the corresponding subbands of higher/finer resolution. Note that DE is not performed in every subband due to the high overhead bits that could be required for the coding of disparity vectors of all subbands. This method is being used in CODEC II. In the second method, DEJDC is performed m the wavelet-block domain. This enables disparity estimation to be performed m all subbands simultaneously without increasing the overhead bits required for the coding disparity vectors. This method is used by CODEC III. However, performing disparity estimation/compensation in all subbands would result in a significant improvement of CODEC III. To further improve the performance of CODEC ill, pioneering wavelet-block search technique is implemented in CODEC IV. The pioneering wavelet-block search technique enables the right/predicted image to be reconstructed at the decoder end without the need of transmitting the disparity vectors. In proposed CODEC V, pioneering block search is performed in all subbands of DWT decomposition which results in an improvement of its performance. Further, the CODEC IV and V are able to perform at very low bit rates(< 0.15 bpp). In CODEC VI and CODEC VII, Overlapped Block Disparity Compensation (OBDC) is used with & without the need of coding disparity vector. Our experiment results showed that no significant coding gains could be obtained for these CODECs over CODEC IV & V. All proposed CODECs m this thesis are wavelet-based stereo image coding algorithms that maximise the flexibility and benefits offered by wavelet transform technology when applied to stereo imaging. In addition the use of a baseline-JPEG coding architecture would enable the easy adaptation of the proposed algorithms within systems originally built for DCT-based coding. This is an important feature that would be useful during an era where DCT-based technology is only slowly being phased out to give way for DWT based compression technology. In addition, this thesis proposed a stereo image coding algorithm that uses JPEG-2000 technology as the basic compression engine. The proposed CODEC, named RASTER is a rate scalable stereo image CODEC that has a unique ability to preserve the image quality at binocular depth boundaries, which is an important requirement in the design of stereo image CODEC. The experimental results have shown that the proposed CODEC is able to achieve PSNR gains of up to 3.7 dB as compared to directly transmitting the right frame using JPEG-2000