Dynamic Volume Rendering of Functional Medical Data on Dissimilar Hardware Platforms

In the last 30 years, medical imaging has become one of the most used diagnostic tools in the medical profession. Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) technologies have become widely adopted because of their ability to capture the human body in a non-invasive manner. A volumetric dataset is a series of orthogonal 2D slices captured at a regular interval, typically along the axis of the body from the head to the feet. Volume rendering is a computer graphics technique that allows volumetric data to be visualized and manipulated as a single 3D object. Iso-surface rendering, image splatting, shear warp, texture slicing, and raycasting are volume rendering methods, each with associated advantages and disadvantages. Raycasting is widely regarded as the highest quality renderer of these methods. Originally, CT and MRI hardware was limited to providing a single 3D scan of the human body. The technology has improved to allow a set of scans capable of capturing anatomical movements like a beating heart. The capturing of anatomical data over time is referred to as functional imaging. Functional MRI (fMRI) is used to capture changes in the human body over time. While fMRI’s can be used to capture any anatomical data over time, one of the more common uses of fMRI is to capture brain activity. The fMRI scanning process is typically broken up into a time consuming high resolution anatomical scan and a series of quick low resolution scans capturing activity. The low resolution activity data is mapped onto the high resolution anatomical data to show changes over time. Academic research has advanced volume rendering and specifically fMRI volume rendering. Unfortunately, academic research is typically a one-off solution to a singular medical case or set of data, causing any advances to be problem specific as opposed to a general capability. Additionally, academic volume renderers are often designed to work on a specific device and operating system under controlled conditions. This prevents volume rendering from being used across the ever expanding number of different computing devices, such as desktops, laptops, immersive virtual reality systems, and mobile computers like phones or tablets. This research will investigate the feasibility of creating a generic software capability to perform real-time 4D volume rendering, via raycasting, on desktop, mobile, and immersive virtual reality platforms. Implementing a GPU-based 4D volume raycasting method for mobile devices will harness the power of the increasing number of mobile computational devices being used by medical professionals. Developing support for immersive virtual reality can enhance medical professionals’ interpretation of 3D physiology with the additional depth information provided by stereoscopic 3D. The results of this research will help expand the use of 4D volume rendering beyond the traditional desktop computer in the medical field. Developing the same 4D volume rendering capabilities across dissimilar platforms has many challenges. Each platform relies on their own coding languages, libraries, and hardware support. There are tradeoffs between using languages and libraries native to each platform and using a generic cross-platform system, such as a game engine. Native libraries will generally be more efficient during application run-time, but they require different coding implementations for each platform. The decision was made to use platform native languages and libraries in this research, whenever practical, in an attempt to achieve the best possible frame rates. 4D volume raycasting provides unique challenges independent of the platform. Specifically, fMRI data loading, volume animation, and multiple volume rendering. Additionally, real-time raycasting has never been successfully performed on a mobile device. Previous research relied on less computationally expensive methods, such as orthogonal texture slicing, to achieve real-time frame rates. These challenges will be addressed as the contributions of this research. The first contribution was exploring the feasibility of generic functional data input across desktop, mobile, and immersive virtual reality. To visualize 4D fMRI data it was necessary to build in the capability to read Neuroimaging Informatics Technology Initiative (NIfTI) files. The NIfTI format was designed to overcome limitations of 3D file formats like DICOM and store functional imagery with a single high-resolution anatomical scan and a set of low-resolution anatomical scans. Allowing input of the NIfTI binary data required creating custom C++ routines, as no object oriented APIs freely available for use existed. The NIfTI input code was built using C++ and the C++ Standard Library to be both light weight and cross-platform. Multi-volume rendering is another challenge of fMRI data visualization and a contribution of this work. fMRI data is typically broken into a single high-resolution anatomical volume and a series of low-resolution volumes that capture anatomical changes. Visualizing two volumes at the same time is known as multi-volume visualization. Therefore, the ability to correctly align and scale the volumes relative to each other was necessary. It was also necessary to develop a compositing method to combine data from both volumes into a single cohesive representation. Three prototype applications were built for the different platforms to test the feasibility of 4D volume raycasting. One each for desktop, mobile, and virtual reality. Although the backend implementations were required to be different between the three platforms, the raycasting functionality and features were identical. Therefore, the same fMRI dataset resulted in the same 3D visualization independent of the platform itself. Each platform uses the same NIfTI data loader and provides support for dataset coloring and windowing (tissue density manipulation). The fMRI data can be viewed changing over time by either animation through the time steps, like a movie, or using an interface slider to “scrub” through the different time steps of the data. The prototype applications data load times and frame rates were tested to determine if they achieved the real-time interaction goal. Real-time interaction was defined by achieving 10 frames per second (fps) or better, based on the work of Miller [1]. The desktop version was evaluated on a 2013 MacBook Pro running OS X 10.12 with a 2.6 GHz Intel Core i7 processor, 16 GB of RAM, and a NVIDIA GeForce GT 750M graphics card. The immersive application was tested in the C6 CAVE™, a 96 graphics node computer cluster comprised of NVIDIA Quadro 6000 graphics cards running Red Hat Enterprise Linux. The mobile application was evaluated on a 2016 9.7” iPad Pro running iOS 9.3.4. The iPad had a 64-bit Apple A9X dual core processor with 2 GB of built in memory. Two different fMRI brain activity datasets with different voxel resolutions were used as test datasets. Datasets were tested using both the 3D structural data, the 4D functional data, and a combination of the two. Frame rates for the desktop implementation were consistently above 10 fps, indicating that real-time 4D volume raycasting is possible on desktop hardware. The mobile and virtual reality platforms were able to perform real-time 3D volume raycasting consistently. This is a marked improvement for 3D mobile volume raycasting that was previously only able to achieve under one frame per second [2]. Both VR and mobile platforms were able to raycast the 4D only data at real-time frame rates, but did not consistently meet 10 fps when rendering both the 3D structural and 4D functional data simultaneously. However, 7 frames per second was the lowest frame rate recorded, indicating that hardware advances will allow consistent real-time raycasting of 4D fMRI data in the near future

MiCellAnnGELo: Annotate microscopy time series of complex cell surfaces with 3D Virtual Reality

Summary: Advances in 3D live cell microscopy are enabling high-resolution capture of previously unobserved processes. Unleashing the power of modern machine learning methods to fully benefit from these technologies is, however, frustrated by the difficulty of manually annotating 3D training data. MiCellAnnGELo virtual reality software offers an immersive environment for viewing and interacting with 4D microscopy data, including efficient tools for annotation. We present tools for labelling cell surfaces with a wide range of applications, including cell motility, endocytosis, and transmembrane signalling. Availability and implementation: MiCellAnnGELo employs the cross platform (Mac/Unix/Windows) Unity game engine and is available under the MIT licence at https://github.com/CellDynamics/MiCellAnnGELo.git, together with sample data and demonstration movies. MiCellAnnGELo can be run in desktop mode on a 2D screen or in 3D using a standard VR headset with compatible GPU.Comment: For associated code and sample data, see https://github.com/CellDynamics/MiCellAnnGELo.gi

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

Big Data Visualization Platform for Mixed Reality

The visualization of data helps to provide faster and deeper insight into the data. In this work, a system for visualizing and analyzing big data in an interactive mixed reality environment is proposed. Such a system can be used for representing different types of data such as temporal, geospatial, network graph, and high dimensional. Also, an implementation of this system for four different data types are created. The data types include network data, volumetric data, high dimensional, and spectral data for different mixed reality devices such as Microsoft HoloLens, Oculus Rift, Samsung Gear VR, and Android ARCore were created. It was shown that such a system could store and use billions of samples and represent millions of them at once

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness

Ubiquitous volume rendering in the web platform

176 p.The main thesis hypothesis is that ubiquitous volume rendering can be achieved using WebGL. The thesis enumerates the challenges that should be met to achieve that goal. The results allow web content developers the integration of interactive volume rendering within standard HTML5 web pages. Content developers only need to declare the X3D nodes that provide the rendering characteristics they desire. In contrast to the systems that provide specific GPU programs, the presented architecture creates automatically the GPU code required by the WebGL graphics pipeline. This code is generated directly from the X3D nodes declared in the virtual scene. Therefore, content developers do not need to know about the GPU.The thesis extends previous research on web compatible volume data structures for WebGL, ray-casting hybrid surface and volumetric rendering, progressive volume rendering and some specific problems related to the visualization of medical datasets. Finally, the thesis contributes to the X3D standard with some proposals to extend and improve the volume rendering component. The proposals are in an advance stage towards their acceptance by the Web3D Consortium

Augmented Reality

Augmented Reality (AR) is a natural development from virtual reality (VR), which was developed several decades earlier. AR complements VR in many ways. Due to the advantages of the user being able to see both the real and virtual objects simultaneously, AR is far more intuitive, but it's not completely detached from human factors and other restrictions. AR doesn't consume as much time and effort in the applications because it's not required to construct the entire virtual scene and the environment. In this book, several new and emerging application areas of AR are presented and divided into three sections. The first section contains applications in outdoor and mobile AR, such as construction, restoration, security and surveillance. The second section deals with AR in medical, biological, and human bodies. The third and final section contains a number of new and useful applications in daily living and learning

Organ printing as an information technology

Funding Information: This work has been sponsored by the São Paulo Research Foundation (FAPESP), The Brazilian Institute of Biofabrication (INCT-BIOFABRIS) and National Council for Scientific and Technological Development (CNPq). Publisher Copyright: © 2015 Published by Elsevier Ltd.Organ printing is defined as a layer by layer additive robotic computer-aided biofabrication of functional 3D organ constructs with using self-assembling tissue spheroids according to digital model. Information technology and computer-aided design softwares are instrumental in the transformation of virtual 3D bioimaging information about human tissue and organs into living biological reality during 3D bioprinting. Information technology enables design blueprints for bioprinting of human organs as well as predictive computer simulation both printing and post-printing processes. 3D bioprinting is now considered as an emerging information technology and the effective application of existing information technology tools and development of new technological platforms such as human tissue and organ informatics, design automation, virtual human organs, virtual organ biofabrication line, mathematical modeling and predictive computer simulations of bioprinted tissue fusion and maturation is an important technological imperative for advancing organ bioprinting.publishersversionPeer reviewe

Ubiquitous volume rendering in the web platform

176 p.The main thesis hypothesis is that ubiquitous volume rendering can be achieved using WebGL. The thesis enumerates the challenges that should be met to achieve that goal. The results allow web content developers the integration of interactive volume rendering within standard HTML5 web pages. Content developers only need to declare the X3D nodes that provide the rendering characteristics they desire. In contrast to the systems that provide specific GPU programs, the presented architecture creates automatically the GPU code required by the WebGL graphics pipeline. This code is generated directly from the X3D nodes declared in the virtual scene. Therefore, content developers do not need to know about the GPU.The thesis extends previous research on web compatible volume data structures for WebGL, ray-casting hybrid surface and volumetric rendering, progressive volume rendering and some specific problems related to the visualization of medical datasets. Finally, the thesis contributes to the X3D standard with some proposals to extend and improve the volume rendering component. The proposals are in an advance stage towards their acceptance by the Web3D Consortium

Exploring multimedia and interactive technologies

The goal of multimedia design strategies and innovation is to produce meaningful learning environments that relate to and build upon what the learner already knows and what the learner seeks. The multimedia tools used to achieve knowledge transfer should activate recall or prior knowledge and help the learner alter and encode new structures. Traditionally, multimedia has been localized to specific delivery systems and demographics based on the government, industry, or academic concentration. The presenter will explore the introduction of immersive telecommunications technologies, constructivist learning methodologies, and adult learning models to standardize networking and multimedia-based services and products capable of adapting to wired and wireless environments, different devices and conditions on a global scale