A Modular and Open-Source Framework for Virtual Reality Visualisation and Interaction in Bioimaging

Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. The advent of new imaging technologies, such as lightsheet microscopy, has resulted in the users being confronted with an ever-growing amount of data, with even terabytes of imaging data created within a day. With the possibility of gentler and more high-performance imaging, the spatiotemporal complexity of the model systems or processes of interest is increasing as well. Visualisation is often the first step in making sense of this data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualisations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we present scenery, a modular and extensible visualisation framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features, and discuss its use with VR/AR hardware and in distributed rendering. In addition to the visualisation framework, we present a series of case studies, where scenery can provide tangible benefit in developmental and systems biology: With Bionic Tracking, we demonstrate a new technique for tracking cells in 4D volumetric datasets via tracking eye gaze in a virtual reality headset, with the potential to speed up manual tracking tasks by an order of magnitude. We further introduce ideas to move towards virtual reality-based laser ablation and perform a user study in order to gain insight into performance, acceptance and issues when performing ablation tasks with virtual reality hardware in fast developing specimen. To tame the amount of data originating from state-of-the-art volumetric microscopes, we present ideas how to render the highly-efficient Adaptive Particle Representation, and finally, we present sciview, an ImageJ2/Fiji plugin making the features of scenery available to a wider audience.:Abstract Foreword and Acknowledgements Overview and Contributions Part 1 - Introduction 1 Fluorescence Microscopy 2 Introduction to Visual Processing 3 A Short Introduction to Cross Reality 4 Eye Tracking and Gaze-based Interaction Part 2 - VR and AR for System Biology 5 scenery — VR/AR for Systems Biology 6 Rendering 7 Input Handling and Integration of External Hardware 8 Distributed Rendering 9 Miscellaneous Subsystems 10 Future Development Directions Part III - Case Studies C A S E S T U D I E S 11 Bionic Tracking: Using Eye Tracking for Cell Tracking 12 Towards Interactive Virtual Reality Laser Ablation 13 Rendering the Adaptive Particle Representation 14 sciview — Integrating scenery into ImageJ2 & Fiji Part IV - Conclusion 15 Conclusions and Outlook Backmatter & Appendices A Questionnaire for VR Ablation User Study B Full Correlations in VR Ablation Questionnaire C Questionnaire for Bionic Tracking User Study List of Tables List of Figures Bibliography Selbstständigkeitserklärun

Augmenting visual perception with gaze-contingent displays

Cheap and easy to use eye tracking can be used to turn a common display into a gaze-contingent display: a system that can react to the user’s gaze and adjust its content based on where an observer is looking. This can be used to enhance the rendering on screens based on perceptual insights and the knowledge about what is currently seen. This thesis investigates how GCDs can be used to support aspects of depth and colour perception. This thesis presents experiments that investigate the effects of simulated depth of field and chromatic aberration on depth perception. It also investigates how changing the colours surrounding the attended area can be used to influence the perceived colour and how this can be used to increase colour differentiation of colour and potentially increase the perceived gamut of the display. The presented investigations and empirical results lay the foundation for future investigations and development of gaze-contingent technologies, as well as for general applications of colour and depth perception. The results show that GCDs can be used to support the user in tasks that are related to visual perception. The presented techniques could be used to facilitate common tasks like distinguishing the depth of objects in virtual environments or discriminating similar colours in information visualisations.EU Marie Curie Program CIG - 30378

Machinima Filmmaking: The Integration of Immersive Technology for Collaborative Machinima Filmmaking

This Digital Media MS project proposes to create a flexible, intuitive, and low-entry barrier virtual cinematography tool that will enable participants engaged in human computer interaction (HCI) activities to quickly stage, choreograph, rehearse, and capture performances in real-time. Heretofore, Machinima developers have used limited forms of expressive input devices to puppeteer characters and record in-game live performances, using a gamepad, keyboard, mouse, and joystick to produce content. This has stagnated Machinima development because machinimators have not embraced the current evolution of input devices to create, capture, and edit content, thereby omitting game engine programming possibilities that could exploit new 3D compositing techniques and alternatives to strengthen interactivity, collaboration, and efficiency in cinematic pipelines. Our system, leveraging consumer-affordable hardware and software, advances the development of Machinima production by providing a foundation for alternative cinematic practices, to create a seamless form of human computer interaction and to positively convince more people toward Machinima filmmaking. We propose to produce an Unreal Engine 4 system plugin which integrates virtual reality and eye tracking, via the Oculus Rift DK2 and Tobii EyeX, respectively. The plugin will enable two people, in the roles of Director and Performer, to navigate and interact within a virtual 3D space to productively affect collaborative Machinima filmmaking.M.S., Digital Media -- Drexel University, 201

Workload-aware systems and interfaces for cognitive augmentation

In today's society, our cognition is constantly influenced by information intake, attention switching, and task interruptions. This increases the difficulty of a given task, adding to the existing workload and leading to compromised cognitive performances. The human body expresses the use of cognitive resources through physiological responses when confronted with a plethora of cognitive workload. This temporarily mobilizes additional resources to deal with the workload at the cost of accelerated mental exhaustion. We predict that recent developments in physiological sensing will increasingly create user interfaces that are aware of the user’s cognitive capacities, hence able to intervene when high or low states of cognitive workload are detected. In this thesis, we initially focus on determining opportune moments for cognitive assistance. Subsequently, we investigate suitable feedback modalities in a user-centric design process which are desirable for cognitive assistance. We present design requirements for how cognitive augmentation can be achieved using interfaces that sense cognitive workload. We then investigate different physiological sensing modalities to enable suitable real-time assessments of cognitive workload. We provide empirical evidence that the human brain is sensitive to fluctuations in cognitive resting states, hence making cognitive effort measurable. Firstly, we show that electroencephalography is a reliable modality to assess the mental workload generated during the user interface operation. Secondly, we use eye tracking to evaluate changes in eye movements and pupil dilation to quantify different workload states. The combination of machine learning and physiological sensing resulted in suitable real-time assessments of cognitive workload. The use of physiological sensing enables us to derive when cognitive augmentation is suitable. Based on our inquiries, we present applications that regulate cognitive workload in home and work settings. We deployed an assistive system in a field study to investigate the validity of our derived design requirements. Finding that workload is mitigated, we investigated how cognitive workload can be visualized to the user. We present an implementation of a biofeedback visualization that helps to improve the understanding of brain activity. A final study shows how cognitive workload measurements can be used to predict the efficiency of information intake through reading interfaces. Here, we conclude with use cases and applications which benefit from cognitive augmentation. This thesis investigates how assistive systems can be designed to implicitly sense and utilize cognitive workload for input and output. To do so, we measure cognitive workload in real-time by collecting behavioral and physiological data from users and analyze this data to support users through assistive systems that adapt their interface according to the currently measured workload. Our overall goal is to extend new and existing context-aware applications by the factor cognitive workload. We envision Workload-Aware Systems and Workload-Aware Interfaces as an extension in the context-aware paradigm. To this end, we conducted eight research inquiries during this thesis to investigate how to design and create workload-aware systems. Finally, we present our vision of future workload-aware systems and workload-aware interfaces. Due to the scarce availability of open physiological data sets, reference implementations, and methods, previous context-aware systems were limited in their ability to utilize cognitive workload for user interaction. Together with the collected data sets, we expect this thesis to pave the way for methodical and technical tools that integrate workload-awareness as a factor for context-aware systems.Tagtäglich werden unsere kognitiven Fähigkeiten durch die Verarbeitung von unzähligen Informationen in Anspruch genommen. Dies kann die Schwierigkeit einer Aufgabe durch mehr oder weniger Arbeitslast beeinflussen. Der menschliche Körper drückt die Nutzung kognitiver Ressourcen durch physiologische Reaktionen aus, wenn dieser mit kognitiver Arbeitsbelastung konfrontiert oder überfordert wird. Dadurch werden weitere Ressourcen mobilisiert, um die Arbeitsbelastung vorübergehend zu bewältigen. Wir prognostizieren, dass die derzeitige Entwicklung physiologischer Messverfahren kognitive Leistungsmessungen stets möglich machen wird, um die kognitive Arbeitslast des Nutzers jederzeit zu messen. Diese sind in der Lage, einzugreifen wenn eine zu hohe oder zu niedrige kognitive Belastung erkannt wird. Wir konzentrieren uns zunächst auf die Erkennung passender Momente für kognitive Unterstützung welche sich der gegenwärtigen kognitiven Arbeitslast bewusst sind. Anschließend untersuchen wir in einem nutzerzentrierten Designprozess geeignete Feedbackmechanismen, die zur kognitiven Assistenz beitragen. Wir präsentieren Designanforderungen, welche zeigen wie Schnittstellen eine kognitive Augmentierung durch die Messung kognitiver Arbeitslast erreichen können. Anschließend untersuchen wir verschiedene physiologische Messmodalitäten, welche Bewertungen der kognitiven Arbeitsbelastung in Realzeit ermöglichen. Zunächst validieren wir empirisch, dass das menschliche Gehirn auf kognitive Arbeitslast reagiert. Es zeigt sich, dass die Ableitung der kognitiven Arbeitsbelastung über Elektroenzephalographie eine geeignete Methode ist, um den kognitiven Anspruch neuartiger Assistenzsysteme zu evaluieren. Anschließend verwenden wir Eye-Tracking, um Veränderungen in den Augenbewegungen und dem Durchmesser der Pupille unter verschiedenen Intensitäten kognitiver Arbeitslast zu bewerten. Das Anwenden von maschinellem Lernen führt zu zuverlässigen Echtzeit-Bewertungen kognitiver Arbeitsbelastung. Auf der Grundlage der bisherigen Forschungsarbeiten stellen wir Anwendungen vor, welche die Kognition im häuslichen und beruflichen Umfeld unterstützen. Die physiologischen Messungen stellen fest, wann eine kognitive Augmentierung sich als günstig erweist. In einer Feldstudie setzen wir ein Assistenzsystem ein, um die erhobenen Designanforderungen zur Reduktion kognitiver Arbeitslast zu validieren. Unsere Ergebnisse zeigen, dass die Arbeitsbelastung durch den Einsatz von Assistenzsystemen reduziert wird. Im Anschluss untersuchen wir, wie kognitive Arbeitsbelastung visualisiert werden kann. Wir stellen eine Implementierung einer Biofeedback-Visualisierung vor, die das Nutzerverständnis zum Verlauf und zur Entstehung von kognitiver Arbeitslast unterstützt. Eine abschließende Studie zeigt, wie Messungen kognitiver Arbeitslast zur Vorhersage der aktuellen Leseeffizienz benutzt werden können. Wir schließen hierbei mit einer Reihe von Applikationen ab, welche sich kognitive Arbeitslast als Eingabe zunutze machen. Die vorliegende wissenschaftliche Arbeit befasst sich mit dem Design von Assistenzsystemen, welche die kognitive Arbeitslast der Nutzer implizit erfasst und diese bei der Durchführung alltäglicher Aufgaben unterstützt. Dabei werden physiologische Daten erfasst, um Rückschlüsse in Realzeit auf die derzeitige kognitive Arbeitsbelastung zu erlauben. Anschließend werden diese Daten analysiert, um dem Nutzer strategisch zu assistieren. Das Ziel dieser Arbeit ist die Erweiterung neuartiger und bestehender kontextbewusster Benutzerschnittstellen um den Faktor kognitive Arbeitslast. Daher werden in dieser Arbeit arbeitslastbewusste Systeme und arbeitslastbewusste Benutzerschnittstellen als eine zusätzliche Dimension innerhalb des Paradigmas kontextbewusster Systeme präsentiert. Wir stellen acht Forschungsstudien vor, um die Designanforderungen und die Implementierung von kognitiv arbeitslastbewussten Systemen zu untersuchen. Schließlich stellen wir unsere Vision von zukünftigen kognitiven arbeitslastbewussten Systemen und Benutzerschnittstellen vor. Durch die knappe Verfügbarkeit öffentlich zugänglicher Datensätze, Referenzimplementierungen, und Methoden, waren Kontextbewusste Systeme in der Auswertung kognitiver Arbeitslast bezüglich der Nutzerinteraktion limitiert. Ergänzt durch die in dieser Arbeit gesammelten Datensätze erwarten wir, dass diese Arbeit den Weg für methodische und technische Werkzeuge ebnet, welche kognitive Arbeitslast als Faktor in das Kontextbewusstsein von Computersystemen integriert

Machinima Filmmaking: The Integration of Immersive Technology for Collaborative Machinima Filmmaking

This Digital Media MS project proposes to create a flexible, intuitive, and low-entry barrier virtual cinematography tool that will enable participants engaged in human computer interaction (HCI) activities to quickly stage, choreograph, rehearse, and capture performances in real-time. Heretofore, Machinima developers have used limited forms of expressive input devices to puppeteer characters and record in-game live performances, using a gamepad, keyboard, mouse, and joystick to produce content. This has stagnated Machinima development because machinimators have not embraced the current evolution of input devices to create, capture, and edit content, thereby omitting game engine programming possibilities that could exploit new 3D compositing techniques and alternatives to strengthen interactivity, collaboration, and efficiency in cinematic pipelines. Our system, leveraging consumer-affordable hardware and software, advances the development of Machinima production by providing a foundation for alternative cinematic practices, to create a seamless form of human computer interaction and to positively convince more people toward Machinima filmmaking. We propose to produce an Unreal Engine 4 system plugin which integrates virtual reality and eye tracking, via the Oculus Rift DK2 and Tobii EyeX, respectively. The plugin will enable two people, in the roles of Director and Performer, to navigate and interact within a virtual 3D space to productively affect collaborative Machinima filmmaking.M.S., Digital Media -- Drexel University, 201

Groupware design : principles, prototypes, and systems

Computers are valuable tools for a wide range of work tasks. A substantial limitation on their value, however, is the predominant focus on enhancing the work of individuals. This fails to account for the issues of collaboration that affect almost all work. Research into computer supported cooperative work (CSCW) aims to eliminate this deficiency, but the promise of computer systems for group work has not been met. This thesis presents four design principles that promote the development of successful groupware. The principles identify the particular problems encountered by groupware, and provide guidelines and strategies to avoid, overcome, or minimise their impact. Derived from several sources, the major influence on the principles development is an investigation into the relationship between factors affecting groupware failure. They are stimulated by observations of groupware use, and by design insights arising from the development of two groupware applications and their prototypes: Mona and TELEFREEK. Mona provides conversation-based email management. Several groupware applications allow similar functionality, but the design principles result in Mona using different mechanisms to achieve its user-support. TELEFREEK provides a platform for accessing computer-supported communication and collaboration facilities. It attends to the problems of initiating interaction, and supports an adaptable and extendible set of "social awareness" assistants. TELEFREEK offers a broader range of facilities than other groupware, and avoids the use of prohibitively high-bandwidth communication networks. TELEFREEK demonstrates that much can be achieved through current and widely accessible technology. Together, Mona and TELEFREEK forcefully demonstrate the use of the design principles, and substantiate the claim of their utility

Money & Trust in Digital Society, Bitcoin and Stablecoins in ML enabled Metaverse Telecollaboration

We present a state of the art and positioning book, about Digital society tools, namely; Web3, Bitcoin, Metaverse, AI/ML, accessibility, safeguarding and telecollaboration. A high level overview of Web3 technologies leads to a description of blockchain, and the Bitcoin network is specifically selected for detailed examination. Suitable components of the extended Bitcoin ecosystem are described in more depth. Other mechanisms for native digital value transfer are described, with a focus on `money'. Metaverse technology is over-viewed, primarily from the perspective of Bitcoin and extended reality. Bitcoin is selected as the best contender for value transfer in metaverses because of it's free and open source nature, and network effect. Challenges and risks of this approach are identified. A cloud deployable virtual machine based technology stack deployment guide with a focus on cybersecurity best practice can be downloaded from GitHub to experiment with the technologies. This deployable lab is designed to inform development of secure value transaction, for small and medium sized companies