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

Functional Magnetic Resonance Imaging

"Functional Magnetic Resonance Imaging - Advanced Neuroimaging Applications" is a concise book on applied methods of fMRI used in assessment of cognitive functions in brain and neuropsychological evaluation using motor-sensory activities, language, orthographic disabilities in children. The book will serve the purpose of applied neuropsychological evaluation methods in neuropsychological research projects, as well as relatively experienced psychologists and neuroscientists. Chapters are arranged in the order of basic concepts of fMRI and physiological basis of fMRI after event-related stimulus in first two chapters followed by new concepts of fMRI applied in constraint-induced movement therapy; reliability analysis; refractory SMA epilepsy; consciousness states; rule-guided behavioral analysis; orthographic frequency neighbor analysis for phonological activation; and quantitative multimodal spectroscopic fMRI to evaluate different neuropsychological states

Large space structures and systems in the space station era: A bibliography with indexes (supplement 03)

Bibliographies and abstracts are listed for 1221 reports, articles, and other documents introduced into the NASA scientific and technical information system between January 1, 1991 and June 30, 1991. Topics covered include large space structures and systems, space stations, extravehicular activity, thermal environments and control, tethering, spacecraft power supplies, structural concepts and control systems, electronics, advanced materials, propulsion, policies and international cooperation, vibration and dynamic controls, robotics and remote operations, data and communication systems, electric power generation, space commercialization, orbital transfer, and human factors engineering

Pilot study for subgroup classification for autism spectrum disorder based on dysmorphology and physical measurements in Chinese children

Poster Sessions: 157 - Comorbid Medical Conditions: abstract 157.058 58BACKGROUND: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder affecting individuals along a continuum of severity in communication, social interaction and behaviour. The impact of ASD significantly varies amongst individuals, and the cause of ASD can originate broadly between genetic and environmental factors. Objectives: Previous ASD researches indicate that early identification combined with a targeted treatment plan involving behavioural interventions and multidisciplinary therapies can provide substantial improvement for ASD patients. Currently there is no cure for ASD, and the clinical variability and uncertainty of the disorder still remains. Hence, the search to unravel heterogeneity within ASD by subgroup classification may provide clinicians with a better understanding of ASD and to work towards a more definitive course of action. METHODS: In this study, a norm of physical measurements including height, weight, head circumference, ear length, outer and inner canthi, interpupillary distance, philtrum, hand and foot length was collected from 658 Typical Developing (TD) Chinese children aged 1 to 7 years (mean age of 4.19 years). The norm collected was compared against 80 ASD Chinese children aged 1 to 12 years (mean age of 4.36 years). We then further attempted to find subgroups within ASD based on identifying physical abnormalities; individuals were classified as (non) dysmorphic with the Autism Dysmorphology Measure (ADM) from physical examinations of 12 body regions. RESULTS: Our results show that there were significant differences between ASD and TD children for measurements in: head circumference (p=0.009), outer (p=0.021) and inner (p=0.021) canthus, philtrum length (p=0.003), right (p=0.023) and left (p=0.20) foot length. Within the 80 ASD patients, 37(46%) were classified as dysmorphic (p=0.00). CONCLUSIONS: This study attempts to identify subgroups within ASD based on physical measurements and dysmorphology examinations. The information from this study seeks to benefit ASD community by identifying possible subtypes of ASD in Chinese population; in seek for a more definitive diagnosis, referral and treatment plan.published_or_final_versio

Life Sciences Program Tasks and Bibliography for FY 1997

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1997. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive internet web page