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

Mobile Wound Assessment and 3D Modeling from a Single Image

The prevalence of camera-enabled mobile phones have made mobile wound assessment a viable treatment option for millions of previously difficult to reach patients. We have designed a complete mobile wound assessment platform to ameliorate the many challenges related to chronic wound care. Chronic wounds and infections are the most severe, costly and fatal types of wounds, placing them at the center of mobile wound assessment. Wound physicians assess thousands of single-view wound images from all over the world, and it may be difficult to determine the location of the wound on the body, for example, if the wound is taken at close range. In our solution, end-users capture an image of the wound by taking a picture with their mobile camera. The wound image is segmented and classified using modern convolution neural networks, and is stored securely in the cloud for remote tracking. We use an interactive semi-automated approach to allow users to specify the location of the wound on the body. To accomplish this we have created, to the best our knowledge, the first 3D human surface anatomy labeling system, based off the current NYU and Anatomy Mapper labeling systems. To interactively view wounds in 3D, we have presented an efficient projective texture mapping algorithm for texturing wounds onto a 3D human anatomy model. In so doing, we have demonstrated an approach to 3D wound reconstruction that works even for a single wound image

The ecomics of ecosystems and biodiversity: scoping the scale

The G8 decided in March 2007 to initiate a “Review on the economics of biodiversity loss”, in the so called Potsdam Initiative: 'In a global study we will initiate the process of analysing the global economic benefit of biological diversity, the costs of the loss of biodiversity and the failure to take protective measures versus the costs of effective conservation. The study is being supported by the European Commission (together with the European Environmental Agency and in cooperation with the German Government. “The objective of the current study is to provide a coherent overview of existing scientific knowledge upon which to base the economics of the Review, and to propose a coherent global programme of scientific work, both for Phase 2 (consolidation) and to enable more robust future iterations of the Review beyond 2010.

Washington University Senior Undergraduate Research Digest (WUURD), Spring 2018

From the Washington University Office of Undergraduate Research Digest (WUURD), Vol. 13, 05-01-2018. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Scienc

Resilient Urban Futures

This open access book addresses the way in which urban and urbanizing regions profoundly impact and are impacted by climate change. The editors and authors show why cities must wage simultaneous battles to curb global climate change trends while adapting and transforming to address local climate impacts. This book addresses how cities develop anticipatory and long-range planning capacities for more resilient futures, earnest collaboration across disciplines, and radical reconfigurations of the power regimes that have institutionalized the disenfranchisement of minority groups. Although planning processes consider visions for the future, the editors highlight a more ambitious long-term positive visioning approach that accounts for unpredictability, system dynamics and equity in decision-making. This volume brings the science of urban transformation together with practices of professionals who govern and manage our social, ecological and technological systems to design processes by which cities may achieve resilient urban futures in the face of climate change

Telemorphosis: Theory in the Era of Climate Change, Vol. 1

The writers in the volume ask, implicitly, how the 21st century horizons that exceed any political, economic, or conceptual models alters or redefines a series of key topoi. These range through figures of sexual difference, bioethics, care, species invasion, war, post-carbon thought, ecotechnics, time, and so on. As such, the volume is also a dossier on what metamorphoses await the legacies of -humanistic- thought in adapting to, or rethinking, the other materialities that impinge of contemporary -life as we know it.- With essays by Robert Markley, J. Hillis Miller, Bernard Stiegler, Justin Read, Timothy Clark, Claire Colebrook, Jason Groves, Joanna Zylinska, Catherine Malabou, Mike Hill, Martin McQuillan, Eduardo Cadava and Tom Cohen

Management Controls for Sustainable Development: Evidence from a Thai Manufacturing Organisation

This thesis aims to empirically investigate the use of management controls in relation to sustainable development within an established manufacturing organisation in Thailand. Situated within the conflicts between formal motivators (e.g., performance measurement and reward systems) which call for economic rationalism and an informally cognitive responsibility for socio-ecological awareness and commitment (Ball and Milne, 2005; Milne, 1996), the existence of formal and informal management controls to support the sustainable development belief and their interplays are examined. An inductive research approach with Laughlin’s (1991) organisational change framework is drawn upon in the analysis of a single case study. The empirical evidence is collected through semi-structured interviews, non-participant observations and document analysis to investigate the organisation's sustainability discourse. This study makes important contributions to the extant social and environmental accounting literature, especially concerning management controls. Little research directs towards how organisations integrate their management controls with the sustainable development concept (Lueg and Radlach, 2016) due to its subjective and disputable nature (Ball and Milne, 2005; Gray, 2010; Milne, 1996). This research goes further to unveil the change journey in quantifiable and religious-based management controls within a Thai manufacturing organisation that encountered complex sustainability challenges. Furthermore, the sustainability concept has been integrated into corporate strategies, organisational culture and key capabilities for value-added activities and innovation. The internal and external disturbances were managed with proper caution and safeguards. The observed formal and informal management controls worked interdependently in line with the organisation’s core values (i.e., interpretive schemes – Laughlin, 1991). These control tools are shown to be built on “measure what can be managed” or achievable-based outcomes with support from multiple specialist work groups

Life Cycle Sustainability Assessment of the Hydrogen Fuel Cell Buses in the European Context. Evaluation of relevant measures to support low-carbon mobility in the public transport sector

Goal and Background. Transport represents 27% of Europe's Greenhouse Gas (GHG) emissions and is the main cause of air pollution in cities. With the global shift towards a low-carbon economy, the EU set forth a lowemission mobility strategy with the aim of reducing the overall emissions in the transport sector. The High V.LO.-City project is part of this overarching strategy and addresses the integration of hydrogen fuel cell (H2FC) buses in the public transport. Methods. In this thesis, the environmental assessment of one H2FC bus and the related refuelling station is carried out using the Life Cycle Assessment (LCA) methodology, taking into account the following phases: (1) bus production, (2) hydrogen production pathways (water electrolysis, chlor-alkali electrolysis, and steam methane reforming), (3) hydrogen consumption during bus operation, and (4) the vehicles' end of life. The potential impacts are evaluated for magnitude and signi cance in the life cycle impact assessment (LCIA) phase, using Environmental Footprint (EF) method which is part of the Product Environmental Footprint (PEF) method, established by the European Union (EU) in 2013. The calculated fuel economy is around 10.54 KgH2/100Km and the energy demand of a refuelling infrastructure may vary between 6 and 9 KWh/KgH2. Results. The results show that H2FC buses have the potential to reduce emissions during the use phase if renewables resources are used. The expected Global Warming Potential (GWP) bene t is about 85% in comparison to a diesel bus. Additionally, the emissions of the selected patterns of hydrogen production depend on how electricity is produced and on the chemical-based or fossil-based feedstocks used to drive the production process. Conclusions and Outlook. The improvement of the environmental pro le of hydrogen production requires to promote clean electricity sources to supply a low-carbon hydrogen and to sharpen policy focus with regard to life cycle management, and to counter potential setbacks, in particular those related to problem-shifting and to grid improvement

Drones and Geographical Information Technologies in Agroecology and Organic Farming

Although organic farming and agroecology are normally not associated with the use of new technologies, it’s rapid growth, new technologies are being adopted to mitigate environmental impacts of intensive production implemented with external material and energy inputs. GPS, satellite images, GIS, drones, help conventional farming in precision supply of water, pesticides, fertilizers. Prescription maps define the right place and moment for interventions of machinery fleets. Yield goal remains the key objective, integrating a more efficient use or resources toward an economic-environmental sustainability. Technological smart farming allows extractive agriculture entering the sustainability era. Societies that practice agroecology through the development of human-environmental co-evolutionary systems represent a solid model of sustainability. These systems are characterized by high-quality agroecosystems and landscapes, social inclusion, and viable economies. This book explores the challenges posed by the new geographic information technologies in agroecology and organic farming. It discusses the differences among technology-laden conventional farming systems and the role of technologies in strengthening the potential of agroecology. The first part reviews the new tools offered by geographic information technologies to farmers and people. The second part provides case studies of most promising application of technologies in organic farming and agroecology: the diffusion of hyperspectral imagery, the role of positioning systems, the integration of drones with satellite imagery. The third part of the book, explores the role of agroecology using a multiscale approach from the farm to the landscape level. This section explores the potential of Geodesign in promoting alliances between farmers and people, and strengthening food networks, whether through proximity urban farming or asserting land rights in remote areas in the spirit of agroecological transition. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons 4.0 license