Ensembles of wrappers for automated feature selection in fish age classification

In feature selection, the most important features must be chosen so as to decrease the number thereof while retaining their discriminatory information. Within this context, a novel feature selection method based on an ensemble of wrappers is proposed and applied for automatically select features in fish age classification. The effectiveness of this procedure using an Atlantic cod database has been tested for different powerful statistical learning classifiers. The subsets based on few features selected, e.g. otolith weight and fish weight, are particularly noticeable given current biological findings and practices in fishery research and the classification results obtained with them outperforms those of previous studies in which a manual feature selection was performed.Peer ReviewedPostprint (author's final draft

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

Neural plasticity and the limits of scientific knowledge

Western science claims to provide unique, objective information about the world. This is supported by the observation that peoples across cultures will agree upon a common description of the physical world. Further, the use of scientific instruments and mathematics is claimed to enable the objectification of science. In this work, carried out by reviewing the scientific literature, the above claims are disputed systematically by evaluating the definition of physical reality and the scientific method, showing that empiricism relies ultimately upon the human senses for the evaluation of scientific theories and that measuring instruments cannot replace the human sensory system. Nativist and constructivist theories of human sensory development are reviewed, and it is shown that nativist claims of core conceptual knowledge cannot be supported by the findings in the literature, which shows that perception does not simply arise from a process of maturation. Instead, sensory function requires a long process of learning through interactions with the environment. To more rigorously define physical reality and systematically evaluate the stability of perception, and thus the basis of empiricism, the development of the method of dimension analysis is reviewed. It is shown that this methodology, relied upon for the mathematical analysis of physical quantities, is itself based upon empiricism, and that all of physical reality can be described in terms of the three fundamental dimensions of mass, length and time. Hereafter the sensory modalities that inform us about these three dimensions are systematically evaluated. The following careful analysis of neuronal plasticity in these modalities shows that all the relevant senses acquire from the environment the capacity to apprehend physical reality. It is concluded that physical reality is acquired rather than given innately, and leads to the position that science cannot provide unique results. Rather, those it can provide are sufficient for a particular environmental setting

A Multiagent System for Edge Detection and Continuity Perception on Fish Otolith Images

We present an algorithm for fish otolith growth ring detection using a multiagent system. Up to now, the identification of growth rings, for age estimation, is routinely achieved by human readers, but this task is tedious and depends on the reader subjectivity. One of the major problems encountered during an automatic contour detection is the lack of ring continuity perception. We present an approach to improve this continuity perception based on a 2D reconstruction of rings using a multiagent system. The originality of the approach is to use local edge detection achieved by agents and combine it with continuity perception that active contours allow