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Globally, billions of flying animals undergo seasonal migrations, many of which occur at night. The temporal and spatial scales at which migrations occur and our inability to directly observe these nocturnal movements makes monitoring and characterizing this critical period in migratory animals' life cycles difficult. Remote sensing, therefore, has played an important role in our understanding of large-scale nocturnal bird migrations. Weather surveillance radar networks in Europe and North America have great potential for long-term low-cost monitoring of bird migration at scales that have previously been impossible to achieve. Such long-term monitoring, however, poses a number of challenges for the ornithological and ecological communities: how does one take advantage of this vast data resource, integrate information across multiple sensors and large spatial and temporal scales, and visually represent the data for interpretation and dissemination, considering the dynamic nature of migration? We assembled an interdisciplinary team of ecologists, meteorologists, computer scientists, and graphic designers to develop two different flow visualizations, which are interactive and open source, in order to create novel representations of broad-front nocturnal bird migration to address a primary impediment to long-term, large-scale nocturnal migration monitoring. We have applied these visualization techniques to mass bird migration events recorded by two different weather surveillance radar networks covering regions in Europe and North America. These applications show the flexibility and portability of such an approach. The visualizations provide an intuitive representation of the scale and dynamics of these complex systems, are easily accessible for a broad interest group, and are biologically insightful. Additionally, they facilitate fundamental ecological research, conservation, mitigation of human-wildlife conflicts, improvement of meteorological products, and public outreach, education, and engagement.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

In this data paper, Bird tracking - GPS tracking of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast is described, a species occurrence dataset published by the Research Institute for Nature and Forest (INBO). The dataset (version 5.5) contains close to 2.5 million occurrences, recorded by 101 GPS trackers mounted on 75 Lesser Black-backed Gulls and 26 Herring Gulls breeding at the Belgian and Dutch coast. The trackers were developed by the University of Amsterdam Bird Tracking System (UvA-BiTS, http://www.uva-bits.nl). These automatically record and transmit bird movements, which allows us and others to study their habitat use and migration behaviour in great detail. Our bird tracking network is operational since 2013. It is funded for LifeWatch by the Hercules Foundation and maintained in collaboration with UvA-BiTS and the Flanders Marine Institute (VLIZ). The recorded data are periodically released in bulk as open data (http://dataset.inbo.be/bird-tracking-gull-occurrences), and are also accessible through CartoDB and the Global Biodiversity Information Facility (GBIF).

The recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets. Large 3D electron microscopy data sets frequently contain noisy data due to accelerated imaging, and denoising techniques require specialised skill sets. Here the authors introduce DenoisEM, an ImageJ plugin that democratises denoising EM data sets, enabling fast parameter tuning and processing through parallel computing.

Most digital cameras use an array of alternating color filters to capture the varied colors in a scene with a single sensor chip. Reconstruction of a full color image from such a color mosaic is what constitutes demosaicing. In this paper, a technique is proposed that performs this demosaicing in a way that incurs a very low computational cost. This is done through a (dual-tree complex) wavelet interpretation of the demosaicing problem. By using a novel locally adaptive approach for demosaicing (complex) wavelet coefficients, we show that many of the common demosaicing artifacts can be avoided in an efficient way. Results demonstrate that the proposed method is competitive with respect to the current state of the art, but incurs a lower computational cost. The wavelet approach also allows for computationally effective denoising or deblurring approaches.

Today, many MRI reconstruction techniques exist for undersampled MRI data. Regularization-based techniques inspired by compressed sensing allow for the reconstruction of undersampled data that would lead to an ill-posed reconstruction problem. Parallel imaging enables the reconstruction of MRI images from undersampled multi-coil data that leads to a well-posed reconstruction problem. Autocalibrating pMRI techniques encompass pMRI techniques where no explicit knowledge of the coil sensivities is required. A first purpose of this paper is to derive a novel autocalibration approach for pMRI that allows for the estimation and use of smooth, but high-bandwidth coil profiles instead of a compactly supported kernel. These high-bandwidth models adhere more accurately to the physics of an antenna system. The second purpose of this paper is to demonstrate the feasibility of a parameter-free reconstruction algorithm that combines autocalibrating pMRI and compressed sensing. Therefore, we present several techniques for automatic parameter estimation in MRI reconstruction. Experiments show that a higher reconstruction accuracy can be had using high-bandwidth coil models and that the automatic parameter choices yield an acceptable result.

Due to the ongoing miniaturization of digital camera sensors and the steady increase of the “number of megapixels”, individual sensor elements of the camera become more sensitive to noise, even deteriorating the final image quality. To go around this problem, sophisticated processing algorithms in the devices, can help to maximally exploit the knowledge on the sensor characteristics (e.g., in terms of noise), and offer a better image reconstruction. Although a lot of research focuses on rather simplistic noise models, such as stationary additive white Gaussian noise, only limited attention has gone to more realistic digital camera noise models. In this article, we first present a digital camera noise model that takes several processing steps in the camera into account, such as sensor signal amplification, clipping, post-processing,.. We then apply this noise model to the reconstruction problem of high dynamic range (HDR) images from a small set of low dynamic range (LDR) exposures of a static scene. In literature, HDR reconstruction is mostly performed by computing a weighted average, in which the weights are directly related to the observer pixel intensities of the LDR image. In this work, we derive a Bayesian probabilistic formulation of a weighting function that is near-optimal in the MSE sense (or SNR sense) of the reconstructed HDR image, by assuming exponentially distributed irradiance values. We define the weighting function as the probability that the observed pixel intensity is approximately unbiased . The weighting function can be directly computed based on the noise model parameters, which gives rise to different symmetric and asymmetric shapes when electronic noise or photon noise is dominant. We also explain how to deal with the case that some of the noise model parameters are unknown and explain how the camera response function can be estimated using the presented noise model. Finally, experimental results are provided to support our findings.

Due to the ongoing miniaturization of digital camera sensors and the steady increase of the \"number of megapixels\", individual sensor elements of the camera become more sensitive to noise, even deteriorating the final image quality. To go around this problem, sophisticated processing algorithms in the devices, can help to maximally exploit the knowledge on the sensor characteristics (e.g., in terms of noise), and offer a better image reconstruction. Although a lot of research focuses on rather simplistic noise models, such as stationary additive white Gaussian noise, only limited attention has gone to more realistic digital camera noise models. In this article, we first present a digital camera noise model that takes several processing steps in the camera into account, such as sensor signal amplification, clipping, post-processing,.. We then apply this noise model to the reconstruction problem of high dynamic range (HDR) images from a small set of low dynamic range (LDR) exposures of a static scene. In literature, HDR reconstruction is mostly performed by computing a weighted average, in which the weights are directly related to the observer pixel intensities of the LDR image. In this work, we derive a Bayesian probabilistic formulation of a weighting function that is near-optimal in the MSE sense (or SNR sense) of the reconstructed HDR image, by assuming exponentially distributed irradiance values. We define the weighting function as the probability that the observed pixel intensity is approximately unbiased. The weighting function can be directly computed based on the noise model parameters, which gives rise to different symmetric and asymmetric shapes when electronic noise or photon noise is dominant. We also explain how to deal with the case that some of the noise model parameters are unknown and explain how the camera response function can be estimated using the presented noise model. Finally, experimental results are provided to support our findings.[PUBLICATION ABSTRACT]

Abstract Given the complexity of societal, technological, and economic challenges encountered by schools and teachers, one may wonder whether and how teachers can still optimally motivate their students. To adopt a motivating role in today’s ever-changing, even stormy, educational landscape, teachers need more than a checklist of motivating practices. They also need a fundamental theoretical perspective that can serve as a general source of inspiration for their everyday classroom practices across various situations and in interaction with different students. Herein, we argue that self-determination theory represents such a valuable perspective. In Part I, we discuss the satisfaction of learners’ psychological needs for autonomy, competence, and relatedness as a source of student motivation, engagement, and resilience. We also present a recently developed circular model involving a broad variety of motivating (i.e., need-supportive) and demotivating (i.e., need-thwarting) teaching practices appealing to these three needs. In Part II, we discuss several implications of this circular model, thereby discussing the diverse pathways that lead to student need satisfaction, motivation, and engagement as well as highlighting teachers’ capacity for calibration to deal with uncertainty and change. We conclude that school principals and teachers do well to invest in both students’ and teachers’ psychological need experiences, such that they become skilled in flexibly adjusting themselves to diversity, uncertainty, and change.

The recent advent of 3D in Electron Microscopy (EM) has allowed for detection of detailed sub-cellular nanometer resolution structures. While being a scientific breakthrough, this has also caused an explosion in dataset size, necessitating the development of automated workflows. Automated workflows typically benefit reproducibility and throughput compared to manual analysis. The risk of automation is that it ignores the expertise of the microscopy user that comes with manual analysis. To mitigate this risk, this paper presents a hybrid paradigm. We propose a \"human-in-the-loop\" (HITL) model that combines expert microscopy knowledge with the power of large-scale parallel computing to improve EM image quality through advanced image restoration algorithms. An interactive graphical user interface, publicly available as an ImageJ plugin, was developed to allow biologists to use our framework in an intuitive and user-friendly fashion. We show that this plugin improves visualization of EM ultrastructure and subsequent (semi-)automated segmentation and image analysis. Footnotes * https://bioimagingcore.be/DenoisEM * https://bioimagingcore.be/DenoisEM/data/