6 results
Search Results
Now showing 1 - 6 of 6
- ItemComputational design and optimization of electro-physiological sensors([London] : Nature Publishing Group UK, 2021) Nittala, Aditya Shekhar; Karrenbauer, Andreas; Khan, Arshad; Kraus, Tobias; Steimle, JürgenElectro-physiological sensing devices are becoming increasingly common in diverse applications. However, designing such sensors in compact form factors and for high-quality signal acquisition is a challenging task even for experts, is typically done using heuristics, and requires extensive training. Our work proposes a computational approach for designing multi-modal electro-physiological sensors. By employing an optimization-based approach alongside an integrated predictive model for multiple modalities, compact sensors can be created which offer an optimal trade-off between high signal quality and small device size. The task is assisted by a graphical tool that allows to easily specify design preferences and to visually analyze the generated designs in real-time, enabling designer-in-the-loop optimization. Experimental results show high quantitative agreement between the prediction of the optimizer and experimentally collected physiological data. They demonstrate that generated designs can achieve an optimal balance between the size of the sensor and its signal acquisition capability, outperforming expert generated solutions.
- ItemSynthesizing long-term sea level rise projections – the MAGICC sea level model v2.0(München : European Geopyhsical Union, 2017) Nauels, Alexander; Meinshausen, Malte; Mengel, Matthias; Lorbacher, Katja; Wigley, Tom M.L.Sea level rise (SLR) is one of the major impacts of global warming; it will threaten coastal populations, infrastructure, and ecosystems around the globe in coming centuries. Well-constrained sea level projections are needed to estimate future losses from SLR and benefits of climate protection and adaptation. Process-based models that are designed to resolve the underlying physics of individual sea level drivers form the basis for state-of-the-art sea level projections. However, associated computational costs allow for only a small number of simulations based on selected scenarios that often vary for different sea level components. This approach does not sufficiently support sea level impact science and climate policy analysis, which require a sea level projection methodology that is flexible with regard to the climate scenario yet comprehensive and bound by the physical constraints provided by process-based models. To fill this gap, we present a sea level model that emulates global-mean long-term process-based model projections for all major sea level components. Thermal expansion estimates are calculated with the hemispheric upwelling-diffusion ocean component of the simple carbon-cycle climate model MAGICC, which has been updated and calibrated against CMIP5 ocean temperature profiles and thermal expansion data. Global glacier contributions are estimated based on a parameterization constrained by transient and equilibrium process-based projections. Sea level contribution estimates for Greenland and Antarctic ice sheets are derived from surface mass balance and solid ice discharge parameterizations reproducing current output from ice-sheet models. The land water storage component replicates recent hydrological modeling results. For 2100, we project 0.35 to 0.56m (66% range) total SLR based on the RCP2.6 scenario, 0.45 to 0.67m for RCP4.5, 0.46 to 0.71m for RCP6.0, and 0.65 to 0.97m for RCP8.5. These projections lie within the range of the latest IPCC SLR estimates. SLR projections for 2300 yield median responses of 1.02m for RCP2.6, 1.76m for RCP4.5, 2.38m for RCP6.0, and 4.73m for RCP8.5. The MAGICC sea level model provides a flexible and efficient platform for the analysis of major scenario, model, and climate uncertainties underlying long-term SLR projections. It can be used as a tool to directly investigate the SLR implications of different mitigation pathways and may also serve as input for regional SLR assessments via component-wise sea level pattern scaling.
- ItemCorrecting systematic errors by hybrid 2D correlation loss functions in nonlinear inverse modelling(San Francisco, California, US : PLOS, 2023) Mayerhöfer, Thomas G.; Noda, Isao; Pahlow, Susanne; Heintzmann, Rainer; Popp, JürgenRecently a new family of loss functions called smart error sums has been suggested. These loss functions account for correlations within experimental data and force modeled data to obey these correlations. As a result, multiplicative systematic errors of experimental data can be revealed and corrected. The smart error sums are based on 2D correlation analysis which is a comparably recent methodology for analyzing spectroscopic data that has found broad application. In this contribution we mathematically generalize and break down this methodology and the smart error sums to uncover the mathematic roots and simplify it to craft a general tool beyond spectroscopic modelling. This reduction also allows a simplified discussion about limits and prospects of this new method including one of its potential future uses as a sophisticated loss function in deep learning. To support its deployment, the work includes computer code to allow reproduction of the basic results.
- ItemIMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images(San Francisco, California, US : PLOS, 2022) Gupta, Yubraj; Costa, Carlos; Pinho, Eduardo; A. Bastião Silva, Luís; Heintzmann, RainerAdvances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since “seeing is believing”, it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital work-flows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer.
- ItemColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data(San Francisco, California, US : PLOS, 2019) Smit, Jochem H.; Li, Yichen; Warszawik, Eliza M.; Herrmann, Andreas; Cordes, Thorben; Gilestro, Giorgio FSingle-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique. With the cost of microscopes dropping and the availability of fully automated microscopes, the volume of microscopy data produced has increased tremendously. These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis. Furthermore, requirements for analysis procedures have become more stringent given the demand of various journals to make data and analysis procedures available. To address these issues we have developed a new data analysis package for analysis of fluorescence microscopy data from rod-like cells. Our software ColiCoords structures microscopy data at the single-cell level and implements a coordinate system describing each cell. This allows for the transformation of Cartesian coordinates from transmission light and fluorescence images and single-molecule localization microscopy (SMLM) data to cellular coordinates. Using this transformation, many cells can be combined to increase the statistical power of fluorescence microscopy datasets of any kind. ColiCoords is open source, implemented in the programming language Python, and is extensively documented. This allows for modifications for specific needs or to inspect and publish data analysis procedures. By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research. The source code and documentation can be found via the project’s GitHub page.
- ItemAnalogue pattern recognition with stochastic switching binary CMOS-integrated memristive devices([London] : Macmillan Publishers Limited, part of Springer Nature, 2020) Zahari, Finn; Pérez, Eduardo; Mahadevaiah, Mamathamba Kalishettyhalli; Kohlstedt, Hermann; Wenger, Christian; Ziegler, MartinBiological neural networks outperform current computer technology in terms of power consumption and computing speed while performing associative tasks, such as pattern recognition. The analogue and massive parallel in-memory computing in biology differs strongly from conventional transistor electronics that rely on the von Neumann architecture. Therefore, novel bio-inspired computing architectures have been attracting a lot of attention in the field of neuromorphic computing. Here, memristive devices, which serve as non-volatile resistive memory, are employed to emulate the plastic behaviour of biological synapses. In particular, CMOS integrated resistive random access memory (RRAM) devices are promising candidates to extend conventional CMOS technology to neuromorphic systems. However, dealing with the inherent stochasticity of resistive switching can be challenging for network performance. In this work, the probabilistic switching is exploited to emulate stochastic plasticity with fully CMOS integrated binary RRAM devices. Two different RRAM technologies with different device variabilities are investigated in detail, and their potential applications in stochastic artificial neural networks (StochANNs) capable of solving MNIST pattern recognition tasks is examined. A mixed-signal implementation with hardware synapses and software neurons combined with numerical simulations shows that the proposed concept of stochastic computing is able to process analogue data with binary memory cells. © 2020, The Author(s).