A control algorithm for autonomous optimization of extracellular recordings

This paper develops a control algorithm that can autonomously position an electrode so as to find and then maintain an optimal extracellular recording position. The algorithm was developed and tested in a two-neuron computational model representative of the cells found in cerebral cortex. The algorithm is based on a stochastic optimization of a suitably defined signal quality metric and is shown capable of finding the optimal recording position along representative sampling directions, as well as maintaining the optimal signal quality in the face of modeled tissue movements. The application of the algorithm to acute neurophysiological recording experiments and its potential implications to chronic recording electrode arrays are discussed

VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

Low-dimensional representations of neural time-series data with applications to peripheral nerve decoding

Bioelectronic medicines, implanted devices that influence physiological states by peripheral neuromodulation, have promise as a new way of treating diverse conditions from rheumatism to diabetes. We here explore ways of creating nerve-based feedback for the implanted systems to act in a dynamically adapting closed loop. In a first empirical component, we carried out decoding studies on in vivo recordings of cat and rat bladder afferents. In a low-resolution data-set, we selected informative frequency bands of the neural activity using information theory to then relate to bladder pressure. In a second high-resolution dataset, we analysed the population code for bladder pressure, again using information theory, and proposed an informed decoding approach that promises enhanced robustness and automatic re-calibration by creating a low-dimensional population vector. Coming from a different direction of more general time-series analysis, we embedded a set of peripheral nerve recordings in a space of main firing characteristics by dimensionality reduction in a high-dimensional feature-space and automatically proposed single efficiently implementable estimators for each identified characteristic. For bioelectronic medicines, this feature-based pre-processing method enables an online signal characterisation of low-resolution data where spike sorting is impossible but simple power-measures discard informative structure. Analyses were based on surrogate data from a self-developed and flexibly adaptable computer model that we made publicly available. The wider utility of two feature-based analysis methods developed in this work was demonstrated on a variety of datasets from across science and industry. (1) Our feature-based generation of interpretable low-dimensional embeddings for unknown time-series datasets answers a need for simplifying and harvesting the growing body of sequential data that characterises modern science. (2) We propose an additional, supervised pipeline to tailor feature subsets to collections of classification problems. On a literature standard library of time-series classification tasks, we distilled 22 generically useful estimators and made them easily accessible.Open Acces

In-Vitro Biological Tissue State Monitoring based on Impedance Spectroscopy

The relationship between post-mortem state and changes of biological tissue impedance has been investigated to serve as a basis for developing an in-vitro measurement method for monitoring the freshness of meat. The main challenges thereby are the reproducible measurement of the impedance of biological tissues and the classification method of their type and state. In order to realize reproducible tissue bio-impedance measurements, a suitable sensor taking into account the anisotropy of the biological tissue has been developed. It consists of cylindrical penetrating multi electrodes realizing good contacts between electrodes and the tissue. Experimental measurements have been carried out with different tissues and for a long period of time in order to monitor the state degradation with time. Measured results have been evaluated by means of the modified Fricke-Cole-Cole model. Results are reproducible and correspond to the expected behavior due to aging. An appropriate method for feature extraction and classification has been proposed using model parameters as features as input for classification using neural networks and fuzzy logic. A Multilayer Perceptron neural network (MLP) has been proposed for muscle type computing and the age computing and respectively freshness state of the meat. The designed neural network is able to generalize and to correctly classify new testing data with a high performance index of recognition. It reaches successful results of test equal to 100% for 972 created inputs for each muscle. An investigation of the influence of noise on the classification algorithm shows, that the MLP neural network has the ability to correctly classify the noisy testing inputs especially when the parameter noise is less than 0.6%. The success of classification is 100% for the muscles Longissimus Dorsi (LD) of beef, Semi-Membraneous (SM) of beef and Longissimus Dorsi (LD) of veal and 92.3% for the muscle Rectus Abdominis (RA) of veal. Fuzzy logic provides a successful alternative for easy classification. Using the Gaussian membership functions for the muscle type detection and trapezoidal member function for the classifiers related to the freshness detection, fuzzy logic realized an easy method of classification and generalizes correctly the inputs to the corresponding classes with a high level of recognition equal to 100% for meat type detection and with high accuracy for freshness computing equal to 84.62% for the muscle LD beef, 92.31 % for the muscle RA beef, 100 % for the muscle SM veal and 61.54% for the muscle LD veal.  Auf der Basis von Impedanzspektroskopie wurde ein neuartiges in-vitro-Messverfahren zur Überwachung der Frische von biologischem Gewebe entwickelt. Die wichtigsten Herausforderungen stellen dabei die Reproduzierbarkeit der Impedanzmessung und die Klassifizierung der Gewebeart sowie dessen Zustands dar. Für die Reproduzierbarkeit von Impedanzmessungen an biologischen Geweben, wurde ein zylindrischer Multielektrodensensor realisiert, der die 2D-Anisotropie des Gewebes berücksichtigt und einen guten Kontakt zum Gewebe realisiert. Experimentelle Untersuchungen wurden an verschiedenen Geweben über einen längeren Zeitraum durchgeführt und mittels eines modifizierten Fricke-Cole-Cole-Modells analysiert. Die Ergebnisse sind reproduzierbar und entsprechen dem physikalisch-basierten erwarteten Verhalten. Als Merkmale für die Klassifikation wurden die Modellparameter genutzt

Processing and analysis of multichannel extracellular neuronal signals: state-of-the-art and challenges

In recent years multichannel neuronal signal acquisition systems have allowed scientists to focus on research questions which were otherwise impossible. They act as a powerful means to study brain (dys)functions in in-vivo and in in-vitro animal models. Typically, each session of electrophysiological experiments with multichannel data acquisition systems generate large amount of raw data. For example, a 128 channel signal acquisition system with 16 bits A/D conversion and 20 kHz sampling rate will generate approximately 17 GB data per hour (uncompressed). This poses an important and challenging problem of inferring conclusions from the large amounts of acquired data. Thus, automated signal processing and analysis tools are becoming a key component in neuroscience research, facilitating extraction of relevant information from neuronal recordings in a reasonable time. The purpose of this review is to introduce the reader to the current state-of-the-art of open-source packages for (semi)automated processing and analysis of multichannel extracellular neuronal signals (i.e., neuronal spikes, local field potentials, electroencephalogram, etc.), and the existing Neuroinformatics infrastructure for tool and data sharing. The review is concluded by pinpointing some major challenges that are being faced, which include the development of novel benchmarking techniques, cloud-based distributed processing and analysis tools, as well as defining novel means to share and standardize data