A framework for the comparative assessment of neuronal spike sorting algorithms towards more accurate off-line and on-line microelectrode arrays data analysis

Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting "building blocks" into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis

Parallel Counting Sort: A Modified of Counting Sort Algorithm

Sorting is one of a classic problem in computer engineer. One well-known sorting algorithm is a Counting Sort algorithm. Counting Sort had one problem, it can’t sort a positive and negative number in the same input list. Then, Modified Counting Sort created to solve that’s problem. The algorithm will split the numbers before the sorting process begin. This paper will tell another modification of this algorithm. The algorithm called Parallel Counting Sort. Parallel Counting Sort able to increase the execution time about 70% from Modified Counting Sort, especially in a big dataset (around 1000 and 10.000 numbers)

Pattern recognition of neural data: methods and algorithms for spike sorting and their optimal performance in prefrontal cortex recordings

Programa de Doctorado en NeurocienciasPattern recognition of neuronal discharges is the electrophysiological basis of the functional characterization of brain processes, so the implementation of a Spike Sorting algorithm is an essential step for the analysis of neural codes and neural interactions in a network or brain circuit. Extracted information from the neural action potential can be used to characterize neural activity events and correlate them during behavioral and cognitive processes, including different types of associative learning tasks. In particular, feature extraction is a critical step in the spike sorting procedure, which is prior to the clustering step and subsequent to the spike detection-identification step in a Spike Sorting algorithm. In the present doctoral thesis, the implementation of an automatic and unsupervised computational algorithm, called 'Unsupervised Automatic Algorithm', is proposed for the detection, identification and classification of the neural action potentials distributed across the electrophysiological recordings; and for clustering of these potentials in function of the shape, phase and distribution features, which are extracted from the first-order derivative of the potentials under study. For this, an efficient and unsupervised clustering method was developed, which integrate the K-means method with two clustering measures (validity and error indices) to verify both the cohesion-dispersion among neural spike during classification and the misclassification of clustering, respectively. In additions, this algorithm was implemented in a customized spike sorting software called VISSOR (Viability of Integrated Spike Sorting of Real Recordings). On the other hand, a supervised grouping method of neural activity profiles was performed to allow the recognition of specific patterns of neural discharges. Validity and effectiveness of these methods and algorithms were tested in this doctoral thesis by the classification of the detected action potentials from extracellular recordings of the rostro-medial prefrontal cortex of rabbits during the classical eyelid conditioning. After comparing the spike-sorting methods/algorithms proposed in this work with other methods also based on feature extraction of the action potentials, it was observed that this one had a better performance during the classification. That is, the methods/algorithms proposed here allowed obtaining: (1) the optimal number of clusters of neuronal spikes (according to the criterion of the maximum value of the cohesion-dispersion index) and (2) the optimal clustering of these spike-events (according to the criterion of the minimum value of the error index). The analytical implication of these results was that the feature extraction based on the shape, phase and distribution features of the action potential, together with the application of an alternative method of unsupervised classification with validity and error indices; guaranteed an efficient classification of neural events, especially for those detected from extracellular or multi-unitary recordings. Rabbits were conditioned with a delay paradigm consisting of a tone as conditioned stimulus. The conditioned stimulus started 50, 250, 500, 1000, or 2000 ms before and co-terminated with an air puff directed at the cornea as unconditioned stimulus. The results obtained indicated that the firing rate of each recorded neuron presented a single peak of activity with a frequency dependent on the inter-stimulus interval (i.e., ¿ 12 Hz for 250 ms, ¿ 6 Hz for 500 ms, and ¿ 3 Hz for 1000 ms). Interestingly, the recorded neurons from the rostro-medial prefrontal cortex presented their dominant firing peaks at three precise times evenly distributed with respect to conditioned stimulus start, and also depending on the duration of the inter-stimulus interval (only for intervals of 250, 500, and 1000 ms). No significant neural responses were recorded at very short (50 ms) or long (2000 ms) conditioned stimulus-unconditioned stimulus time intervals. Furthermore, the eyelid movements were recorded with the magnetic search coil technique and the electromyographic (EMG) activity of the orbicularis oculi muscle. Reflex and conditioned eyelid responses presented a dominant oscillatory frequency of ¿ 12 Hz. The experimental implication of these results is that the recorded neurons from the rostro-medial prefrontal cortex seem not to encode the oscillatory properties characterizing conditioned eyelid responses in rabbits. As a general experimental conclusion, it could be said that rostro-medial prefrontal cortex neurons are probably involved in the determination of CS-US intervals of an intermediate range (250-1000 ms).Universidad Pablo de Olavide. Departamento de Fisiología, Anatomía y Biología CelularPostprin