18,739 research outputs found
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
An Adaptive Sampling Scheme to Efficiently Train Fully Convolutional Networks for Semantic Segmentation
Deep convolutional neural networks (CNNs) have shown excellent performance in
object recognition tasks and dense classification problems such as semantic
segmentation. However, training deep neural networks on large and sparse
datasets is still challenging and can require large amounts of computation and
memory. In this work, we address the task of performing semantic segmentation
on large data sets, such as three-dimensional medical images. We propose an
adaptive sampling scheme that uses a-posterior error maps, generated throughout
training, to focus sampling on difficult regions, resulting in improved
learning. Our contribution is threefold: 1) We give a detailed description of
the proposed sampling algorithm to speed up and improve learning performance on
large images. We propose a deep dual path CNN that captures information at fine
and coarse scales, resulting in a network with a large field of view and high
resolution outputs. We show that our method is able to attain new
state-of-the-art results on the VISCERAL Anatomy benchmark
Open Source Software for Automatic Detection of Cone Photoreceptors in Adaptive Optics Ophthalmoscopy Using Convolutional Neural Networks
Imaging with an adaptive optics scanning light ophthalmoscope (AOSLO) enables direct visualization of the cone photoreceptor mosaic in the living human retina. Quantitative analysis of AOSLO images typically requires manual grading, which is time consuming, and subjective; thus, automated algorithms are highly desirable. Previously developed automated methods are often reliant on ad hoc rules that may not be transferable between different imaging modalities or retinal locations. In this work, we present a convolutional neural network (CNN) based method for cone detection that learns features of interest directly from training data. This cone-identifying algorithm was trained and validated on separate data sets of confocal and split detector AOSLO images with results showing performance that closely mimics the gold standard manual process. Further, without any need for algorithmic modifications for a specific AOSLO imaging system, our fully-automated multi-modality CNN-based cone detection method resulted in comparable results to previous automatic cone segmentation methods which utilized ad hoc rules for different applications. We have made free open-source software for the proposed method and the corresponding training and testing datasets available online
Three-Dimensional GPU-Accelerated Active Contours for Automated Localization of Cells in Large Images
Cell segmentation in microscopy is a challenging problem, since cells are
often asymmetric and densely packed. This becomes particularly challenging for
extremely large images, since manual intervention and processing time can make
segmentation intractable. In this paper, we present an efficient and highly
parallel formulation for symmetric three-dimensional (3D) contour evolution
that extends previous work on fast two-dimensional active contours. We provide
a formulation for optimization on 3D images, as well as a strategy for
accelerating computation on consumer graphics hardware. The proposed software
takes advantage of Monte-Carlo sampling schemes in order to speed up
convergence and reduce thread divergence. Experimental results show that this
method provides superior performance for large 2D and 3D cell segmentation
tasks when compared to existing methods on large 3D brain images
Sequential Monte Carlo samplers for semilinear inverse problems and application to magnetoencephalography
We discuss the use of a recent class of sequential Monte Carlo methods for
solving inverse problems characterized by a semi-linear structure, i.e. where
the data depend linearly on a subset of variables and nonlinearly on the
remaining ones. In this type of problems, under proper Gaussian assumptions one
can marginalize the linear variables. This means that the Monte Carlo procedure
needs only to be applied to the nonlinear variables, while the linear ones can
be treated analytically; as a result, the Monte Carlo variance and/or the
computational cost decrease. We use this approach to solve the inverse problem
of magnetoencephalography, with a multi-dipole model for the sources. Here,
data depend nonlinearly on the number of sources and their locations, and
depend linearly on their current vectors. The semi-analytic approach enables us
to estimate the number of dipoles and their location from a whole time-series,
rather than a single time point, while keeping a low computational cost.Comment: 26 pages, 6 figure
Feature extraction using extrema sampling of discrete derivatives for spike sorting in implantable upper-limb neural prostheses
Next generation neural interfaces for upper-limb (and other) prostheses aim to develop implantable interfaces for one or more nerves, each interface having many neural signal channels that work reliably in the stump without harming the nerves. To achieve real-time multi-channel processing it is important to integrate spike sorting on-chip to overcome limitations in transmission bandwidth. This requires computationally efficient algorithms for feature extraction and clustering suitable for low-power hardware implementation. This paper describes a new feature extraction method for real-time spike sorting based on extrema analysis (namely positive peaks and negative peaks) of spike shapes and their discrete derivatives at different frequency bands. Employing simulation across different datasets, the accuracy and computational complexity of the proposed method are assessed and compared with other methods. The average classification accuracy of the proposed method in conjunction with online sorting (O-Sort) is 91.6%, outperforming all the other methods tested with the O-Sort clustering algorithm. The proposed method offers a better tradeoff between classification error and computational complexity, making it a particularly strong choice for on-chip spike sorting
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