scholarly journals Spatial information in large-scale neural recordings

2015 ◽  
Vol 8 ◽  
Author(s):  
Thaddeus R. Cybulski ◽  
Joshua I. Glaser ◽  
Adam H. Marblestone ◽  
Bradley M. Zamft ◽  
Edward S. Boyden ◽  
...  
Keyword(s):  
Large Scale ◽  
Spatial Information ◽  
Neural Recordings

scholarly journals Spatial Information in Large-Scale Neural Recordings

2014 ◽  
Author(s):  
Thaddeus R Cybulski ◽  
Joshua I Glaser ◽  
Adam H Marblestone ◽  
Bradley M Zamft ◽  
Edward S Boyden ◽  
...  
Keyword(s):  
Information Content ◽  
Information Flow ◽  
Fisher Information ◽  
Large Scale ◽  
Spatial Information ◽  
Neural Recording ◽  
Central Issue ◽  
Neural Recordings ◽  
Analytic Expressions ◽  
Potential Applications

A central issue in neural recording is that of distinguishing the activities of many neurons. Here, we develop a framework, based on Fisher information, to quantify how separable a neuron's activity is from the activities of nearby neurons. We (1) apply this framework to model information flow and spatial distinguishability for several electrical and optical neural recording methods, (2) provide analytic expressions for information content, and (3) demonstrate potential applications of the approach. This method generalizes to many recording devices that resolve objects in space and thus may be useful in the design of next-generation scalable neural recording systems.

scholarly journals Building population models for large-scale neural recordings: Opportunities and pitfalls

2021 ◽  
Vol 70 ◽  
pp. 64-73
Author(s):  
Cole Hurwitz ◽  
Nina Kudryashova ◽  
Arno Onken ◽  
Matthias H. Hennig
Keyword(s):  
Large Scale ◽  
Population Models ◽  
Neural Recordings

Out in the wash: spatial ecology of a temperate marine shallow rocky-reef species derived using acoustic telemetry

2015 ◽  
Vol 66 (6) ◽  
pp. 559 ◽  
Author(s):  
Jerom R. Stocks ◽  
Charles A. Gray ◽  
Matthew D. Taylor
Keyword(s):  
Spatial Ecology ◽  
Large Scale ◽  
Spatial Information ◽  
Activity Space ◽  
Rocky Reef ◽  
Temperate Reef ◽  
Detection Frequency ◽  
Detection Depth ◽  
Eastern Australia ◽  
Temperate Reef Fish

Characterising the movement and habitat affinities of fish is a fundamental component in understanding the functioning of marine ecosystems. A comprehensive array of acoustic receivers was deployed at two near-shore coastal sites in south-eastern Australia, to examine the movements, activity-space size and residency of a temperate rocky-reef, herbivorous species Girella elevata. Twenty-four G. elevata individuals were internally tagged with pressure-sensing acoustic transmitters across these two arrays and monitored for up to 550 days. An existing network of coastal receivers was used to examine large-scale movement patterns. Individuals exhibited varying residency, but all had small activity-space sizes within the arrays. The species utilised shallow rocky-reef habitat, displaying unimodal or bimodal patterns in depth use. A positive correlation was observed between wind speed and the detection depth of fish, with fish being likely to move to deeper water to escape periods of adverse conditions. Detection frequency data, corrected using sentinel tags, generally illustrated diurnal behaviour. Patterns of habitat usage, residency and spatial utilisation highlighted the susceptibility of G. elevata to recreational fishing pressure. The results from the present study will further contribute to the spatial information required in the zoning of effective marine protected areas, and our understanding of temperate reef fish ecology.

scholarly journals Semantic overlay network for large-scale spatial information indexing

2013 ◽  
Vol 57 ◽  
pp. 208-217 ◽  
Author(s):  
Zhiqiang Zou ◽  
Yue Wang ◽  
Kai Cao ◽  
Tianshan Qu ◽  
Zhongmin Wang
Keyword(s):  
Large Scale ◽  
Spatial Information ◽  
Overlay Network

scholarly journals Multiscale Semantic Feature Optimization and Fusion Network for Building Extraction Using High-Resolution Aerial Images and LiDAR Data

2021 ◽  
Vol 13 (13) ◽  
pp. 2473
Author(s):  
Qinglie Yuan ◽  
Helmi Zulhaidi Mohd Shafri ◽  
Aidi Hizami Alias ◽  
Shaiful Jahari Hashim
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
Spatial Information ◽  
Feature Fusion ◽  
Aerial Images ◽  
Semantic Gap ◽  
Superior Performance ◽  
Lidar Data ◽  
Building Extraction ◽  
Hierarchical Features

Automatic building extraction has been applied in many domains. It is also a challenging problem because of the complex scenes and multiscale. Deep learning algorithms, especially fully convolutional neural networks (FCNs), have shown robust feature extraction ability than traditional remote sensing data processing methods. However, hierarchical features from encoders with a fixed receptive field perform weak ability to obtain global semantic information. Local features in multiscale subregions cannot construct contextual interdependence and correlation, especially for large-scale building areas, which probably causes fragmentary extraction results due to intra-class feature variability. In addition, low-level features have accurate and fine-grained spatial information for tiny building structures but lack refinement and selection, and the semantic gap of across-level features is not conducive to feature fusion. To address the above problems, this paper proposes an FCN framework based on the residual network and provides the training pattern for multi-modal data combining the advantage of high-resolution aerial images and LiDAR data for building extraction. Two novel modules have been proposed for the optimization and integration of multiscale and across-level features. In particular, a multiscale context optimization module is designed to adaptively generate the feature representations for different subregions and effectively aggregate global context. A semantic guided spatial attention mechanism is introduced to refine shallow features and alleviate the semantic gap. Finally, hierarchical features are fused via the feature pyramid network. Compared with other state-of-the-art methods, experimental results demonstrate superior performance with 93.19 IoU, 97.56 OA on WHU datasets and 94.72 IoU, 97.84 OA on the Boston dataset, which shows that the proposed network can improve accuracy and achieve better performance for building extraction.

scholarly journals T-SNE visualization of large-scale neural recordings

2016 ◽  
Author(s):  
George Dimitriadis ◽  
Joana Neto ◽  
Adam R. Kampff
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Brain Regions ◽  
Data Sets ◽  
Neural Recordings ◽  
Sorting Problem ◽  
Feature Spaces ◽  
High Degree

AbstractElectrophysiology is entering the era of ‘Big Data’. Multiple probes, each with hundreds to thousands of individual electrodes, are now capable of simultaneously recording from many brain regions. The major challenge confronting these new technologies is transforming the raw data into physiologically meaningful signals, i.e. single unit spikes. Sorting the spike events of individual neurons from a spatiotemporally dense sampling of the extracellular electric field is a problem that has attracted much attention [22, 23], but is still far from solved. Current methods still rely on human input and thus become unfeasible as the size of the data sets grow exponentially.Here we introduce the t-student stochastic neighbor embedding (t-sne) dimensionality reduction method [27] as a visualization tool in the spike sorting process. T-sne embeds the n-dimensional extracellular spikes (n = number of features by which each spike is decomposed) into a low (usually two) dimensional space. We show that such embeddings, even starting from different feature spaces, form obvious clusters of spikes that can be easily visualized and manually delineated with a high degree of precision. We propose that these clusters represent single units and test this assertion by applying our algorithm on labeled data sets both from hybrid [23] and paired juxtacellular/extracellular recordings [15]. We have released a graphical user interface (gui) written in python as a tool for the manual clustering of the t-sne embedded spikes and as a tool for an informed overview and fast manual curration of results from other clustering algorithms. Furthermore, the generated visualizations offer evidence in favor of the use of probes with higher density and smaller electrodes. They also graphically demonstrate the diverse nature of the sorting problem when spikes are recorded with different methods and arise from regions with different background spiking statistics.

scholarly journals 3DViewGraph: Learning Global Features for 3D Shapes from A Graph of Unordered Views with Attention

2019 ◽  
Author(s):  
Zhizhong Han ◽  
Xiyang Wang ◽  
Chi Man Vong ◽  
Yu-Shen Liu ◽  
Matthias Zwicker ◽  
...  
Keyword(s):  
Spatial Pattern ◽  
Large Scale ◽  
Spatial Information ◽  
Dimensional Space ◽  
Spatial Relationship ◽  
Global Features ◽  
Pattern Correlation ◽  
3D Shape Analysis ◽  
3D Shapes ◽  
Learned Features

Learning global features by aggregating information over multiple views has been shown to be effective for 3D shape analysis. For view aggregation in deep learning models, pooling has been applied extensively. However, pooling leads to a loss of the content within views, and the spatial relationship among views, which limits the discriminability of learned features. We propose 3DViewGraph to resolve this issue, which learns 3D global features by more effectively aggregating unordered views with attention. Specifically, unordered views taken around a shape are regarded as view nodes on a view graph. 3DViewGraph first learns a novel latent semantic mapping to project low-level view features into meaningful latent semantic embeddings in a lower dimensional space, which is spanned by latent semantic patterns. Then, the content and spatial information of each pair of view nodes are encoded by a novel spatial pattern correlation, where the correlation is computed among latent semantic patterns. Finally, all spatial pattern correlations are integrated with attention weights learned by a novel attention mechanism. This further increases the discriminability of learned features by highlighting the unordered view nodes with distinctive characteristics and depressing the ones with appearance ambiguity. We show that 3DViewGraph outperforms state-of-the-art methods under three large-scale benchmarks.

scholarly journals A time-stamp mechanism may provide temporal information necessary for egocentric to allocentric spatial transformations

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Avner Wallach ◽  
Erik Harvey-Girard ◽  
James Jaeyoon Jun ◽  
André Longtin ◽  
Len Maler
Keyword(s):  
Spatial Learning ◽  
Spatial Organization ◽  
Spatial Information ◽  
Spatial Relations ◽  
Temporal Information ◽  
Accurate Estimation ◽  
Neural Recordings ◽  
Brain Circuitry ◽  
Learning Circuits ◽  
Thalamic Region

Learning the spatial organization of the environment is essential for most animals’ survival. This requires the animal to derive allocentric spatial information from egocentric sensory and motor experience. The neural mechanisms underlying this transformation are mostly unknown. We addressed this problem in electric fish, which can precisely navigate in complete darkness and whose brain circuitry is relatively simple. We conducted the first neural recordings in the preglomerular complex, the thalamic region exclusively connecting the optic tectum with the spatial learning circuits in the dorsolateral pallium. While tectal topographic information was mostly eliminated in preglomerular neurons, the time-intervals between object encounters were precisely encoded. We show that this reliable temporal information, combined with a speed signal, can permit accurate estimation of the distance between encounters, a necessary component of path-integration that enables computing allocentric spatial relations. Our results suggest that similar mechanisms are involved in sequential spatial learning in all vertebrates.

scholarly journals Spatio-temporal deep learning model for distortion classification in laparoscopic video

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1010
Author(s):  
Nouar AlDahoul ◽  
Hezerul Abdul Karim ◽  
Abdulaziz Saleh Ba Wazir ◽  
Myles Joshua Toledo Tan ◽  
Mohammad Faizal Ahmad Fauzi
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Spatial Information ◽  
Short Term Memory ◽  
Learning Model ◽  
Motion Blur ◽  
Video Frame ◽  
Video Enhancement ◽  
Deep Learning Model ◽  
Laparoscopic Videos

Background: Laparoscopy is a surgery performed in the abdomen without making large incisions in the skin and with the aid of a video camera, resulting in laparoscopic videos. The laparoscopic video is prone to various distortions such as noise, smoke, uneven illumination, defocus blur, and motion blur. One of the main components in the feedback loop of video enhancement systems is distortion identification, which automatically classifies the distortions affecting the videos and selects the video enhancement algorithm accordingly. This paper aims to address the laparoscopic video distortion identification problem by developing fast and accurate multi-label distortion classification using a deep learning model. Current deep learning solutions based on convolutional neural networks (CNNs) can address laparoscopic video distortion classification, but they learn only spatial information. Methods: In this paper, utilization of both spatial and temporal features in a CNN-long short-term memory (CNN-LSTM) model is proposed as a novel solution to enhance the classification. First, pre-trained ResNet50 CNN was used to extract spatial features from each video frame by transferring representation from large-scale natural images to laparoscopic images. Next, LSTM was utilized to consider the temporal relation between the features extracted from the laparoscopic video frames to produce multi-label categories. A novel laparoscopic video dataset proposed in the ICIP2020 challenge was used for training and evaluation of the proposed method. Results: The experiments conducted show that the proposed CNN-LSTM outperforms the existing solutions in terms of accuracy (85%), and F1-score (94.2%). Additionally, the proposed distortion identification model is able to run in real-time with low inference time (0.15 sec). Conclusions: The proposed CNN-LSTM model is a feasible solution to be utilized in laparoscopic videos for distortion identification.

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