NeuroChaT: A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo

Islam, Nurul; Martin, Sean; Aggleton, John P.; O’Mara, Shane M.

doi:10.12688/wellcomeopenres.15533.1

Cited by 7 publications

(7 citation statements)

References 34 publications

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“…Standard statistical testing was performed using an open-source custom-written suite in Python (NeuroChaT; available for download at https://github.com/shanemomara/omaraneurolab , https://github.com/shanemomara/NeuroChaT ) ( Islam et al, 2019 ), and additional custom codes in R (R Foundation for Statistical computing; https://www.r-project.org ). Units were classified based on the spatiotemporal features of their activity in the arena during pellet-chasing, as described below.…”

Section: Methodsmentioning

confidence: 99%

Anterior Thalamic Inputs Are Required for Subiculum Spatial Coding, with Associated Consequences for Hippocampal Spatial Memory

et al. 2021

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Just as hippocampal lesions are principally responsible for “temporal lobe” amnesia, lesions affecting the anterior thalamic nuclei seem principally responsible for a similar loss of memory, “diencephalic” amnesia. Compared with the former, the causes of diencephalic amnesia have remained elusive. A potential clue comes from how the two sites are interconnected, as within the hippocampal formation, only the subiculum has direct, reciprocal connections with the anterior thalamic nuclei. We found that both permanent and reversible anterior thalamic nuclei lesions in male rats cause a cessation of subicular spatial signaling, reduce spatial memory performance to chance, but leave hippocampal CA1 place cells largely unaffected. We suggest that a core element of diencephalic amnesia stems from the information loss in hippocampal output regions following anterior thalamic pathology. SIGNIFICANCE STATEMENT At present, we know little about interactions between temporal lobe and diencephalic memory systems. Here, we focused on the subiculum, as the sole hippocampal formation region directly interconnected with the anterior thalamic nuclei. We combined reversible and permanent lesions of the anterior thalamic nuclei, electrophysiological recordings of the subiculum, and behavioral analyses. Our results were striking and clear: following permanent thalamic lesions, the diverse spatial signals normally found in the subiculum (including place cells, grid cells, and head-direction cells) all disappeared. Anterior thalamic lesions had no discernible impact on hippocampal CA1 place fields. Thus, spatial firing activity within the subiculum requires anterior thalamic function, as does successful spatial memory performance. Our findings provide a key missing part of the much bigger puzzle concerning why anterior thalamic damage is so catastrophic for spatial memory in rodents and episodic memory in humans.

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Section: Methodsmentioning

confidence: 99%

Anterior Thalamic Inputs Are Required for Subiculum Spatial Coding, with Associated Consequences for Hippocampal Spatial Memory

et al. 2021

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“…NeuroChaT (Islam et al, 2019)). The pyqtgraph GUI library has many capabilities that could expand neurotic's interactive and annotation features.…”

Section: Discussionmentioning

confidence: 99%

neurotic: Neuroscience Tool for Interactive Characterization

Gill

Garcia

Ting

et al. 2020

eNeuro

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A software tool for synchronization of video with signals would be of broad general use to behavioral neuroscientists. A new program, called neurotic, allows users to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, is easy to use, and supports a variety of file formats. The program also facilitates collaborations by using a portable specification for loading and processing data and retrieving data files from online sources. Two examples are shown in which the software is used to explore experimental datasets with extracellular nerve or muscle recordings and simultaneous video of behavior. The configuration specification for controlling how data are located, loaded, processed, and plotted is also summarized. Algorithms for spike detection and burst detection are demonstrated. This new program could be used in many applications in which behavior and signals need to be analyzed together. Significance Statement Behavioral neuroscience would benefit from a tool that allows easy visualization of both behavior and neural or other signals. A new tool, called neurotic, is described that is free and open-source, and can make data visualization, analysis, and collaboration much easier.

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“…To assess whether place cells had a stable place field between successive sessions, we computed, using NeuroChat (Islam et al, 2019) spatial coherence along the L1/D/L2 sequence to establish place field stability. In addition, the equation L1DL2 (angle) was used to assess the measure of the angle (degrees) between the place field in darkness (D) and the two place fields in light (L1 and L2) using the COM of each place field: L1DL2 (angle) = cos -1 DL1.DL2…”

Section: Spatial Firing Stabilitymentioning

confidence: 99%

“…The software GraphPad Prism 8 was used for statistical analysis (t test and Wilcoxon signed-rank test) and graphs. NeuroChaT (Islam et al, 2019) was used to analyse spike properties and relative theta power (see "spike units" and "LFP" sections, respectively). The analysis for the total power in the 30 minutes LFP recording was written in Python (v3.7), extending NeuroChaT.…”

Section: |Dl1|| * ||Dl2||mentioning

confidence: 99%

Place Cells in the Claustrum Remap Under NMDA Receptor Control

Rizello

Martin

Rouine

et al. 2021

Preprint

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Place cells are cells exhibiting location-dependent responses; they have mostly been studied in the hippocampus. Place cells have also been reported in the rat claustrum, an underexplored paracortical region with extensive corto-cortical connectivity. It has been hypothesised that claustral neuronal responses are anchored to cortical visual inputs. We show rat claustral place cells remap when visual inputs are eliminated from the environment and that this remapping is NMDA-receptor-dependent. Eliminating visual input enhances delta-band oscillatory activity in the claustrum, without affecting simultaneously-recorded visual cortical activity. We conclude that, like the hippocampus, claustral place field remapping might be mediated by NMDA receptor activity, and is modulated by visual cortical inputs. (106 words)

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NeuroChaT: A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo

Cited by 7 publications

References 34 publications

Anterior Thalamic Inputs Are Required for Subiculum Spatial Coding, with Associated Consequences for Hippocampal Spatial Memory

Anterior Thalamic Inputs Are Required for Subiculum Spatial Coding, with Associated Consequences for Hippocampal Spatial Memory

neurotic: Neuroscience Tool for Interactive Characterization

Place Cells in the Claustrum Remap Under NMDA Receptor Control

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