NeuroInfoViewer: A Software Package for Analysis of Miniscope Data

Ерофеев, А. И.; Barinov, D. S.; Gerasimov, E. I.; Pchitskaya, Ekaterina; Bolsunovskaya, Marina; Власова, О. Л.; Bezprozvanny, Ilya

doi:10.1007/s11055-021-01179-y

Cited by 4 publications

(1 citation statement)

References 18 publications

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“…The choice of correlation coefficient calculation method was crucial for the accurate interpretation of the miniscope data (Figure S2 and Table 2). The less strict way is to use the signal method (Figure S2A,B), in which its correlation map is enriched with various strongly connected pairs of neurons, while the strictest method is active_acc (Figure S2G,H), in which only periods of simultaneous activity are examined [28]. Neurons were also clustered based on their correlation values, so that a pair of neurons belong to the same group if their connections are stronger than 80% of others in the network.…”

Section: Pairwise Neuronal-activity Correlation In the Neuronal Networkmentioning

confidence: 99%

NeuroActivityToolkit—Toolbox for Quantitative Analysis of Miniature Fluorescent Microscopy Data

Gerasimov,

Mitenev,

Pchitskaya

et al. 2023

J. Imaging

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The visualization of neuronal activity in vivo is an urgent task in modern neuroscience. It allows neurobiologists to obtain a large amount of information about neuronal network architecture and connections between neurons. The miniscope technique might help to determine changes that occurred in the network due to external stimuli and various conditions: processes of learning, stress, epileptic seizures and neurodegenerative diseases. Furthermore, using the miniscope method, functional changes in the early stages of such disorders could be detected. The miniscope has become a modern approach for recording hundreds to thousands of neurons simultaneously in a certain brain area of a freely behaving animal. Nevertheless, the analysis and interpretation of the large recorded data is still a nontrivial task. There are a few well-working algorithms for miniscope data preprocessing and calcium trace extraction. However, software for further high-level quantitative analysis of neuronal calcium signals is not publicly available. NeuroActivityToolkit is a toolbox that provides diverse statistical metrics calculation, reflecting the neuronal network properties such as the number of neuronal activations per minute, amount of simultaneously co-active neurons, etc. In addition, the module for analyzing neuronal pairwise correlations is implemented. Moreover, one can visualize and characterize neuronal network states and detect changes in 2D coordinates using PCA analysis. This toolbox, which is deposited in a public software repository, is accompanied by a detailed tutorial and is highly valuable for the statistical interpretation of miniscope data in a wide range of experimental tasks.

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Section: Pairwise Neuronal-activity Correlation In the Neuronal Networkmentioning

confidence: 99%