Determining the optimal expression method for dual-color imaging

Norman, Jacob F.; Rahsepar, Bahar; Noueihed, Jad; White, John A.

doi:10.1016/j.jneumeth.2020.109064

Cited by 1 publication

(3 citation statements)

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“…To investigate the application of each DR technique to in vivo recordings, we also consider calcium imaging data recorded from 36 awake mice. Briefly, recordings in layer 2/3 of murine S1 [57] were collected during the awake, resting state [8]. Traces representing calcium transients were extracted from the recordings and processed using standard techniques [57].…”

Section: Awake-state Datamentioning

confidence: 99%

“…For example, calcium imaging allows simultaneous recording from hundreds of neurons in a single brain region in vivo, while maintaining single cell-resolution 3,4 . Other tools allow cell "tagging" based on factors, including activity during a specified time window and molecular genotype [5][6][7][8] .…”

Section: Introductionmentioning

confidence: 99%

“…For example, calcium imaging allows simultaneous recording from hundreds of neurons in a single brain region in vivo , while maintaining single cell-resolution [3,4]. Other tools allow cell “tagging” based on factors, including activity during a specified time window and molecular genotype [5–8]. The resultant data set consists of several hundred time series thousands of points long, multiplicatively increasing per experimental condition added, in addition to any tagging data.…”

Section: Introductionmentioning

confidence: 99%

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Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings

Carbonero,

Noueihed,

Kramer

et al. 2023

Preprint

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Calcium imaging allows recording from hundreds of neurons in vivo with the ability to resolve single cell activity. Evaluating and analyzing neuronal responses, while also considering all dimensions of the data set to make specific conclusions, is extremely difficult. Often, descriptive statistics are used to analyze these forms of data. These analyses, however, remove variance by averaging the responses of single neurons across recording sessions, or across combinations of neurons to create single quantitative metrics, losing the temporal dynamics of neuronal activity, and their responses relative to each other. Dimensionally Reduction (DR) methods serve as a good foundation for these analyses because they reduce the dimensions of the data into components, while still maintaining the variance. Non-negative Matrix Factorization (NMF) is an especially promising DR analysis method for calcium imaging because of its mathematical constraints, which include positivity and linearity. We adapt NMF for our analyses and compare its performance to alternative dimensionality reduction methods on both artificial and in vivo data. We find that NMF is well-suited for analyzing calcium imaging recordings, accurately capturing the underlying dynamics of the data, and outperforming alternative methods in common use.

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Section: Awake-state Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings

Carbonero,

Noueihed,

Kramer

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Determining the optimal expression method for dual-color imaging

Cited by 1 publication

References 58 publications

Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings

Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings

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