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. 2021 Feb 1;2(1):100306. doi: 10.1016/j.xpro.2021.100306

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© 2021 The Author(s)

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Analysis of time series calcium traces

(A) Depiction of raw fluorescence traces for 5 focal planes for the ROI, the annular background region, and the background-subtracted fluorescence (arbitrary units). X axis reports the datapoint number in the trace. Red indicates the focal plane defined as the “best” focal plane for this ROI.

(B) Calculation of ΔF/F values for the best focal plane defined as (F − F₀)/F₀. F₀ is calculated by smoothing the background-subtracted fluorescence and then taking a running minimum.

(C) Preparation of the ΔF/F trace for peak detection. The ΔF/F trace is heavily smoothed to find the red shape of the trace. The difference between the ΔF/F and the smoothed trace reveals transients without any baseline shift. A two-cycle thresholding that considers the mean and standard deviation of the 5^th through 95^th percentile of datapoints reveals the signal component (red) above the noise. Peak detection algorithms can then proceed using this threshold.