Fig. 3: CITE-On online cell detection performance. | Nature Communications

Fig. 3: CITE-On online cell detection performance.

From: A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging

Fig. 3

a Best parameter search for frame downsampling: F-1 score (pseudocolor) as a function of score threshold (vertical axis) and number of frames in the sliding average (horizontal axis) for LIV (left), CA1 jRCaMP1a (middle), and CA1 GCaMP6f (right). The maximal F-1 is indicated with the black rectangle. b Fluorescence median projections of one representative FOV for CA1 jRCaMP1a (left) and one FOV for CA1 GCaMP6f (middle). GT (magenta) and online detections at the end of the t-series (Det, green) are also shown. In the rightmost panel, the online detections of jRCaMP1a (cyan) and GCaMP6f (magenta) at the end of the t-series are shown. c Same as in b but for a representative LIV t-series. d Top: boxplots showing online performance as Precision (gray), Recall (white), and F-1 (black) for all t-series in the validation datasets (LIV, N = 13; CA1 jRCaMP1a, N = 12; CA1 GCaMP6f, N = 12). No motion correction was performed. Bottom: same as top, but for the motion-corrected t-series. The orange line in all boxplots (in top and bottom panels) is the median, the bounds of the boxes are the 75th and 25th percentiles (i.e., the interquartile range (IQR)), and the whiskers correspond to the highest value or lowest value of the distribution. If the lowest or highest values are outliers (i.e., >1.5 *IQR from the bounds of the boxes), the whiskers correspond to 1.5 *IQR. Outliers are represented as black diamonds. Results of Kolmogorov–Smirnov test for performance in not motion-corrected t-series vs. motion-corrected t-series from LIV: p = 0.54 for F-1, p = 0.15 for Precision, p = 0.38 for Recall, N = 13 t-series. Results of two-sided Kolmogorov–Smirnov test for performance in not motion-corrected t-series vs. motion-corrected t-series from CA1 jRCaMP1a: p = 0.16 for F-1, p = 0.20 for Precision, p = 0.20 for Recall, N = 12 t-series. Results of Kolmogorov–Smirnov test for performance in not motion corrected vs. motion-corrected t-series from CA1 GCaMP6f: p = 0.18 for F-1, p = 0.28 for Precision, p = 0.22 for Recall, N = 12 t-series. e F-1 values as a function of the fraction of the total length of the t-series for not-motion corrected data (N = 13 t-series for LIV, N = 24 t-series for CA1, including N = 12 t-series for CA1 jRCaMP1a and N = 12 t-series for CA1 GCaMP6f t-series).

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