An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
Fig 4
Toolbox performance in inferring neuronal activity from calcium imaging data.
(A) Two examples with different signal-to-noise ratios (SNRs) from different neurons in the cai-1 ground-truth dataset[28,39]. For each example, we show: top, GCaMP6f ΔF/F0 traces (black) and the significant fluorescent transients detected by the module (red); bottom, ticks representing the simultaneously recorded spikes (those associated with a significant calcium event are highlighted in red; asterisks mark single spikes); middle, spiking rate of the neuron calculated by temporally convolving spikes with a Gaussian filter of σ = 20 ms. Imaging was performed at 60 Hz. A spike was considered as associated with a significant calcium event if it was followed by an event of significant fluorescence within 40 ms (GCaMP6f rise time τpeak = 45± 4 ms, for 1 spike[28]). Significant transients were calculated with default toolbox parameters in Dynamic threshold mode, with a GCaMP6f τdecay = 250 ms[28]. (B) Boxplot summary of performance for all recordings (n = 37). Top: coefficients obtained when correlating the spiking rates with the raw fluorescence traces or with the ΔF/F0 traces of significant transients (where non-significant fluctuations were set to 0). Bottom: Percentage of “detected” spikes (i.e., those associated with a significant calcium event), for all recorded spikes or for single spikes only.