Find Fluopeaks, ImageJ/Fiji tool for automatic detection of fluorescence Ca2+ transients within x-y-t confocal image stacks.

Automated analysis of intracellular Ca2+ transients. This ImageJ macro has been developed for the automatic detection of Ca2+ transients within x-y-t confocal image stacks (design reference formats *.lif and *.tif, other formats possibly also compatible) making use of the peak finding plugin tool by Tiago Ferreira (http://fiji.sc/Find_Peaks) included in the BAR collection by the same author (https://imagej.net/BAR). Temporal Ca2+ transients are evaluated within a user-defined region of interest (using ImageJ selection tools). Fluorescence (F) signals are reported as a ratio (ΔF/F0 %) of the change in fluorescence (ΔF = F-F0) relative to the baseline (F0). F0 is automatically estimated on the base of the amplitude frequency distribution sampled over a user-selectable number of bins of the fluorescence signal, and hence calculated as the average value (or, optionally, the maximum value) of those signal contributes which are characterized by both high occurence and low amplitude value. The algorithm is designed to detect the Ca2+ spikes in the time frame between 50 and 250 seconds, which can be modified by the user. Peaks with amplitude lower than standard deviation of (F-F0)/F0*100 (optionally, 2*basal signal standard deviation) or value lower than 2*standard deviation of F0 (condition optionally not considered) are discarded as noise.