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Background  Repeated oscillations in intracellular calcium (Ca 2+ ) concentration, known as Ca 2+  spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca 2+  spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools.    Results  As a contribution, we have developed automated Ca 2+  spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern.  We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in  Medicago truncatula  root epidermal cells by exudates of the AM fungus  Gigaspora margarita  as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca 2+  signature.    Conclusions  We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca 2+  spiking.

Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses