Matlab code for example for five-step wavelet analysis (GaMoSEC) of rhythmic dynamics, example from Yeast time series

CODE:  Herein, the time series data were consecutively analyzed by the five types of transformations, coined GaMoSEC, an acronym describing the methodology used (i.e., Gaussian, Morlet, Synchrosqueezing, Empirical Wavelet Decomposition, and Wavelet Coherence).  

EWT was made available thanks to Jerome Gilless. refer to - J.Gilles, "Empirical wavelet transform" to appear in IEEE Trans. Signal Processing, Vol.61, No.16, 3999--4010, 2013. - J.Gilles, G.Tran, S.Osher "2D Empirical transforms. Wavelets, Ridgelets and Curvelets Revisited", SIAM Journal on Imaging Sciences, Vol.7, No.1, 157--186, 2014. - J.Gilles, K. Heal, "A parameterless scale-space approach to find meaningful modes in histograms - Application to image and spectrum segmentation", International Journal of Wavelets, Multiresolution and Information Processing, Vol.12, No.6, 1450044-1--1450044-17, 2014.

TIME SERIES: An autonomously oscillating culture of S. cerevisiae under constant environmental conditions (temperature, illumination, pH) was monitored by membrane-inlet mass spectrometry. Data were collected every 12 s at m/z = 32, 34, 40 and 44 corresponding to oxygen, H2S, argon and carbon dioxide. Argon m/z = 40 was used to correct for long-term drift in the instrument's response.

Spontaneous, synchronized oscillations in a contiguous layer of S. cerevisiae cells loaded with 2 µM MitoSox (Invitrogen-Molecular Probes, Eugene, OR) incubated at 30°C with aeration of the perfusion buffer, were monitored by two-photon scanning laser microscopy. Yeasts were attached to a coverslip which had been coated with poly-L-lysine with unrestricted access to atmospheric oxygen on the stage of a Nikon E600FN upright microscope which was maintained at 30°C.

Analysis was presented in Kembro et al (2023) A dynamically coherent pattern of rhythms that matches

between distant species across the evolutionary scale. Sci Rep.

https://doi.org/10.1038/s41598-023-32286-0