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Grid-based, Automated Analysis of Bioluminescence Time-lapse Images

Jihwan Myung
Organization: Okinawa Institute of Science and Technology (OIST)
Department: Computational Neuroscience Unit
Revision date


ImagingAnalysis is a Mathematica packages that performs grid-based analysis of time-lapse images. The package creates time series from individual cell-sized grids and extracts unwrapped phases that can be directly adapted to Kuramoto-type modelling. It also estimates periods based on three independent measures: Fast Fourier Transform, slopes of the unwrapped phase, and peak-to-peak intervals. It detects peak positions and plot them as raster plots and histograms. It also plots spatial distribution of oscillatory parameters, e.g. period. The package detrends the time series using the Hodrick-Prescott filter and normalizes the detrended time series by dimensional embedding or envelope curve estimation. It finds clusters using spectral clustering and partial correlations. It calculates time-dependent phase coherence by Kuramoto Synchronization Index. It produces animations for the phase development in a clock-like format.

Put ImagingAnalysis.m in the Applications folder in the Mathematica library (Mac OSX) or put it in any equivalent directory (Linux/Windows). See the Mathematica notebook SampleAnalysisNoteBook.nb as an example of how the package is used. Sample dataset (BmalLD-processed.zip) is available at: https://sourceforge.net/projects/imaginganalysis/files/Sample%20Imaging%20Dataset/

*Wolfram Technology > Image Processing

SCN, Imaging analysis, Time series analysis, Circadian clock
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ImagingAnalysis.m (179.4 KB) - Mathematica Package
SampleAnalysisNoteBook_NoOutput.nb (85.7 KB) - Mathematica Notebook