This is the Linux app named ImagingAnalysis whose latest release can be downloaded as BmalLD-processed.zip. It can be run online in the free hosting provider OnWorks for workstations.
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ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0.
Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11.
- Extracts time series from individual grids (cells) and plots in various formats
- Detects peak positions and plot them as raster plots and histograms
- Displays spatial distribution of oscillatory parameters, e.g. period
- Estimates period using three independent measures (FFT/peak-peak/unwrapping)
- Extracts time-dependent phases by using dimensional embedding
- Detrends and normalizes raw time series
- Reconstruct time-lapse images using normalized oscillations
- Find clusters using spectral clustering and partial correlations
- Calculates time-dependent phase coherence by Kuramoto Synchronization Index
- Performs phase unwrapping
- Animates phase development in a clock-like format
Healthcare Industry, Science/Research, by End-User Class
This is an application that can also be fetched from https://sourceforge.net/projects/imaginganalysis/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.