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.

Features

  • 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

Project Samples

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License

Academic Free License (AFL)

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ImagingAnalysis Web Site

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Additional Project Details

Languages

English

Intended Audience

Healthcare Industry, Science/Research, by End-User Class

User Interface

Other toolkit

Programming Language

Mathematica

Related Categories

Mathematica Bio-Informatics Software, Mathematica Data Visualization Software, Mathematica Medical Physics Software

Registered

2011-08-30