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ImagingAnalysis is a Mathematica packages that performs grid-based analysis of time-lapse images.

Installation

Put ImagingAnalysis.m in the Applications folder in the Mathematica library (Mac OSX) or put it in any equivalent directory (Linux/Windows).

Import Data Format

Image sequence: either 8-bit or 16-bit TIFF.

Export Data Formats

Analyzed Data: Tab-separated variables (TSV) text file
Processed Images: 8-bit TIFF

Versions

There are three major variations of this package:
ImagingAnalysis.m ... For use with image sequences created by LV200.
ImagingAnalysisFN.m ... For use with image sequences created by LV200 or FN1-R2.
PMTAnalysis.m ... For use with photometry data created by Hamamatsu 24-channel.

Mathematica versions

Recommended Mathematica versions are 7.0 and above. ImagingAnalysis was originally developed on Mathematica 6.0 and most of the codes should run under 6.0 without problems. However, subsequent developments have been performed on Mathematica 7.0 and 8.0 and some 7.0-specific functions may have been used.

Release

This software has been used for analyzing bioluminescence images from cultured suprachiasmatic nucleus tissue explants. The release date of the software, along with sample data, will be announced after a related paper is accepted for publication.

Credits

The ImagingAnalysis and its variants are created by Jihwan Myung.
The Partial Correlation and Spectral Clustering functions are created by Sungho Hong.
The HPFilter function is created by Johannes Ludsteck.

License

The software is distributed for academic use. Although the author is currently affiliated with Hiroshima University, Japan, this software was not financially supported during the development by any organization.

Last updated on 2011/8/30 by Jihwan Myung