ImagingAnalysis Home

ImagingAnalysis is a Mathematica packages that performs grid-based analysis of time-lapse images.
This is the final release verion (2017/05/14) of the package under this name. Previous inconsistency errors (caused by legacy commands) are resolved in this release. A more comprehensive package that includes new commands will be released under a different name.

Installation
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. Use the accompanying datasets (raw images and preprocessed images).

Import Data Format
Image sequence: either 8-bit or 16-bit TIFF.
The raw images should be preprocessed and made compact through grid transformation (see Preprocessing). The ImageJ macro that performs the transformation is released with this package (see Downloads under Preprocessing_ImageJ).

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. (Released on 2012/08/01)
ImagingAnalysisFN.m ... For use with image sequences created by LV200 or FN1-R2. (Unreleased)
PMTAnalysis.m ... For use with photometry data created by Hamamatsu 24-channel. (Unreleased)

There are two updated versions of ImagingAnalysis.m:
ImagingAnalysis.wl ... For Mathematica 11. (Released on 2017/05/14)
ImagingAnalysis.m ... For use with image sequences created by LV200 and FN1-R2. (Released on 2017/05/14)

Mathematica versions
Release 2017/05/14:
The debugging has been done on Mathematica 11.0.

Release 2012/08/01:
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 full release of the software, along with sample data, has been made on 2012/8/1 following the publication of the paper on which this software is based:

Jihwan Myung, Sungho Hong, Fumiyuki Hatanaka, Yoshihiro Nakajima, Erik De Schutter, and Toru Takumi (2012). Period Coding of Bmal1 Oscillators in the Suprachiasmatic Nucleus. Journal of Neuroscience. 32: 8900-8918; doi: 10.1523/​JNEUROSCI.5586-11.2012

The same software, or an internal unreleased update of it, was used for the following paper:

Jihwan Myung, Sungho Hong, Daniel DeWoskin, Erik De Schutter, Daniel B Forger, Toru Takumi (2015). GABA-mediated repulsive coupling between circadian clock neurons in the SCN encodes seasonal time. Proceedings of the National Academy of Sciences. 112: E3920-E3929; doi: 10.1073/pnas.1421200112

Credits
The ImagingAnalysis and its variants are created and maintained by Jihwan Myung (OIST). Jihwan Myung is currently a fellow at Berliner Antike-Kolleg in Berlin.
The Partial Correlation and Spectral Clustering functions are created by Sungho Hong (OIST).
The HPFilter function is created by Johannes Ludsteck.

License
The software is distributed for academic use.

Last updated on 2017/05/14 by JM
Previous update on 2012/08/01 by JM
Created on 2011/08/30 by Jihwan Myung