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Home modified by Jihwan Myung

Jihwan Myung — Sun, 14 May 2017 19:40:45 -0000

--- v14
+++ v15
@@ -1,4 +1,5 @@
 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).
@@ -16,23 +17,35 @@

 Versions
 There are three major variations of this package:
-ImagingAnalysis.m ... For use with image sequences created by LV200. (Released on 2012/8/1)
+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
+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 by Jihwan Myung (Hiroshima Univ.).
+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.

@@ -41,5 +54,6 @@
 The software is distributed for academic use.

-Last updated on 2012/8/1 by JM
-Created on 2011/8/30 by Jihwan Myung
+Last updated on 2017/05/14 by JM
+Previous update on 2012/08/01 by JM
+Created on 2011/08/30 by Jihwan Myung

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Wed, 01 Aug 2012 19:32:32 -0000

--- v13
+++ v14
@@ -41,5 +41,5 @@
 The software is distributed for academic use.
 
 
-Last updated on 2012/8/1 by Jihwan Myung
+Last updated on 2012/8/1 by JM
 Created on 2011/8/30 by Jihwan Myung

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Wed, 01 Aug 2012 19:30:33 -0000

--- v12
+++ v13
@@ -1,7 +1,7 @@
 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).
+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
@@ -16,9 +16,9 @@
 
 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.
+ImagingAnalysis.m ... For use with image sequences created by LV200. (Released on 2012/8/1)
+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)
 
 
 Mathematica versions
@@ -26,7 +26,9 @@
 
 
 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.
+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
 
 
 Credits
@@ -39,4 +41,5 @@
 The software is distributed for academic use.
 
 
-Last updated on 2011/8/30 by Jihwan Myung
+Last updated on 2012/8/1 by Jihwan Myung
+Created on 2011/8/30 by Jihwan Myung

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:33:05 -0000

--- v11 
+++ v12 
@@ -6,7 +6,7 @@
 
 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 publication). The ImageJ macro that performs the transformation is released with this package (see Downloads).
+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

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:26:33 -0000

--- v10 
+++ v11 
@@ -36,7 +36,7 @@
 
 
 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.
+The software is distributed for academic use.
 
 
 Last updated on 2011/8/30 by Jihwan Myung

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:26:03 -0000

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:25:01 -0000

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:24:02 -0000

--- v7 
+++ v8 
@@ -6,6 +6,7 @@
 
 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 publication). The ImageJ macro that performs the transformation is released with this package (see Downloads).
 
 
 Export Data Formats

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:20:42 -0000

--- v6 
+++ v7 
@@ -1,47 +1,40 @@
-ImagingAnalysis is a Mathematica packages that performs grid-based analysis of time-lapse images. 
-
-Installation
-
+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
-
+Import Data Format
 Image sequence: either 8-bit or 16-bit TIFF.
 
 
-Export Data Formats
-
+Export Data Formats
 Analyzed Data: Tab-separated variables (TSV) text file
 Processed Images: 8-bit TIFF
 
 
-Versions
-
+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
-
+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
-
+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.
+Credits
+The ImagingAnalysis and its variants are created by Jihwan Myung (Hiroshima Univ.).
+The Partial Correlation and Spectral Clustering functions are created by Sungho Hong (OIST).
 The HPFilter function is created by Johannes Ludsteck.
 
 
-License
-
+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.

WikiPage Home modified by Jihwan Myung

Jihwan Myung — Tue, 30 Aug 2011 06:18:38 -0000

--- v5 
+++ v6 
@@ -1,3 +1,48 @@
-ImagingAnalysis is a Mathematica packages that performs grid-based analysis of time-lapse images. 
-
+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