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Installation
Download the latest version and unzip.
In the ImageJ directory..
Fiji is a distribution of the popular Open Source software ImageJ focused on biological image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image processing algorithms. 目次 目次 ImageJ について Fiji について Fiji のインストール Windows へのインストールについて Mac へのインストールについて Linux へのインストールについて 論文への引用 ImageJについての書籍やリンク ImageJ について ImageJとは、Java というプログラミング言. ImageJ and Fiji 13 13.1 The ImageJ Universe – 188 13.2 Fiji – 188 13.3 Plugins – 190. All of the source code for Fiji can be downloaded. Installation of Fiji is straightforward because it has been configured as a. Updated Java Archive files (.jar files) and offer to download and install them for the user. Figure 13.1b shows an exam. BaSiC is a retrospective image correction method for optical microscopy, available as a Fiji/ImageJ Plugin. It is based on low rank and sparse decomposition, which corrects both shading (uneven illumination) in space and background bleaching in time. Download.mp4 (169.33 MB). Divisions are readily identifiable by the condensation and increase in brightness of chromatin as the metaphase plate appears, followed.
- Put the OSOV folder in the plugins directory (e.g. c:ImageJpluginsOSOV)
- Put the OSOV Toolbox.ijm in the macros/toolsets folder (e.g. c:ImageJmacrostoolsetsOSOV Toolbox.ijm)
- Restart ImageJ
On Mac systems the easiest way to get to the ImageJ application folder is to go to Applications in Finder (usually accessible from the Favorites list on the left panel) and right-click the Image J app (e.g. 'Fiji.app') and click 'Show Package Contents'.
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Once installed you can access the macros and plugins from the toolsets menu or the normal plugin menu (under 'OSOV'). To add the toolset to the toolbar use the More Tools icon (>>) at the far right of the toolbar (See the ImageJ User Guide - Custom Tools for more information) and select 'OSOV Toolbox'.
Problems
- If you're getting any sort of 'Not Found' errors when trying to run commands, or if the Plugin > OSOV menu doesn't list a number of items then you may have issue with the version of ImageJ. This version of ImageJ from https://imagej.net/Fiji/Downloads#Life-Line_Fiji_versions will work:
Credits
All plugins developed by OpenSourceOV except for the Stack Contrast Adjustment plugin developed by Jan Michalek, Martin Capek, Jiri Janacek.
Detailed tutorial
Detailed description and tutorial can be find here (might be lengthy...)
Updates
#2015/02/07: Updated to use the latest javacv version 0.10
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#2014/07/23: Updated to match more recent javacv/opencv library files (support win32, win64, mac64, linux32, linux64 now)
#2012/12/17: Fixed a bug causing the wrong magnitude in the Cross-correlation version.
#2012/11/16: Added macro script examples for analyzing stacks with more than 2 slices.
#2012/09/03: Fixed a bug when no correlation peak was found at first round. (Which will cause the error: java.lang.ArrayIndexOutOfBoundsException: -61938....)
#2011/11/18: Force the output number format to override the system locale setting to avoid the error interpretation of comma for different locale (ex: French / US).
#2011/7/24: Fixed a bug related to the subpixel interpolation.
#2011/7/13: Fixed a bug caused by the completely blank image region.
#2011/5/30: Fixed the memory leak issue cause by the OpenCV interface.
Troubleshooting
#Q:The plugin launched correctly, but after entering the parameters in the dialog window I got a error message saying 'java.lang.ArrayIndexOutOfBoundsException: .......... at ij.process.FloatProcessor.getf(FloatProcessor.java:271)...' A: Are you using an old version of ImageJ ? Try to update it to at least version 1.44 or later.
#Q:I would like to use this PIV plugin to analyze stacks with more than 2 slices, is it possible ?
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The plugin itself only handle 2 slices at this moment. But since multiple slice analysis is a repetitive task, it can be easily done by using a macro script which automatically split the whole stack pair-wise (1-2, 2-3, 3-4...) and do the PIV. You can find the example macro script here.#Q:How to plot the results obtained from above multi-slice PIV macro ?
A: Please check this macro script example for batch ploting PIV result macro Here is
References
1. Tseng, Q. et al. Spatial Organization of the Extracellular Matrix Regulates Cell–cell Junction Positioning. PNAS (2012).doi:10.1073/pnas.11063771092. Tseng, Qingzong. 2011. “Study of multicellular architecture with controlled microenvironment”. Ph.D. dissertation, Université de Grenoble. http://tel.archives-ouvertes.fr/tel-00622264.
Credit
This plugin is largely inspired by the JPIV from Peter Vennemann. For the vector interpolation between each PIV iteration, I used the library from the Open Source Physics.
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Thanks to Samual Audit and his javacv library which allows me to use the very powerful OpenCV library from java.
If you find this plugin useful or have questions or comment, feel free to contact me (qztseng at gmail dot com). Or through my Linkedin tw.linkedin.com/pub/qingzong-tseng/58/807/b41/