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Initial site content.
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‎.gitignore‎

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_site
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.sass-cache
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.jekyll-metadata
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/.idea/
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*.iml
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*.lock

‎404.html‎

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---
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layout: default
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---
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<style type="text/css" media="screen">
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.container {
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margin: 10px auto;
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max-width: 600px;
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text-align: center;
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}
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h1 {
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margin: 30px 0;
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font-size: 4em;
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line-height: 1;
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letter-spacing: -1px;
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}
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</style>
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<div class="container">
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<h1>404</h1>
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<p><strong>Page not found :(</strong></p>
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<p>The requested page could not be found.</p>
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</div>

‎Gemfile‎

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source "https://rubygems.org"
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# Hello! This is where you manage which Jekyll version is used to run.
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# When you want to use a different version, change it below, save the
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# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
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#
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# bundle exec jekyll serve
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#
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# This will help ensure the proper Jekyll version is running.
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# Happy Jekylling!
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gem "jekyll", "~> 3.8.5"
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# This is the default theme for new Jekyll sites. You may change this to anything you like.
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gem "minima", "~> 2.0"
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# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
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# uncomment the line below. To upgrade, run `bundle update github-pages`.
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# gem "github-pages", group: :jekyll_plugins
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# If you have any plugins, put them here!
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.6"
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end
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# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
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gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
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# Performance-booster for watching directories on Windows
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gem "wdm", "~> 0.1.0" if Gem.win_platform?
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‎_config.yml‎

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# Welcome to Jekyll!
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#
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# This config file is meant for settings that affect your whole blog, values
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# which you are expected to set up once and rarely edit after that. If you find
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# yourself editing this file very often, consider using Jekyll's data files
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# feature for the data you need to update frequently.
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#
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# For technical reasons, this file is *NOT* reloaded automatically when you use
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# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
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# Site settings
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# These are used to personalize your new site. If you look in the HTML files,
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# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
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# You can create any custom variable you would like, and they will be accessible
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# in the templates via {{ site.myvariable }}.
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title: IJ-Plugins Project
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email: jpsacha@gmail.com
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description: >- # this means to ignore newlines until "baseurl:"
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The ImageJ Plugins project is a source of custom plugins for the ImageJ software package.
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baseurl: "" # the subpath of your site, e.g. /blog
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url: "" # the base hostname & protocol for your site, e.g. http://example.com
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github_username: ij-plugins
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# Build settings
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markdown: kramdown
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theme: minima
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plugins:
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- jekyll-feed
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# Exclude from processing.
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# The following items will not be processed, by default. Create a custom list
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# to override the default setting.
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# exclude:
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# - Gemfile
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# - Gemfile.lock
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# - node_modules
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# - vendor/bundle/
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# - vendor/cache/
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# - vendor/gems/
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# - vendor/ruby/

‎_posts/2019-01-03-welcome-to-new-ij-plugins-site.md‎

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---
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layout: post
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title: "Welcome to new IJ-Plugins Site!"
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date: 2019-03-01 17:00:00 -0500
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categories: update
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---
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The new IJ-Plugins site is staring its operation.
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The IJ-Plugins project started in January of 2002 with mission of hosting plugins for [ImageJ][imagej]. It was originally hosted at [Source Forge](https://ij-plugins.sourceforge.net/).
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Source code for several projects ([ijp-toolkit](https://github.com/ij-plugins), [ijp-imageio](https://github.com/ij-plugins/ijp-imageio), [ijp-scala-console](https://github.com/ij-plugins/ijp-scala-console)) moved to GitHub some time ago. Some new projects ([ijp-color](https://github.com/ij-plugins/ijp-color), [ijp-DeBayer2SX](https://github.com/ij-plugins/ijp-DeBayer2SX)) were added on GitHub.
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After a long wait [the original website](https://ij-plugins.sourceforge.net/) is moving piece-by-piece to [this new location](http://ij-plugins.github.io/). It should be getting more regular updates here. Stay posted.
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[imagej]: https://imagej.nih.gov/ij/

‎about.md‎

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---
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layout: page
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title: About
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permalink: /about/
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---
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The ImageJ Plugins project is a source of custom plugins for the [ImageJ][imagej] software package. [ImageJ][imagej] is a public domain image processing and analysis program developed in Java.
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[imagej]: https://imagej.nih.gov/ij/

‎index.md‎

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---
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# Feel free to add content and custom Front Matter to this file.
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# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults
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layout: home
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---
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## News
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* Mar 1, 2019 - the IJ-Plugins website started its transition from the [old location](https://ij-plugins.sourceforge.net/) to here
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## ImageJ Plugin Bundles and Libraries
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* **[ij-Plugins Toolkit](https://github.com/ij-plugins)** - Set of ImageJ plugins and library for: reading and writing of 3D images, morphological operations on 3D images, color space conversion, color edge detection, various anisotropic diffusion filters, fast median filters, image quilting, image segmentation through clustering and region growing, and more.
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* **[ijp-color](https://github.com/ij-plugins/ijp-color)** - Operations on color spaces and color images, color conversion, and color calibration.
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* **[ijp-DeBayer2SX](https://github.com/ij-plugins/ijp-DeBayer2SX)** - Bayer-pattern image to color image converters.
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* **[ijp-scala-console](https://github.com/ij-plugins/ijp-scala-console)** - edit and run Scala scripts from ImageJ, have full access to ImageJ API and API's of all installed plugins.
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* **[ijp-imageio](https://github.com/ij-plugins/ijp-imageio)** - adds support for additional image file formats and sub-formats: BMP, FlashPIX, GIF, JPEG, PNG, PNM, and TIFF. Improves mapping of sample sizes, e.g., a 16 bit PNG or compressed TIFF images are read into ImageJ's ShortProcessor (16 bits per pixel). Enables reading and writing of 1 bit, 8 bit, 16 bit, 32 bit, tiled, compressed, and multi-page TIFF images. The I/O operations are performed using JAI codec.
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## Past Projects
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For details see [the old website](https://ij-plugins.sourceforge.net/).
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### ImageJ Plugin Bundles and Libraries
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* **ij-DCRaw** - open in ImageJ raw images from digital cameras with a help of DCRaw tool. Control how raw or how processed the opened image is.
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* **ij-VTK** - The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization written in C++ with bindings for Tcl/Tk, Java, Python, and .NET. ij-VTK provides plugins for running VTK image processing filters from ImageJ and helper classes for using VTK in Java applications.
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* **MRIAnalysisPak** - is a plugin collection for ImageJ for the analysis of MRI and fMRI data. This package is maintained by members of the Center for Comparative Neuroimaging (CCNI) at the University of Massachusetts Medical School and The Small Animal MRI Laboratory at Harvard Medical School/Brigham & Women's Hospital. The MRIAnalysisPak can be downloaded here.
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### VTK Examples for Java
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* **VTK-Examples** - Port of Tcl and Python VTK examples to Java.

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