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6 changes: 3 additions & 3 deletions _pages/Open_an_image.md
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Expand Up @@ -9,9 +9,9 @@ description: test description

The answer to this question depends on how you use ImageJ.

- Do you want the open an image using the graphical user interface? ([\#From the GUI](#From_the_GUI "wikilink"))
- Are you writing a script? ([\#From a Script](#From_a_Script "wikilink"))
- Are you using Java, to develop an ImageJ2 plug-in or do write your one program using ImgLib2 and ImageJ libraries? ([\#From Java](#From_Java "wikilink"))
- Do you want the open an image using the graphical user interface? ([\#From the GUI](#From_the_GUI))
- Are you writing a script? ([\#From a Script](#From_a_Script))
- Are you using Java, to develop an ImageJ2 plug-in or do write your one program using ImgLib2 and ImageJ libraries? ([\#From Java](#From_Java))

From the GUI
------------
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32 changes: 16 additions & 16 deletions _pages/about/governance.md
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40 changes: 20 additions & 20 deletions _pages/about/index.md
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Expand Up @@ -12,7 +12,7 @@ ImageJ is an open source Java image processing program inspired by [NIH Image](/
Flavors
-------

There are a few different flavors of ImageJ with very similar names, and some confusion is inevitable. Below is a table which should help to clarify the purpose of each. For the historical context of these projects, see [History](#History "wikilink") below.
There are a few different flavors of ImageJ with very similar names, and some confusion is inevitable. Below is a table which should help to clarify the purpose of each. For the historical context of these projects, see [History](#History) below.

<table>
<tbody>
Expand All @@ -26,33 +26,33 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="even">
<td><img src="/media/Fiji-icon.png" width="64"/></td>
<td><a href="/fiji" title="wikilink">Fiji</a></td>
<td><a href="/about/contributors" title="wikilink">Fiji contributors</a></td>
<td><a href="/fiji">Fiji</a></td>
<td><a href="/about/contributors">Fiji contributors</a></td>
<td><strong>F</strong>iji <strong>i</strong>s <strong>J</strong>ust
<strong>I</strong>mageJ, with extras. It is a distribution of ImageJ with
many plugins useful for scientific image analysis in fields such as life
sciences. It is actively maintained, with updates released
often.<br><br>We recommend Fiji as the preferred version of ImageJ.</td>
<td><a href="User:Schindelin#A_short_story_about_Fiji" title="wikilink">Dec. 2007</a></td>
<td><a href="User:Schindelin#A_short_story_about_Fiji">Dec. 2007</a></td>
<td>Active</td>
</tr>
<tr class="odd">
<td><img src="/media/Imagej2-icon.png" width="64"/></td>
<td><a href="/software/imagej2" title="wikilink">ImageJ2</a></td>
<td><a href="/about/contributors" title="wikilink">ImageJ developers</a></td>
<td><a href="/software/imagej2">ImageJ2</a></td>
<td><a href="/about/contributors">ImageJ developers</a></td>
<td>A new version of ImageJ targeting scientific multidimensional image
data. It is a complete rewrite of ImageJ, but includes <a
href="/software/imagej1" title="wikilink">ImageJ1</a> with a compatibility layer,
href="/software/imagej1">ImageJ1</a> with a compatibility layer,
so that old-style plugins and macros can run the same as always.
ImageJ2 provides several significant new features, such as an automatic
<a href="updater" title="wikilink">updater</a>, and improved <a
href="scripting" title="wikilink">scripting</a> capabilities.</td>
<a href="updater">updater</a>, and improved <a
href="scripting">scripting</a> capabilities.</td>
<td>Dec. 2009</td>
<td>Active</td>
</tr>
<tr class="even">
<td><img src="/media/Imagej1-icon.png" width="64"/></td>
<td><a href="/software/imagej1" title="wikilink">ImageJ1</a></td>
<td><a href="/software/imagej1">ImageJ1</a></td>
<td>{% include person content='Rasband' %}</td>
<td>A stable version of ImageJ which has been in development since 1997.
It has a strong, established user base, with thousands of plugins and
Expand All @@ -62,8 +62,8 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="odd">
<td><img src="/media/Imagej1-icon.png" width="64"/></td>
<td><a href="/software/imageja" title="wikilink">ImageJA</a></td>
<td><a href="/about/contributors" title="wikilink">ImageJ developers</a></td>
<td><a href="/software/imageja">ImageJA</a></td>
<td><a href="/about/contributors">ImageJ developers</a></td>
<td>ImageJA is a project that provides a clean <a href="Git">Git</a>
history of ImageJ1, with a proper 'pom.xml' file so that it can be used
with Maven without hassles.<br><br>It is what ImageJ2's legacy support
Expand All @@ -73,7 +73,7 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="even">
<td></td>
<td><a href="/software/imagejfx" title="wikilink">ImageJFX</a></td>
<td><a href="/software/imagejfx">ImageJFX</a></td>
<td>{% include person content='cmongis' %}</td>
<td>ImageJFX is a new user interface for ImageJ, built using
{% include wikipedia title='JavaFX' text='JavaFX' %}.</td>
Expand All @@ -82,7 +82,7 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="odd">
<td><img src="/media/Imagesxm-icon.png" width="64"/></td>
<td><a href="/software/imagesxm" title="wikilink">ImageSXM</a></td>
<td><a href="/software/imagesxm">ImageSXM</a></td>
<td>Steve Barrett</td>
<td>Image SXM is a version of NIH Image that has been extended to handle
the loading, display and analysis of scanning microscope images.</td>
Expand Down Expand Up @@ -124,7 +124,7 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="odd">
<td></td>
<td><a href="/software/mbf-imagej" title="wikilink">MBF ImageJ</a></td>
<td><a href="/software/mbf-imagej">MBF ImageJ</a></td>
<td>Tony Collins</td>
<td>The MBF "ImageJ for Microscopy" bundle (formerly
<a href="http://www.uhnres.utoronto.ca/facilities/wcif/imagej/">WCIF
Expand All @@ -134,16 +134,16 @@ There are a few different flavors of ImageJ with very similar names, and some co
with light microscopy image data. It was a great resource by
microscopists, for microscopists. Unfortunately, the manual went
offline in late 2012. In response, the software team at
<a href="/orgs/loci" title="wikilink">LOCI</a> created the
<a href="/cookbook" title="wikilink">Cookbook</a> user guide and
<a href="update_site" title="wikilink">update site</a>, which
<a href="/orgs/loci">LOCI</a> created the
<a href="/cookbook">Cookbook</a> user guide and
<a href="update_site">update site</a>, which
includes most of the same plugins.</td>
<td>2005</td>
<td>Defunct<br>(Last update:<br>Dec. 2009)</td>
</tr>
<tr class="even">
<td></td>
<td><a href="/software/imagejx" title="wikilink">ImageJX</a></td>
<td><a href="/software/imagejx">ImageJX</a></td>
<td>{% include person content='Harris' %}</td>
<td>ImageJX was created as a means to discuss and explore
improvements to ImageJ. There was an
Expand All @@ -160,7 +160,7 @@ There are a few different flavors of ImageJ with very similar names, and some co
</tr>
<tr class="odd">
<td><img src="/media/nih-image-logo.png"/></td>
<td><a href="/software/nih-image" title="wikilink">NIH Image</a></td>
<td><a href="/software/nih-image">NIH Image</a></td>
<td>{% include person content='Rasband' %}</td>
<td>NIH Image is a public domain image processing and analysis
program for the Macintosh. It is the direct predecessor of ImageJ,
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2 changes: 1 addition & 1 deletion _pages/cookbook/image-intensity-processing.md
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Expand Up @@ -72,7 +72,7 @@ Ratio Analysis

![](/media/Intensity ratio analysis.jpg "fig:intensity_ratio_analysis.jpg") Ratiometric imaging compares the recordings of two different signals to see if there are any similarities between them. It is done by dividing one channel by another channel to produce a third ratiometric channel. This technique is useful because it corrects for dye leakage, unequal dye loading, and photo-bleaching. An example application would be measuring intracellular ion, pH, and voltage dynamics in real time.

Background subtraction is needed before analysis of dual-channel ratio images. See also the [background correction](#Background_correction "wikilink") section. The *Ratio\_Profiler* plugin will perform ratiometric analysis of a single ROI on a dual-channel interleaved stack. The odd-slices are channel 1 images and the even slices are channel 2 images. If your two channels are opened as separate stacks, such as Zeiss, the two channels can be interleaved (mixed together by alternating between them) with the menu command {% include bc path='Plugins | Stacks - Shuffling | Stack Interleaver'%}.
Background subtraction is needed before analysis of dual-channel ratio images. See also the [background correction](#Background_correction) section. The *Ratio\_Profiler* plugin will perform ratiometric analysis of a single ROI on a dual-channel interleaved stack. The odd-slices are channel 1 images and the even slices are channel 2 images. If your two channels are opened as separate stacks, such as Zeiss, the two channels can be interleaved (mixed together by alternating between them) with the menu command {% include bc path='Plugins | Stacks - Shuffling | Stack Interleaver'%}.

The plugin will generate a green-plot of the ratio values. Ch1÷Ch2 is the default and you can get Ch2÷Ch1 if the plugin is run with the {% include key content='Alt' %} key down. It will also generate a second plot of the intensities of the individual channels, Ch1 and Ch2, as well as a results table.

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2 changes: 1 addition & 1 deletion _pages/develop/architecture.md
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Expand Up @@ -89,7 +89,7 @@ Maven component structure

All components in these organizations use [Maven](/develop/maven) for [project management](Project_Management). Each organization has its own Maven [groupId](http://books.sonatype.com/mvnref-book/reference/pom-relationships-sect-project-relationships.html#pom-relationships-sect-more-coordinates). Each component extends the {% include github org='scijava' repo='pom-scijava' label='pom-scijava' %} [parent POM](http://books.sonatype.com/mvnref-book/reference/pom-relationships-sect-project-relationships.html#pom-relationships-sect-project-inheritance), which provides sensible build defaults and compatible dependency versions (see "Bill of Materials" below).

<table><tbody><tr class="odd"><td><p><strong>Logo</strong></p></td><td><p><strong>Project</strong></p></td><td><p><strong>Organization</strong></p></td><td><p><strong>groupId</strong></p></td></tr><tr class="even"><td><p> {% include logo content='SciJava' %}</p></td><td><p><a href="SciJava" title="wikilink">SciJava</a></p></td><td><p><a href="https://github.com/scijava">scijava</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~org.scijava">org.scijava</a></p></td></tr><tr class="odd"><td><p> {% include logo content='ImageJ2' %}</p></td><td><p><a href="/about" title="wikilink">ImageJ</a></p></td><td><p><a href="https://github.com/imagej">imagej</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~net.imagej">net.imagej</a></p></td></tr><tr class="even"><td><p> {% include logo content='ImgLib2' %}</p></td><td><p><a href="/imglib2" title="wikilink">ImgLib2</a></p></td><td><p><a href="https://github.com/imglib">imglib</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~net.imglib2">net.imglib2</a></p></td></tr><tr class="odd"><td><p> {% include logo content='SCIFIO' %}</p></td><td><p><a href="/software/scifio" title="wikilink">SCIFIO</a></p></td><td><p><a href="https://github.com/scifio">scifio</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~io.scif">io.scif</a></p></td></tr><tr class="even"><td rowspan=3 style="vertical-align: middle"><p> {% include logo content='Fiji' %}</p></td><td><p><a href="/fiji" title="wikilink">Fiji</a></p></td><td><p><a href="https://github.com/fiji">fiji</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td></tr><tr class="odd"><td><p><a href="/plugins/bdv" title="wikilink">BigDataViewer</a></p></td><td><p><a href="https://github.com/bigdataviewer">bigdataviewer</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td><td></td></tr><tr class="even"><td><p><a href="/plugins/trakem2" title="wikilink">TrakEM2</a></p></td><td><p><a href="https://github.com/trakem2">trakem2</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td><td></td></tr></tbody></table>
<table><tbody><tr class="odd"><td><p><strong>Logo</strong></p></td><td><p><strong>Project</strong></p></td><td><p><strong>Organization</strong></p></td><td><p><strong>groupId</strong></p></td></tr><tr class="even"><td><p> {% include logo content='SciJava' %}</p></td><td><p><a href="SciJava">SciJava</a></p></td><td><p><a href="https://github.com/scijava">scijava</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~org.scijava">org.scijava</a></p></td></tr><tr class="odd"><td><p> {% include logo content='ImageJ2' %}</p></td><td><p><a href="/about">ImageJ</a></p></td><td><p><a href="https://github.com/imagej">imagej</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~net.imagej">net.imagej</a></p></td></tr><tr class="even"><td><p> {% include logo content='ImgLib2' %}</p></td><td><p><a href="/imglib2">ImgLib2</a></p></td><td><p><a href="https://github.com/imglib">imglib</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~net.imglib2">net.imglib2</a></p></td></tr><tr class="odd"><td><p> {% include logo content='SCIFIO' %}</p></td><td><p><a href="/software/scifio">SCIFIO</a></p></td><td><p><a href="https://github.com/scifio">scifio</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~io.scif">io.scif</a></p></td></tr><tr class="even"><td rowspan=3 style="vertical-align: middle"><p> {% include logo content='Fiji' %}</p></td><td><p><a href="/fiji">Fiji</a></p></td><td><p><a href="https://github.com/fiji">fiji</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td></tr><tr class="odd"><td><p><a href="/plugins/bdv">BigDataViewer</a></p></td><td><p><a href="https://github.com/bigdataviewer">bigdataviewer</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td><td></td></tr><tr class="even"><td><p><a href="/plugins/trakem2">TrakEM2</a></p></td><td><p><a href="https://github.com/trakem2">trakem2</a></p></td><td><p><a href="https://maven.scijava.org/index.html#nexus-search;gav~sc.fiji">sc.fiji</a></p></td><td></td></tr></tbody></table>

Bill of Materials
-----------------
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2 changes: 1 addition & 1 deletion _pages/develop/cpp-tips.md
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Expand Up @@ -33,7 +33,7 @@ Java's generics are implemented using erasure, which means that generics help ca

The upside of this limitation is that you will never get as cryptic multi-page long error messages as with C++.

A downside is that the Java compiler just cannot optimize generics as much as C++ can do with templates, also due to the fact that Java does not recompile the base classes of the generics -- in contrast to what C++ does with templates. However, due to the [compile time](#Compile_time "wikilink") being fuzzy, Java can optimize a lot in the Just-In-Time compiler, especially when you use the *final* keyword wisely; a method marked as final cannot be overridden in subclasses, and is therefore a prime candidate for Just-In-Time optimization.
A downside is that the Java compiler just cannot optimize generics as much as C++ can do with templates, also due to the fact that Java does not recompile the base classes of the generics -- in contrast to what C++ does with templates. However, due to the [compile time](#Compile_time) being fuzzy, Java can optimize a lot in the Just-In-Time compiler, especially when you use the *final* keyword wisely; a method marked as final cannot be overridden in subclasses, and is therefore a prime candidate for Just-In-Time optimization.

Java has no pointers
--------------------
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