Annotate many pages with project: front matter

And make related opportunistic changes along the way:

* Change imagejdocu.tudor.lu to imagejdocu.list.lu
* Change a few javadoc.imagej.net to javadoc.scijava.org
* Use the term "ImageJ2" when talking about ImageJ2 features
* Use the term "SciJava" when talking about SciJava features
* Create a new /tutorials/notebooks page for the ImageJ2 tutorial
  notebooks, and fix outstanding broken links to those notebooks.
* Clean up and vet a bunch of the /scripting/* pages.

_includes/warning/importing-classes

@@ -1,6 +1,6 @@
 To reference Java classes from {{include.lang}} you will need to import them.
 <br>
-{% include notice icon="warning" content='Unlike the original [ImageJ](/software/imagej), [ImageJ2](/software/imagej2) (and therefore [Fiji](/software/fiji)) does not automatically import any classes. Consequently, scripts written for ImageJ will not run in ImageJ2 without adding the proper imports. The rationale is that the auto-import feature is not safe. What if two classes of the same name live in two different packages? Or if a new class is introduced that makes formerly unique names ambiguous? All of a sudden, all of the scripts that reference the original class no longer work. In short: auto-imports are dangerously imprecise.' %}
+{% include notice icon="imagej2" content='Unlike the original [ImageJ](/software/imagej), [ImageJ2](/software/imagej2) (and therefore [Fiji](/software/fiji)) does not automatically import any classes. Consequently, scripts written for ImageJ will not run in ImageJ2 without adding the proper imports. The rationale is that the auto-import feature is not safe. What if two classes of the same name live in two different packages? Or if a new class is introduced that makes formerly unique names ambiguous? All of a sudden, all of the scripts that reference the original class no longer work. In short: auto-imports are dangerously imprecise.' %}
 <br>
 
 {%- comment -%}

_pages/contribute/distributing.md

@@ -345,11 +345,11 @@ Useful extensions deserve corresponding documentation explaining how to use them
 <tr>
 <td style="vertical-align: top">
 <ul><li> Request an account from an IIDP administrator.</li>
-<li> <a rel="nofollow" class="external text" href="http://imagejdocu.tudor.lu/doku.php?id=create_new_content">Create a page</a> for your extension.</li></ul>
+<li> <a rel="nofollow" class="external text" href="http://imagejdocu.list.lu/doku.php?id=create_new_content">Create a page</a> for your extension.</li></ul>
 </td>
 <td style="vertical-align: top">
-<ul><li> The <a rel="nofollow" class="external text" href="http://imagejdocu.tudor.lu/">ImageJ Information and Documentation Portal</a> predates the ImageJ wiki, and many extensions are still primarily documented there.</li>
-<li> The IIDP is a fairly <a rel="nofollow" class="external text" href="http://imagejdocu.tudor.lu/doku.php?id=start&amp;do=recent">active</a> wiki (but not <a href="https://github.com/imagej/imagej.github.io/commits/main" title="Recent changes">compared to this one</a>!).</li>
+<ul><li> The <a rel="nofollow" class="external text" href="http://imagejdocu.list.lu/">ImageJ Information and Documentation Portal</a> predates the ImageJ wiki, and many extensions are still primarily documented there.</li>
+<li> The IIDP is a fairly <a rel="nofollow" class="external text" href="http://imagejdocu.list.lu/doku.php?id=start&amp;do=recent">active</a> wiki (but not <a href="https://github.com/imagej/imagej.github.io/commits/main" title="Recent changes">compared to this one</a>!).</li>
 <li> The ImageJ developers hope to unify these two wikis in the future.</li></ul>
 </td>
 <td style="vertical-align: top">

_pages/contribute/fiji.md

@@ -1,6 +1,7 @@
 ---
 title: Contributing to Fiji
 section: Contribute
+project: /software/fiji
 nav-links: true
 nav-title: Fiji
 ---

_pages/contribute/project-ideas.md

@@ -345,4 +345,4 @@ This project requires a bit of knowledge in compiling C++ code on Linux, macOS a
 
 # Other resources
 
-There is a wish list on the [ImageJ Documentation Wiki](http://imagejdocu.tudor.lu/doku.php?id=wishlist:start&s%5b%5d=ideas).
+There is a wish list on the [ImageJ Documentation Wiki](http://imagejdocu.list.lu/doku.php?id=wishlist:start&s%5b%5d=ideas).

_pages/develop/index.md

@@ -10,7 +10,7 @@ This page provides an overview of ImageJ2 from the perspective of software devel
 
 ## Quick start
 
--   **Learn to write [scripts](/scripting)** from the [tutorial notebooks](/tutorials).
+-   **Learn to write [scripts](/scripting)** from the [tutorial notebooks](/tutorials/notebooks).
 -   **Learn to use ImageJ2 from Java** with the [tutorial Maven projects](https://github.com/imagej/tutorials/tree/master/maven-projects).
 
 ## What is ImageJ2?
@@ -152,7 +152,7 @@ See the [source code](source) page for further details.
 
 ## Tutorials
 
-Start with the [tutorial notebooks](/tutorials)!
+Start with the [ImageJ2 tutorial notebooks](/tutorials/notebooks)!
 
 {::nomarkdown}
 <table class="top striped-columns">

_pages/editing/dokuwiki-migration.md

@@ -12,7 +12,7 @@ These instructions will be updated very soon so that ImageJ Documentation Wiki p
 
 **Legacy Text Follows**
 
-The ImageJ Documentation Wiki will no longer be available at location <https://imagejdocu.tudor.lu>, as the CRP Henri Tudor has merged to become the Luxembourg Institute of Science and Technology five years ago and the old domain will be discontinued. We want to take this as an opportunity to merge the resources on <https://imagejdocu.tudor.lu> with those here at <https://imagej.net>.
+The ImageJ Documentation Wiki will no longer be available at location <https://imagejdocu.list.lu>, as the CRP Henri Tudor has merged to become the Luxembourg Institute of Science and Technology five years ago and the old domain will be discontinued. We want to take this as an opportunity to merge the resources on <https://imagejdocu.list.lu> with those here at <https://imagej.net>.
 
 This guide covers the process of migrating a page from the ImageJ Documentation Wiki ([DocuWiki](https://www.dokuwiki.org/dokuwiki)) to this ImageJ wiki ([GitHub Pages with Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/about-github-pages-and-jekyll)).
 

_pages/events/learnathon-2017.md

@@ -68,7 +68,7 @@ Details of your assignment:
 
 -   Create a [Git](/develop/git) repository.
 -   Create a [Maven](/develop/maven) project. (hints: [1](https://github.com/imagej/example-imagej-command), [2](/develop/building-a-pom))
--   Implement a `Command` plugin in your [IDE](/develop/ides), which calculates the *mean* across an image. (hints: [1](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1_-_Using_ImageJ/2_-_Introduction_to_ImageJ_Ops.ipynb), [2](https://github.com/imagej/tutorials/tree/master/maven-projects/simple-commands/src/main/java))
+-   Implement a `Command` plugin in your [IDE](/develop/ides), which calculates the *mean* across an image. (hints: [1](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb), [2](https://github.com/imagej/tutorials/tree/master/maven-projects/simple-commands/src/main/java))
 -   Push to [GitHub](/develop/github) (hints: [1](https://help.github.com/articles/pushing-to-a-remote/), [2](https://git-man-page-generator.lokaltog.net/)).
 
 If you get that far, YOU WIN. {% include person id='fjug' %} has a reward for you.
@@ -120,8 +120,8 @@ Git repos to clone:
 -   Afternoon Ops Session:
     -   [`https://github.com/imagej/tutorials`](https://github.com/imagej/tutorials)
         -   Import the `maven-projects/using-ops` into your IDE
-    -   [Introduction to ImageJ Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1_-_Using_ImageJ/2_-_Introduction_to_ImageJ_Ops.ipynb) Jupyter notebook
-    -   [Extending ImageJ: Writing Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2_-_Extending_ImageJ/4_-_Writing_Op_plugins.ipynb) Jupyter notebook
+    -   [Introduction to ImageJ Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb) Jupyter notebook
+    -   [Extending ImageJ: Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/2-Ops.ipynb) Jupyter notebook
 -   Afternoon Session on KNIME:
     -   Download & Install KNIME (app with all extensions)
         -   https://www.knime.org/downloads/overview?quicktabs_knimed=1#quicktabs-knimed

_pages/events/learnathon-2018.md

@@ -67,7 +67,7 @@ Git repos to clone:
 
 ### ImageJ2 Ops
 
--   [ImageJ Tutorial Notebooks](/tutorials)
+-   [ImageJ2 Tutorial Notebooks](/tutorials/notebooks)
 
 ### ImageJ Legacy
 
@@ -79,7 +79,7 @@ The ImageJ Legacy Course covered the topics: images, tables, regions of interest
 
 ### Jupyter Notebooks
 
--   [ImageJ Tutorials](https://github.com/imagej/tutorials)
+-   [ImageJ2 Tutorial Notebooks](/tutorials/notebooks)
 -   Installation:
     -   [Anaconda](https://conda.io/miniconda.html) (we suggest miniconda) should be installed on your system.
     -   Clone to a place of your choice: `git clone `[`https://github.com/imagej/tutorials`](https://github.com/imagej/tutorials)
@@ -111,7 +111,7 @@ The ImageJ Legacy Course covered the topics: images, tables, regions of interest
 -   Clone https://github.com/imagej/tutorials (but you already have it, right?)
 -   Import `maven-projects/create-a-new-op` in Eclipse.
 -   See also the [Adding new ops](/develop/writing-ops) guide
--   See also the "Extending ImageJ: Ops" notebook linked from [here](/tutorials)
+-   See also the "Extending ImageJ: Ops" notebook linked from [here](/tutorials/notebooks)
 
 ### ImageJ Server
 

_pages/formats/lsm.md

@@ -17,6 +17,6 @@ In Fiji, corresponding commands are:
 -   {% include bc path='File | Import | Show LSMToolbox'%} which displays the toolbox, from which all commands can be called;
 -   {% include bc path='Help | About Plugins | LSMToolbox...'%} which displays information about the plugin.
 
-For more info see [LSM ToolBox documentation on ImageJ documentation Wiki](http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start).
+For more info see [LSM ToolBox documentation on ImageJ documentation Wiki](http://imagejdocu.list.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start).
 
 

_pages/imaging/visualization.md

@@ -210,8 +210,8 @@ Here we summarize some of the 3D visualization plugins in ImageJ.
 
 ### Available Plugins for Making Figures in ImageJ
 
-1.  [Magic Montage](http://imagejdocu.tudor.lu/doku.php?id=video:utilities:creating_montages_with_magic_montage)
-2.  [FigureJ](http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start)
+1.  [Magic Montage](http://imagejdocu.list.lu/doku.php?id=video:utilities:creating_montages_with_magic_montage)
+2.  [FigureJ](http://imagejdocu.list.lu/doku.php?id=plugin:utilities:figurej:start)
 3.  [ScientiFig](https://grr.gred-clermont.fr/labmirouse/software/)
 4.  [Figure Maker](https://github.com/quantixed/imagej-macros#figure-maker)
 

_pages/imaging/watershed.md

@@ -32,7 +32,7 @@ separate ones. It is often useful on blob-like structures such as cell nuclei.
 
     {% include img src="nucleidapiconfocal" width=250 %}
 
--   Run a [Gaussian Blur filter](http://imagejdocu.tudor.lu/doku.php?id=gui:process:filters) on the image to blur out the "speckle", actually Poisson distributed, statistical "photon {% include wikipedia title='Shot noise' text='shot noise'%}", and also to smooth out the inhomogeneity of the nuclear staining. We will use a large sigma value of 3 for this task. A value of sigma too small will mean that the segmentation will be disturbed by the noise and staining pattern. Too high a sigma value, and the objects will be too blurred, making it harder to find their edges precisely and separate them later. Run menu command: Process - Filters - Gaussian Blur, with a sigma value of 3 pixels. You can preview other values to see how they look also. You should get an image that looks like this:
+-   Run a [Gaussian Blur filter](http://imagejdocu.list.lu/doku.php?id=gui:process:filters) on the image to blur out the "speckle", actually Poisson distributed, statistical "photon {% include wikipedia title='Shot noise' text='shot noise'%}", and also to smooth out the inhomogeneity of the nuclear staining. We will use a large sigma value of 3 for this task. A value of sigma too small will mean that the segmentation will be disturbed by the noise and staining pattern. Too high a sigma value, and the objects will be too blurred, making it harder to find their edges precisely and separate them later. Run menu command: Process - Filters - Gaussian Blur, with a sigma value of 3 pixels. You can preview other values to see how they look also. You should get an image that looks like this:
 
     {% include img src="nucleidapiconfocalgauss3pxsigma" width=250 %}
 

_pages/libs/imagej-ops/index.md

@@ -24,7 +24,7 @@ Ops has three major design goals:
 Start by reading these Jupyter notebooks:
 
 -   [Using ImageJ Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb) - to call ops from your scripts.
--   [Writing Op plugins](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/4-Ops.ipynb) - to write your own ops.
+-   [Extending ImageJ: Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/2-Ops.ipynb) - to write your own ops.
 
 Ops are a special type of ImageJ plugin, so a basic understanding of the [SciJava plugin framework](/develop/plugins) is strongly recommended.
 
@@ -37,7 +37,7 @@ In addition to cloning the [imagej-ops](https://github.com/imagej/imagej-ops) it
 
 -   [Step-by-step guide: Adding new ops](/develop/writing-ops)
 -   [ImageJ Tutorial: Introduction to ImageJ Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb)
--   [Extending ImageJ: Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/4-Ops.ipynb)
+-   [Extending ImageJ: Ops](https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/2-Ops.ipynb)
 -   "Scripting in ImageJ - An introduction to ImageJ Ops" (February 2017 NEUBIAS2020) – [slides](/presentations/2017-02-12-imagej-ops-neubias/#/)
 -   "ImageJ2 scripts: Parameters + ImageJ Ops" (ImageJ conference 2015) – [slides](/presentations/2015-09-04-imagej2-scripting/), [video 1](https://vimeo.com/140098817), [video 2](https://vimeo.com/140098835)
 -   "The ImageJ Ops Framework: Image processing made easy" (January 2015) – [slides](/presentations/2015-01-12-imagej-ops/)

_pages/news/2013-08-09-analyze-stripes-v2-4-1-released.md

@@ -6,6 +6,6 @@ Analyze\_Stripes\_v2.4.1 has just been released!
 
 Analyze\_Stripes is a Fiji (or ImageJ) macro designed to automatically measure the width, edge roughness, and orientation angle of stripes.
 
-Check out its [Fiji page](https://fiji.sc/Analyze_Stripes) or its [ImageJ page](http://imagejdocu.tudor.lu/doku.php?id=macro:analyze_stripes).
+Check out its [Fiji page](https://fiji.sc/Analyze_Stripes) or its [ImageJ page](http://imagejdocu.list.lu/doku.php?id=macro:analyze_stripes).
 
 

_pages/news/2013-11-04-plugins-for-making-scientific-figures.md

@@ -6,7 +6,7 @@ Writing papers and making figures is and always will be a big part of what scien
 
 Two groups have recently introduced plugins that leverage the tools available in ImageJ/Fiji to make scientific figures. Both tools are made by scientists introducing innovative concepts specifically designed to make scientific figure making easier and more controlled.
 
-[FigureJ](http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start) from *Jerome Mutterer* and [ScientiFig](http://srv-gred.u-clermont1.fr/labmirouse/software/) from *Benoit Aigouy* are well documented, open source ({% include github org='mutterer' repo='figurej' label='FigureJ' %} {% include github org='baigouy' repo='ScientiFig' label='ScientiFig' %}) and published:
+[FigureJ](http://imagejdocu.list.lu/doku.php?id=plugin:utilities:figurej:start) from *Jerome Mutterer* and [ScientiFig](http://srv-gred.u-clermont1.fr/labmirouse/software/) from *Benoit Aigouy* are well documented, open source ({% include github org='mutterer' repo='figurej' label='FigureJ' %} {% include github org='baigouy' repo='ScientiFig' label='ScientiFig' %}) and published:
 
 {% include citation doi="10.1111/jmi.12069" %}
 

_pages/news/2017-05-30-comprehensive-updates.md

@@ -8,7 +8,7 @@ Today, a lot of work on [ImageJ](/software/imagej), [Fiji](/software/fiji) and [
 
 The most exciting news is that, as [announced on the ImageJ forum](http://forum.imagej.net/t/jupyter-notebook-for-imagej/5421), there is now a {% include github org='hadim' repo='scijava-jupyter-kernel' label='SciJava Jupyter Kernel' %} enabling ImageJ to be used with [Jupyter Notebook](https://jupyter.org/) in all of the [supported scripting languages](/scripting#supported-languages).
 
-Please peruse the [ImageJ Tutorial notebooks](/tutorials) for examples of this kernel in action!
+Please peruse the [ImageJ2 tutorial notebooks](/tutorials/notebooks) for examples of this kernel in action!
 
 ## Sweeping component updates
 

_pages/people/mcib3d.md

@@ -7,4 +7,4 @@ forum: ThomasBoudier
 github: mcib3d
 ---
 
-Thomas Boudier is the developer of the [3D ImageJ Suite](http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start) plugins, and contributed to [SalsaJ](http://www.euhou.net/index.php/salsaj-software-mainmenu-9/) variant of ImageJ.
+Thomas Boudier is the developer of the [3D ImageJ Suite](http://imagejdocu.list.lu/doku.php?id=plugin:stacks:3d_ij_suite:start) plugins, and contributed to [SalsaJ](http://www.euhou.net/index.php/salsaj-software-mainmenu-9/) variant of ImageJ.

_pages/people/tferr.md

@@ -22,8 +22,8 @@ Tiago Ferreira is the author of:
 -   [ImageJ User Guide](https://imagej.nih.gov/ij/docs/guide/) ({% include github org='tferr' repo='IJ-guide' label='GitHub' %})
 -   [BAR toolbox](/plugins/bar) ({% include github org='tferr' repo='Scripts' label='GitHub' %}), including among others:
     -   [Find Peaks](/plugins/find-peaks)
-    -   [ROI Color Coder](https://imagejdocu.tudor.lu/doku.php?id=macro:roi_color_coder) †
-    -   [Distribution Plotter](https://imagejdocu.tudor.lu/doku.php?id=macro:distribution_plotter) †
+    -   [ROI Color Coder](https://imagejdocu.list.lu/doku.php?id=macro:roi_color_coder) †
+    -   [Distribution Plotter](https://imagejdocu.list.lu/doku.php?id=macro:distribution_plotter) †
     -   [ROI Manager Tools](https://imagej.nih.gov/ij/plugins/roi-manager-tools/) †
 
 You can reach him [here](mailto:tiago_dot_tferr_at_gmail_dot_com) (obviously, replacing *\_dot\_* with a de facto `.`)

_pages/plugins/3d-objects-counter.md

@@ -33,7 +33,7 @@ As ImageJ's "Analyze Particles" function, 3D-OC also has a "redirect to" option,
 
 ## Plugin's manual
 
-The plugin's manual might be downloaded from [ImageJ's wiki.](http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc.pdf)
+The plugin's manual might be downloaded from [ImageJ's wiki.](http://imagejdocu.list.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc.pdf)
 
 ## Install/Update
 

_pages/plugins/analyze-skeleton/index.md

@@ -6,7 +6,7 @@ artifact: sc.fiji:AnalyzeSkeleton_
 doi: 10.1002/jemt.20829
 ---
 
-Analysis of 2D and 3D skeleton images. For the ImageJ 1.x plugin, see [this page](http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start).
+Analysis of 2D and 3D skeleton images. For the ImageJ 1.x plugin, see [this page](http://imagejdocu.list.lu/doku.php?id=plugin:analysis:analyzeskeleton:start).
 
 {::nomarkdown}
 <table>

_pages/plugins/analyze-stripes.md

@@ -6,15 +6,15 @@ categories: [Analysis,Tutorials]
 
 ## Analyze Stripes
 
-{% include info-box software='ImageJ or Fiji' name='Analyze\_Stripes' author='Justin R. Bickford' maintainer='Justin R. Bickford' filename=' [Analyze\_Stripes\_v2.6.ijm](http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=macro:analyze_stripes_v2.6.ijm)' released='9 August 2013' latest-version='14 February 2019' status='stable' category='Analysis' website=' [Analyze\_Stripes website](http://imagejdocu.tudor.lu/doku.php?id=macro:analyze_stripes)' %}
+{% include info-box software='ImageJ or Fiji' name='Analyze\_Stripes' author='Justin R. Bickford' maintainer='Justin R. Bickford' filename=' [Analyze\_Stripes\_v2.6.ijm](http://imagejdocu.list.lu/lib/exe/fetch.php?media=macro:analyze_stripes_v2.6.ijm)' released='9 August 2013' latest-version='14 February 2019' status='stable' category='Analysis' website=' [Analyze\_Stripes website](http://imagejdocu.list.lu/doku.php?id=macro:analyze_stripes)' %}
 
 ## Purpose
 
 Analyze\_Stripes is a Fiji (or ImageJ) macro designed to automatically measure the width, edge roughness, and orientation angle of stripes or edges.
 
 ## Documentation
 
-Complete documentation may be found at the [Analyze\_Stripes website](http://imagejdocu.tudor.lu/doku.php?id=macro:analyze_stripes).
+Complete documentation may be found at the [Analyze\_Stripes website](http://imagejdocu.list.lu/doku.php?id=macro:analyze_stripes).
 
 ## News