Update documentation

CONTRIBUTING.md

@@ -2,14 +2,14 @@
 
 ## Prerequisites
 * Familiarize yourself with GitHub
-* [Java 8]() (newer version is fine, but the project still uses 1.8 bytecode)
-* [Maven](https://imagej.net/Maven)
-* [Git](https://imagej.net/Git)
+* [Java 8](https://openjdk.java.net/) (newer version is fine, but the project still uses 1.8 bytecode)
+* [Maven](https://imagej.github.io/develop/maven)
+* [GitHub](https://imagej.github.io/develop/github) and Git
 * Preferrably an IDE such as [Eclipse](https://www.eclipse.org), [IntelliJ](https://www.jetbrains.com/idea/) or [NetBeans](https://netbeans.org)
   * Eclipse requires the m2e-egit connector to be installed so that you can seamlessly import your BoneJ2 fork from GitHub, but the version in the marketplace is often too old: you may need to [install it from the repository](https://stackoverflow.com/questions/51359823/m2e-egit-connector-for-scm-on-eclipse-photon-failure).
 
 ## Getting started
-1) Create a [fork](https://imagej.net/How_to_contribute_to_an_existing_plugin_or_library)
+1) Create a [fork](https://imagej.github.io/develop/improving-the-code)
 2) [Synchronize](https://help.github.com/articles/syncing-a-fork/) your fork
 3) Create a topic branch for your fix / new feature, e.g. `fix-issue-#1`
 

Legacy/bonej/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ legacy plugins</name>
     <description>Mavenized version of the BoneJ1 plugins</description>
-    <url>https://imagej.net/BoneJ_experimental</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -49,17 +49,17 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
         <contributor>
             <name>Mark Hiner</name>
-            <url>https://imagej.net/User:Hinerm</url>
+            <url>https://imagej.github.io/users/hinerm</url>
             <properties><id>hinerm</id></properties>
         </contributor>
         <contributor>

Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java

@@ -114,7 +114,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  *      </p>
  *      <p>
  *      Several of the methods are based on Ignacio Arganda-Carreras's
- *      Skeletonize3D_ plugin: <a href="https://imagej.net/Skeletonize3D">
+ *      Skeletonize3D_ plugin: <a href="https://imagej.github.io/plugins/skeletonize3d">
  *      Skeletonize3D homepage</a>
  *      </p>
  *

Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java

@@ -194,7 +194,7 @@ public void run(final String arg) {
 		gd.addChoice("Surface colours", items, items[0]);
 		gd.addNumericField("Split value", 0, 3, 7, units + "³");
 		gd.addNumericField("Volume_resampling", 2, 0);
-		gd.addHelp("https://imagej.net/BoneJ#Particle_Analyser");
+		gd.addHelp("https://imagej.github.io/plugins/bonej#particle-analyser");
 		gd.addDialogListener(this);
 		gd.showDialog();
 		if (gd.wasCanceled()) {

Legacy/bonej/src/main/java/org/bonej/plugins/ReporterOptions.java

@@ -78,7 +78,7 @@ public void run(final String arg) {
 			"and promote BoneJ to funders.");
 		dialog.addMessage("If you agree to participate please hit OK\n" +
 			"otherwise, cancel. For more information click Help.");
-		dialog.addHelp("https://imagej.net/BoneJ2#Usage_reporting");
+		dialog.addHelp("https://imagej.github.io/plugins/bonej#usage-reporting");
 		dialog.showDialog();
 		if (dialog.wasCanceled()) {
 			Prefs.set(OPTOUTKEY, false);

Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java

@@ -274,7 +274,7 @@ else if (roi.getType() != Roi.RECTANGLE) {
 		gd.addCheckbox("Partial_volume_compensation", false);
 		gd.addNumericField("Background", thresholds[0], 1, 6, pixUnits + " ");
 		gd.addNumericField("Foreground", thresholds[1], 1, 6, pixUnits + " ");
-		gd.addHelp("https://imagej.net/BoneJ2#Slice_geometry");
+		gd.addHelp("https://imagej.github.io/plugins/bonej#slice-geometry");
 		gd.addDialogListener(this);
 		gd.showDialog();
 		final String bone = gd.getNextChoice();

Legacy/util/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ legacy utilities</name>
     <description>Utility classes for BoneJ1 plugins</description>
-    <url>https://imagej.net/BoneJ_experimental</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -49,17 +49,17 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
         <contributor>
             <name>Mark Hiner</name>
-            <url>https://imagej.net/User:Hinerm</url>
+            <url>https://imagej.github.io/users/hinerm</url>
             <properties><id>hinerm</id></properties>
         </contributor>
     </contributors>

Modern/ops/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ2 Ops</name>
     <description>Ops created for BoneJ2</description>
-    <url>https://imagej.net/BoneJ_experimental</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -64,17 +64,17 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
         <contributor>
             <name>Mark Hiner</name>
-            <url>https://imagej.net/User:Hinerm</url>
+            <url>https://imagej.github.io/users/hinerm</url>
             <properties><id>hinerm</id></properties>
         </contributor>
     </contributors>

Modern/utilities/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ2 utilities</name>
     <description>Utility methods for BoneJ2</description>
-    <url>https://imagej.net/BoneJ_experimental</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -64,12 +64,12 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
     </contributors>

Modern/wrapperPlugins/pom.xml

@@ -16,7 +16,7 @@
         The Domain Presentation Layer (DPL) of BoneJ2, i.e. the commands that wrap the needed ops,
         and present results for skeletal biologists.
     </description>
-    <url>https://imagej.net/BoneJ_experimental</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -67,17 +67,17 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
         <contributor>
             <name>Mark Hiner</name>
-            <url>https://imagej.net/User:Hinerm</url>
+            <url>https://imagej.github.io/users/hinerm</url>
             <properties><id>hinerm</id></properties>
         </contributor>
     </contributors>

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java

@@ -149,7 +149,7 @@ public void run() {
 	@SuppressWarnings("unused")
 	private void showHelpPage() {
 		try {
-			platformService.open(new URL("https://imagej.net/BoneJ2#Usage_reporting"));
+			platformService.open(new URL("https://imagej.github.io/plugins/bonej#usage-reporting"));
 		} catch (final IOException e) {
 			uiService.showDialog("Something went wrong while opening the help page. Please try again.");
 			logService.trace(e);

README.md

@@ -14,7 +14,7 @@ BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides
 For legacy ImageJ1 plug-ins, which are no longer maintained, please visit https://bonej.org/legacy.
 
 ## Overview
-The code is in two main modules: `Legacy` and `Modern`. The code in `Legacy` is originally from [BoneJ1](https://bonej.org/legacy), but it has been refactored to manage its dependencies via Maven. Unlike BoneJ1, the plug-ins in `Legacy` work with Java 8 and the latest version of [Fiji](https://imagej.net/Fiji). However some of them still depend on [3D_Viewer](https://github.com/fiji/3D_Viewer), which is known to have issues with the latest versions of MacOS (see the [forum](https://forum.image.sc)). 
+The code is in two main modules: `Legacy` and `Modern`. The code in `Legacy` is originally from [BoneJ1](https://bonej.org/legacy), but it has been refactored to manage its dependencies via Maven. Unlike BoneJ1, the plug-ins in `Legacy` work with Java 8 and the latest version of [Fiji](https://imagej.github.io/fiji/). However some of them still depend on [3D_Viewer](https://github.com/fiji/3D_Viewer), which is known to have issues with the latest versions of MacOS (see the [forum](https://forum.image.sc)). 
 
 The main development happens in the `Modern` module. It hosts the modernized versions of BoneJ plug-ins, which fully comply with the current ImageJ API. Our goal is that as code matures, `Modern` hosts only "thin" wrapper plug-ins. They should be responsible only for interacting with the user, and collecting and displaying results. The wrappers call algorithms from the [Ops framework](https://imagej.net/ImageJ_Ops), specialised algorithms from BoneJ's own `Ops`, and utility code from `imagej-common`, `scifio` and other such core libraries.
 

pom.xml

@@ -16,7 +16,7 @@
 
     <name>BoneJ Parent POM</name>
     <description>Parent POM for BoneJ components</description>
-    <url>https://imagej.net/BoneJ2</url>
+    <url>https://imagej.github.io/plugins/bonej</url>
     <inceptionYear>2016</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>
@@ -67,18 +67,18 @@
     <contributors>
         <contributor>
             <name>Richard Domander</name>
-            <url>https://imagej.net/User:Rdom</url>
+            <url>https://imagej.github.io/users/rimadoma</url>
             <properties><id>rimadoma</id></properties>
             <roles><role>founder</role></roles>
         </contributor>
         <contributor>
             <name>Curtis Rueden</name>
-            <url>https://imagej.net/User:Rueden</url>
+            <url>https://imagej.github.io/users/ctrueden</url>
             <properties><id>ctrueden</id></properties>
         </contributor>
         <contributor>
             <name>Mark Hiner</name>
-            <url>https://imagej.net/User:Hinerm</url>
+            <url>https://imagej.github.io/users/hinerm</url>
             <properties><id>hinerm</id></properties>
         </contributor>
     </contributors>