diff --git a/.github/workflows/jpackage.yml b/.github/workflows/jpackage.yml
index ae389bc..173edfd 100644
--- a/.github/workflows/jpackage.yml
+++ b/.github/workflows/jpackage.yml
@@ -19,10 +19,10 @@ jobs:
 
     - uses: actions/checkout@v4
 
-    - name: Set up JDK 17 # TODO: check Java version
+    - name: Set up JDK 21 # TODO: check Java version
       uses: actions/setup-java@v4
       with:
-        java-version: '17'
+        java-version: '21'
         distribution: 'temurin'
 
     - name: Validate Gradle wrapper
diff --git a/README.md b/README.md
index 9ccdf0b..038f18f 100644
--- a/README.md
+++ b/README.md
@@ -2,10 +2,15 @@
 
 This repo contains a template and instructions to help create a new extension for [QuPath](https://qupath.github.io).
 
-It already contains two minimal extensions, so the first task is to make sure that they work.
+It already contains two minimal extensions - one using Java, one using Groovy - so the first task is to make sure that they work.
 Then, it's a matter of customizing the code to make it more useful.
 
-> There are two extensions to show that you can use either Java or Groovy.
+> **Update!** 
+> For QuPath v0.6.0 this repo switched to use Kotlin DSL for Gradle build files - 
+> and also to use the [QuPath Gradle Plugin](https://github.com/qupath/qupath-gradle-plugin).
+> 
+> The outcome is that the build files are _much_ simpler.
+
 
 ## Build the extension
 
@@ -33,39 +38,88 @@ QuPath.
 > If you don't do that, you'll need to drag *all* the extra dependences onto QuPath to install them as well.
 
 
-## Set up in an IDE (optional)
+## Configure the extension
 
-During development, things are likely to be much easier if you work within an IDE.
+Edit `settings.gradle.kts` to specify which version of QuPath your extension should be compatible with, e.g.
 
-QuPath itself is developed using IntelliJ, and you can import the extension template there.
+```kotlin
+qupath {
+    version = "0.6.0-SNAPSHOT"
+}
+```
+
+Edit `build.gradle.kts` to specify the details of your extension
 
-However, for development and testing, it can help to import QuPath *and* the extension and have them in your IDE side-by-side.
+```kotlin
+qupathExtension {
+  name = "qupath-extension-template"
+  group = "io.github.qupath"
+  version = "0.1.0-SNAPSHOT"
+  description = "A simple QuPath extension"
+  automaticModule = "io.github.qupath.extension.template"
+}
+```
 
-In IntelliJ, you can do this in a few steps:
-* Get QuPath's source code, as described at https://qupath.readthedocs.io/en/stable/docs/reference/building.html
-* Store your extension code in a directory *beside* QuPath's code. So it should be located next to the `qupath` code directory.
-* Import QuPath into IntelliJ as a Gradle project (you don't need to import the extension yet!)
-   * See https://www.jetbrains.com/help/idea/work-with-gradle-projects.html
-* Within `qupath/settings.gradle` add the line `includeFlat 'your-extension-code-directory'` (updating the code directory as needed)
-* Refresh the Gradle project in IntelliJ, and your extension code should appear
-* Create a [Run configuration](https://www.jetbrains.com/help/idea/run-debug-configuration.html) in IntelliJ to launch QuPath. An example of how that looks is shown below:
 
-<img src="qupath-intellij.png" alt="QuPath run configuration in IntelliJ" width="428" />
+## Run QuPath + the extension
 
-Now when you run QuPath from IntelliJ, your extension should (hopefully) be found - there's no need to add it by drag & drop.
+During development, your probably want to run QuPath easily with your extension installed for debugging.
 
-## Customize the extension
+### 0. Make sure you have Java installed
+You'll need to install Java first.
 
-There are a few fixed steps to customizing the extension, and then the main creative part where you add your own code.
+At the time of writing, we use a Java 21 JDK downloaded from https://adoptium.net/
 
-### Update `settings.gradle`
+> Java 21 is a 'Long Term Support' release - which is why we use it instead of the very latest version.
+
+### 1. Get QuPath's source code
+You can find instructions at https://qupath.readthedocs.io/en/stable/docs/reference/building.html
+
+### 2. Create an `include-extra` file
+Create a file called `include-extra` in the root directory of the QuPath source code (*not* the extension code!).
+
+Set the contents of this file to:
+```
+[includeBuild]
+/path/to/your/extension
+
+[dependencies]
+extension-group:extension-name
+```
+replacing the default lines where needed.
+
+For example, to build the extension with the names given above you'd use
+```
+[includeBuild]
+../qupath-extension-template
 
-Open `settings.gradle` and check the comment lines flagged with `\\TODO`.
-These point you towards parts you may well need to change.
+[dependencies]
+io.github.qupath:qupath-extension-template
+```
+
+### 3. Run QuPath
+Run QuPath from the command line using
+```
+gradlew run
+```
+If all goes well, QuPath should launch and you can check the *Extensions* mention to confirm the extension is installed.
+
+
+## Set up in an IDE (optional)
+
+During development, things are likely to be much easier if you work within an IDE.
+
+QuPath itself is developed using IntelliJ, and you can import the extension template there.
+
+The setup process is as above, and you'll need a a [Run configuration](https://www.jetbrains.com/help/idea/run-debug-configuration.html) 
+to call `gradlew run`.
+
+
+## Customize the extension
 
-### Update `build.gradle`
+Now you're ready for the creative part.
 
-Open `build.gradle` and follow a similar process to with `settings.gradle`, to update the bits flagged with `\\TODO`.
+You can develop the extension using either Java or Groovy - the template includes examples of both.
 
 ### Create the extension Java or Groovy file(s)
 
diff --git a/build.gradle b/build.gradle
deleted file mode 100644
index 23807b0..0000000
--- a/build.gradle
+++ /dev/null
@@ -1,170 +0,0 @@
-plugins {
-    // Main gradle plugin for building a Java library
-    id 'java-library'
-    // Support writing the extension in Groovy (remove this if you don't want to)
-    id 'groovy'
-    // To create a shadow/fat jar that bundle up all dependencies
-    id 'com.github.johnrengelman.shadow' version '8.1.1'
-    // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
-    id 'org.bytedeco.gradle-javacpp-platform'
-    id 'org.openjfx.javafxplugin' version '0.1.0'
-}
-
-// TODO: Change the module name
-ext.moduleName = 'io.github.qupath.extension.template'
-
-// TODO: Define the extension name & version, and provide a short description
-base {
-    archivesName = rootProject.name
-    version = '0.0.1-SNAPSHOT'
-    description = 'A simple QuPath extension template'
-}
-
-// TODO: Specify the QuPath version, compatible with the extension.
-// The default 'gradle.ext.qupathVersion' reads this from settings.gradle.
-ext.qupathVersion = gradle.ext.qupathVersion
-
-// TODO: Specify the Java version compatible with the extension
-// Should be Java 17 for QuPath v0.5.0
-ext.qupathJavaVersion = 17
-
-/**
- * Define dependencies.
- * - Using 'shadow' indicates that they are already part of QuPath, so you don't need
- *   to include them in your extension. If creating a single 'shadow jar' containing your
- *   extension and all dependencies, these won't be added.
- * - Using 'implementation' indicates that you need the dependency for the extension to work,
- *   and it isn't part of QuPath already. If you are creating a single 'shadow jar', the
- *   dependency should be bundled up in the extension.
- * - Using 'testImplementation' indicates that the dependency is only needed for testing,
- *   but shouldn't be bundled up for use in the extension.
- */
-dependencies {
-
-    // Main QuPath user interface jar.
-    // Automatically includes other QuPath jars as subdependencies.
-    shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
-
-    // For logging - the version comes from QuPath's version catalog at
-    // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml
-    // See https://docs.gradle.org/current/userguide/platforms.html
-    shadow libs.slf4j
-
-    // For JavaFX
-    shadow libs.qupath.fxtras
-
-    // If you aren't using Groovy, this can be removed
-    shadow libs.bundles.groovy
-
-    testImplementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
-    testImplementation libs.junit
-}
-
-/*
- * Manifest info
- */
-jar {
-    manifest {
-        attributes("Implementation-Title": project.name,
-                "Implementation-Version": archiveVersion,
-                "Automatic-Module-Name": moduleName)
-    }
-}
-
-/**
- * Copy necessary attributes, see
- * - https://github.com/qupath/qupath-extension-template/issues/9
- * - https://github.com/openjfx/javafx-gradle-plugin#variants
- */
-configurations.shadow  {
-    def runtimeAttributes = configurations.runtimeClasspath.attributes
-    runtimeAttributes.keySet().each { key ->
-        if (key in [Usage.USAGE_ATTRIBUTE, OperatingSystemFamily.OPERATING_SYSTEM_ATTRIBUTE, MachineArchitecture.ARCHITECTURE_ATTRIBUTE])
-            attributes.attribute(key, runtimeAttributes.getAttribute(key))
-    }
-}
-
-/*
- * Copy the LICENSE file into the jar... if we have one (we should!)
- */
-processResources {
-  from ("${projectDir}/LICENSE") {
-    into 'licenses/'
-  }
-}
-
-/*
- * Define extra 'copyDependencies' task to copy dependencies into the build directory.
- */
-tasks.register("copyDependencies", Copy) {
-    description "Copy dependencies into the build directory for use elsewhere"
-    group "QuPath"
-
-    from configurations.default
-    into 'build/libs'
-}
-
-/*
- * Ensure Java 17 compatibility, and include sources and javadocs when building.
- */
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(qupathJavaVersion)
-    }
-    withSourcesJar()
-    withJavadocJar()
-}
-
-/*
- * Create javadocs for all modules/packages in one place.
- * Use -PstrictJavadoc=true to fail on error with doclint (which is rather strict).
- */
-tasks.withType(Javadoc) {
-	options.encoding = 'UTF-8'
-	def strictJavadoc = findProperty('strictJavadoc')
-	if (!strictJavadoc) {
-        options.addStringOption('Xdoclint:none', '-quiet')
-	}
-}
-
-/*
- * Specify that the encoding should be UTF-8 for source files
- */
-tasks.named('compileJava') {
-	options.encoding = 'UTF-8'
-}
-
-/*
- * Avoid 'Entry .gitkeep is a duplicate but no duplicate handling strategy has been set.'
- * when using withSourcesJar()
- */
-tasks.withType(org.gradle.jvm.tasks.Jar) {
-    duplicatesStrategy = DuplicatesStrategy.INCLUDE
-}
-
-/*
- * Support tests with JUnit.
- */
-tasks.named('test') {
-    useJUnitPlatform()
-}
-
-// Looks redundant to include this here and in settings.gradle,
-// but helps overcome some gradle trouble when including this as a subproject
-// within QuPath itself (which is useful during development).
-repositories {
-    // Add this if you need access to dependencies only installed locally
-    //  mavenLocal()
-
-    mavenCentral()
-
-    // Add scijava - which is where QuPath's jars are hosted
-    maven {
-        url "https://maven.scijava.org/content/repositories/releases"
-    }
-
-    maven {
-        url "https://maven.scijava.org/content/repositories/snapshots"
-    }
-
-}
diff --git a/build.gradle.kts b/build.gradle.kts
new file mode 100644
index 0000000..134683f
--- /dev/null
+++ b/build.gradle.kts
@@ -0,0 +1,34 @@
+plugins {
+    // Support writing the extension in Groovy (remove this if you don't want to)
+    groovy
+    // To optionally create a shadow/fat jar that bundle up any non-core dependencies
+    id("com.gradleup.shadow") version "8.3.5"
+    // QuPath Gradle extension convention plugin
+    id("qupath-conventions")
+}
+
+// TODO: Configure your extension here (please change the defaults!)
+qupathExtension {
+    name = "qupath-extension-template"
+    group = "io.github.qupath"
+    version = "0.1.0-SNAPSHOT"
+    description = "A simple QuPath extension"
+    automaticModule = "io.github.qupath.extension.template"
+}
+
+// TODO: Define your dependencies here
+dependencies {
+
+    // Main dependencies for most QuPath extensions
+    shadow(libs.bundles.qupath)
+    shadow(libs.bundles.logging)
+    shadow(libs.qupath.fxtras)
+
+    // If you aren't using Groovy, this can be removed
+    shadow(libs.bundles.groovy)
+
+    // For testing
+    testImplementation(libs.bundles.qupath)
+    testImplementation(libs.junit)
+
+}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index d64cd49..a4b76b9 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 9355b41..cea7a79 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.10-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.12-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
diff --git a/gradlew b/gradlew
index 1aa94a4..f5feea6 100755
--- a/gradlew
+++ b/gradlew
@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -55,7 +57,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -84,7 +86,8 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
diff --git a/gradlew.bat b/gradlew.bat
index 6689b85..9b42019 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -43,11 +45,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -57,11 +59,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
diff --git a/qupath-intellij.png b/qupath-intellij.png
deleted file mode 100644
index bcbd526..0000000
Binary files a/qupath-intellij.png and /dev/null differ
diff --git a/settings.gradle b/settings.gradle
deleted file mode 100644
index ed3fa38..0000000
--- a/settings.gradle
+++ /dev/null
@@ -1,42 +0,0 @@
-pluginManagement {
-    plugins {
-        // Gradle is awkward about declaring versions for plugins
-        // Specifying it here, rather than build.gradle, makes it possible
-        // to include the extension as a subproject of QuPath itself
-        // (which is useful during development)
-        id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9'
-    }
-}
-
-// TODO: Name your QuPath extension here!
-rootProject.name = 'my-qupath-extension'
-
-// TODO: Define the QuPath version compatible with the extension
-// Note that the QuPath API isn't stable; something designed for
-// 0.X.a should work with 0.X.b, but not necessarily with 0.Y.a.
-gradle.ext.qupathVersion = "0.5.0"
-
-dependencyResolutionManagement {
-
-    // Access QuPath's version catalog for dependency versions
-    versionCatalogs {
-        libs {
-            from("io.github.qupath:qupath-catalog:${gradle.ext.qupathVersion}")
-        }
-    }
-
-    repositories {
-
-        mavenCentral()
-
-        // Add scijava - which is where QuPath's jars are hosted
-        maven {
-            url "https://maven.scijava.org/content/repositories/releases"
-        }
-
-        maven {
-            url "https://maven.scijava.org/content/repositories/snapshots"
-        }
-
-    }
-}
diff --git a/settings.gradle.kts b/settings.gradle.kts
new file mode 100644
index 0000000..5c6ca66
--- /dev/null
+++ b/settings.gradle.kts
@@ -0,0 +1,18 @@
+pluginManagement {
+    repositories {
+        gradlePluginPortal()
+        maven {
+            url = uri("https://maven.scijava.org/content/repositories/releases")
+        }
+    }
+}
+
+// TODO: Specify which version of QuPath the extension is targeting here
+qupath {
+    version = "0.5.1"
+}
+
+// Apply QuPath Gradle settings plugin to handle configuration
+plugins {
+    id("io.github.qupath.qupath-extension-settings") version "0.2.1"
+}
diff --git a/src/main/java/qupath/ext/template/ui/InterfaceController.java b/src/main/java/qupath/ext/template/ui/InterfaceController.java
index b0ab335..ef919d6 100644
--- a/src/main/java/qupath/ext/template/ui/InterfaceController.java
+++ b/src/main/java/qupath/ext/template/ui/InterfaceController.java
@@ -2,9 +2,7 @@
 
 import javafx.fxml.FXML;
 import javafx.fxml.FXMLLoader;
-import javafx.scene.control.ChoiceBox;
 import javafx.scene.control.Spinner;
-import javafx.scene.control.TextField;
 import javafx.scene.layout.VBox;
 import qupath.ext.template.DemoExtension;
 import qupath.fx.dialogs.Dialogs;
@@ -22,6 +20,11 @@ public class InterfaceController extends VBox {
     @FXML
     private Spinner<Integer> threadSpinner;
 
+    /**
+     * Create a new instance of the interface controller.
+     * @return a new instance of the interface controller
+     * @throws IOException
+     */
     public static InterfaceController createInstance() throws IOException {
         return new InterfaceController();
     }