From df1ac263ea56fecb80d0b74ee72e06d3e27e7524 Mon Sep 17 00:00:00 2001
From: Stefan Hahmann <stefanhahmann@users.noreply.github.com>
Date: Wed, 23 Apr 2025 13:08:32 +0200
Subject: [PATCH 01/13] Make MainWindow a bit wider

---
 src/main/java/org/mastodon/mamut/MainWindow.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/mastodon/mamut/MainWindow.java b/src/main/java/org/mastodon/mamut/MainWindow.java
index 3e3ea15f4..945195da6 100644
--- a/src/main/java/org/mastodon/mamut/MainWindow.java
+++ b/src/main/java/org/mastodon/mamut/MainWindow.java
@@ -111,7 +111,7 @@ public MainWindow( final ProjectModel appModel )
 
 		// Main Panel
 		final JPanel buttonsPanel = new JPanel();
-		buttonsPanel.setLayout( new MigLayout( "wrap 2", "[150px!]10[150px!]" ) );
+		buttonsPanel.setLayout( new MigLayout( "wrap 2", "[190px!]10[190px!]" ) );
 
 		// Project:
 		final JPanel titlePanel = new JPanel();

From 93d81028d9d82129175c88575333b6562b74a777 Mon Sep 17 00:00:00 2001
From: Stefan Hahmann <stefan.hahmann@tu-dresden.de>
Date: Thu, 24 Apr 2025 10:50:45 +0200
Subject: [PATCH 02/13] Set the smaller font for Buttons and Labels as default
 on Linux/Unix systems and make MainWindow a bit smaller again

---
 .../java/org/mastodon/mamut/MainWindow.java   |  2 +-
 .../mamut/launcher/MastodonLauncher.java      | 24 +++++++++++++++++++
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/mastodon/mamut/MainWindow.java b/src/main/java/org/mastodon/mamut/MainWindow.java
index 945195da6..63c73a478 100644
--- a/src/main/java/org/mastodon/mamut/MainWindow.java
+++ b/src/main/java/org/mastodon/mamut/MainWindow.java
@@ -111,7 +111,7 @@ public MainWindow( final ProjectModel appModel )
 
 		// Main Panel
 		final JPanel buttonsPanel = new JPanel();
-		buttonsPanel.setLayout( new MigLayout( "wrap 2", "[190px!]10[190px!]" ) );
+		buttonsPanel.setLayout( new MigLayout( "wrap 2", "[170px!]10[170px!]" ) );
 
 		// Project:
 		final JPanel titlePanel = new JPanel();
diff --git a/src/main/java/org/mastodon/mamut/launcher/MastodonLauncher.java b/src/main/java/org/mastodon/mamut/launcher/MastodonLauncher.java
index 324b059bc..a2ebc3d87 100644
--- a/src/main/java/org/mastodon/mamut/launcher/MastodonLauncher.java
+++ b/src/main/java/org/mastodon/mamut/launcher/MastodonLauncher.java
@@ -28,6 +28,7 @@
  */
 package org.mastodon.mamut.launcher;
 
+import java.awt.Font;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTarget;
@@ -47,6 +48,7 @@
 import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
+import javax.swing.UIManager;
 
 import org.jdom2.JDOMException;
 import org.mastodon.app.MastodonIcons;
@@ -94,6 +96,7 @@ public class MastodonLauncher extends JFrame
 	public MastodonLauncher( final Context context )
 	{
 		super( "Mastodon launcher" );
+		setFont();
 		this.context = Optional.ofNullable( context ).orElse( new Context() );
 
 		System.setProperty( "apple.laf.useScreenMenuBar", "true" );
@@ -123,6 +126,27 @@ public MastodonLauncher( final Context context )
 		setDropTarget( new LauncherDropTarget() );
 	}
 
+	private static void setFont()
+	{
+		// Determine the OS and set the font
+		String os = System.getProperty( "os.name" ).toLowerCase();
+
+		if ( os.contains( "nix" ) || os.contains( "nux" ) )
+		{
+			Font defaultFont = new Font( "Arial", Font.PLAIN, 12 );
+			// Set the font for UI components
+			UIManager.put( "Label.font", defaultFont );
+			UIManager.put( "Button.font", defaultFont );
+			UIManager.put( "TextField.font", defaultFont );
+			UIManager.put( "TextArea.font", defaultFont );
+			UIManager.put( "ComboBox.font", defaultFont );
+			UIManager.put( "List.font", defaultFont );
+			UIManager.put( "Table.font", defaultFont );
+			UIManager.put( "Menu.font", defaultFont );
+			UIManager.put( "MenuItem.font", defaultFont );
+		}
+	}
+
 	private void importSimi()
 	{
 		gui.clearLog();

From 18a146cf19cf8f6f404a17c84aa2f88695e81421 Mon Sep 17 00:00:00 2001
From: Stefan Hahmann <stefan.hahmann@tu-dresden.de>
Date: Thu, 24 Apr 2025 11:10:21 +0200
Subject: [PATCH 03/13] Use github action setup-java@v4 instead of v2

* The CI Pipeline was not working anymore. Github seems to require this change to allow the CI to be working again
---
 .github/workflows/build-main.yml | 2 +-
 .github/workflows/build-pr.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
index 0b1538578..92bc2f106 100644
--- a/.github/workflows/build-main.yml
+++ b/.github/workflows/build-main.yml
@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'
diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml
index 2df3c51a5..149fd4b4f 100644
--- a/.github/workflows/build-pr.yml
+++ b/.github/workflows/build-pr.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

From 458c7e99195d80e65836f47380cf536c2b1c8217 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Wed, 30 Jul 2025 11:18:23 -0400
Subject: [PATCH 04/13] typo

---
 src/main/java/org/mastodon/mamut/model/Model.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/mastodon/mamut/model/Model.java b/src/main/java/org/mastodon/mamut/model/Model.java
index f4b50ac86..32eaec354 100644
--- a/src/main/java/org/mastodon/mamut/model/Model.java
+++ b/src/main/java/org/mastodon/mamut/model/Model.java
@@ -233,7 +233,7 @@ public FileIdToGraphMap< Spot, Link > loadRaw( final MamutProject.ProjectReader
 	}
 
 	/**
-	 * Saves this model to the specified the specified project folder.
+	 * Saves this model to the specified project folder.
 	 *
 	 * @param writer
 	 *            writer to save the raw project files.

From d3c63c2b6ff865ee0af86e2793a8c4053b598b07 Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 18 Aug 2025 15:12:25 +0200
Subject: [PATCH 05/13] Adapt benchmark for the paper.

---
 .../revised/CreateLargeModelExample.java      | 37 +++++++++++++++++--
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
index e72e29608..c223ad4c0 100644
--- a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
+++ b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -28,14 +28,21 @@
  */
 package org.mastodon.graph.revised;
 
+import java.io.IOException;
+
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.WindowManager;
 import org.mastodon.mamut.io.importer.ModelImporter;
+import org.mastodon.mamut.io.project.MamutProject;
 import org.mastodon.mamut.model.Link;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.Spot;
+import org.mastodon.views.bdv.SharedBigDataViewerData;
+import org.scijava.Context;
 
 public class CreateLargeModelExample
 {
-	private static final int N_STARTING_CELLS = 6;
+	private static final int N_STARTING_CELLS = 10;
 
 	private static final int N_DIVISIONS = 17;
 
@@ -160,8 +167,13 @@ private void addBranch( final Spot start, final double vx, final double vy, fina
 		model.getGraph().releaseRef( link );
 	}
 
-	public static void main( final String[] args )
+	public static void main( final String[] args ) throws IOException
 	{
+		// Print info on the JVM used to run the code.
+		System.out.println( "JVM: " + System.getProperty( "java.vm.name" ) + " " + System.getProperty( "java.vm.version" ) );
+		System.out.println( "Java: " + System.getProperty( "java.version" ) );
+		System.out.println( "OS: " + System.getProperty( "os.name" ) + " " + System.getProperty( "os.version" ) + " " + System.getProperty( "os.arch" ) );
+
 		final CreateLargeModelExample clme = new CreateLargeModelExample();
 		final long start = System.currentTimeMillis();
 		final Model model = clme.run();
@@ -170,5 +182,22 @@ public static void main( final String[] args )
 		System.out.println( "Total number of spots: " + model.getGraph().vertices().size() );
 		System.out.println( String.format( "Total memory used by the model: %.1f MB",
 				( Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory() ) / 1e6d ) );
+
+
+		final Context context = new Context();
+		final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
+		final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
+		final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project  );
+		final WindowManager wm = new WindowManager( appModel  );
+
+//		start = System.currentTimeMillis();
+//		wm.createBigDataViewer();
+//		end = System.currentTimeMillis();
+//		System.out.println( "Rendering in the main viewer done in " + ( end - start ) / 1000. + " s." );
+//
+//		start = System.currentTimeMillis();
+//		wm.createTrackScheme( );
+//		end = System.currentTimeMillis();
+//		System.out.println( "Rendering in TrackScheme done in " + ( end - start ) / 1000. + " s." );
 	}
 }

From 8416b6facdf3891562babdff889c441ce114aadd Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:36:15 +0200
Subject: [PATCH 06/13] Bump to next development cycle

Signed-off-by: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
---
 .../CommonTrackMateFeatureDeclarations.java   |  94 ++++++++++
 .../io/importer/trackmate/MamutExporter.java  | 176 ++++++++++++++++--
 .../importer/trackmate/TrackMateXMLKeys.java  |   2 +
 .../grapher/DataDisplayFrameSupplier.java     |  41 ----
 .../mamut/views/grapher/GrapherGuiState.java  |  49 ++---
 .../views/grapher/GrapherInitializer.java     |  18 ++
 .../views/grapher/MamutBranchViewGrapher.java |   3 +-
 .../MamutBranchViewGrapherFactory.java        |  15 +-
 .../mamut/views/grapher/MamutViewGrapher.java |  17 +-
 .../grapher/MamutViewGrapherFactory.java      |  15 +-
 .../views/bdv/overlay/OverlayNavigation.java  |  27 ++-
 .../grapher/display/DataDisplayFrame.java     |  14 +-
 .../grapher/display/GrapherSidePanel.java     |  21 ++-
 .../views/grapher/display/Plotable.java       |  10 +
 14 files changed, 382 insertions(+), 120 deletions(-)
 create mode 100644 src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
 delete mode 100644 src/main/java/org/mastodon/mamut/views/grapher/DataDisplayFrameSupplier.java
 create mode 100644 src/main/java/org/mastodon/views/grapher/display/Plotable.java

diff --git a/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java b/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
new file mode 100644
index 000000000..5aac6f5cc
--- /dev/null
+++ b/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
@@ -0,0 +1,94 @@
+package org.mastodon.mamut.io.importer.trackmate;
+
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_DIMENSION_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ISINT_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_NAME_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_SHORT_NAME_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_TAG;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import org.jdom2.Element;
+
+public class CommonTrackMateFeatureDeclarations
+{
+
+	public static final List< CommonTrackMateFeatureDeclaration > spotFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.VISIBILITY_FEATURE_NAME, "Visibility", "Visibility", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_X_FEATURE_NAME, "X", "X", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Y_FEATURE_NAME, "Y", "Y", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Z_FEATURE_NAME, "Z", "Z", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_T_FEATURE_NAME, "T", "T", "TIME", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.FRAME_FEATURE_NAME, "Frame", "Frame", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.RADIUS_FEATURE_NAME, "Radius", "R", "LENGTH", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.QUALITY_FEATURE_NAME, "Quality", "Quality", "QUALITY", false ),
+	} );
+
+	public static final List< CommonTrackMateFeatureDeclaration > edgeFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_SOURCE_ATTRIBUTE, "Source spot ID", "Source ID", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_TARGET_ATTRIBUTE, "Target spot ID", "Target ID", "NONE", true ),
+	} );
+
+	public static final List< CommonTrackMateFeatureDeclaration > trackFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.TRACK_ID_ATTRIBUTE, "Track ID", "ID", "NONE", true ),
+	} );
+
+	public static class CommonTrackMateFeatureDeclaration
+	{
+		public final String key;
+
+		public final String name;
+
+		public final String shortName;
+
+		public final String dimension;
+
+		public final boolean isInt;
+
+		public CommonTrackMateFeatureDeclaration( final String key, final String name, final String shortName, final String dimension, final boolean isInt )
+		{
+			this.key = key;
+			this.name = name;
+			this.shortName = shortName;
+			this.dimension = dimension;
+			this.isInt = isInt;
+		}
+		
+		public Element toElement()
+		{
+			final Element fel = new Element( FEATURE_TAG );
+			fel.setAttribute( FEATURE_ATTRIBUTE, key );
+			fel.setAttribute( FEATURE_NAME_ATTRIBUTE, name );
+			fel.setAttribute( FEATURE_SHORT_NAME_ATTRIBUTE, shortName );
+			fel.setAttribute( FEATURE_DIMENSION_ATTRIBUTE, dimension );
+			fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, "" + isInt );
+			return fel;
+		}
+	}
+
+	/**
+	 * List of Mastodon spot projection keys, translated to the TrackMate export
+	 * name, that are not needed in the exported XML file, as they are already
+	 * exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantSpotProjectionKeys = Arrays.asList(
+			"Spot_position_X", "Spot_position_Y", "Spot_position_Z", "Spot_radius", "Spot_frame" );
+
+	/**
+	 * List of Mastodon link projection keys, translated to the TrackMate export
+	 * name, that are not needed in the exported XML file, as they are already
+	 * exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantLinkProjectionKeys = Arrays.asList(
+			"Link_target_IDs_Source_spot_id", "Link_target_IDs_Target_spot_id" );
+
+	/**
+	 * List of Mastodon track projection keys, translated to the TrackMate
+	 * export name, that are not needed in the exported XML file, as they are
+	 * already exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantTrackProjectionKeys = Collections.emptyList();
+}
diff --git a/src/main/java/org/mastodon/mamut/io/importer/trackmate/MamutExporter.java b/src/main/java/org/mastodon/mamut/io/importer/trackmate/MamutExporter.java
index eaf1e69d0..c0b7fb54c 100644
--- a/src/main/java/org/mastodon/mamut/io/importer/trackmate/MamutExporter.java
+++ b/src/main/java/org/mastodon/mamut/io/importer/trackmate/MamutExporter.java
@@ -54,6 +54,7 @@
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FOLDER_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_FEATURE_NAME;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_INTERVAL_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.GUI_STATE_TAG;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.HEIGHT_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.ID_FEATURE_NAME;
@@ -361,6 +362,7 @@ private Element imageDataToXml()
 		attributes.add( new Attribute( PIXEL_WIDTH_ATTRIBUTE, Double.toString( pixelWidth ) ) );
 		attributes.add( new Attribute( PIXEL_HEIGHT_ATTRIBUTE, Double.toString( pixelHeight ) ) );
 		attributes.add( new Attribute( VOXEL_DEPTH_ATTRIBUTE, Double.toString( voxelDepth ) ) );
+		attributes.add( new Attribute( FRAME_INTERVAL_ATTRIBUTE, Double.toString( 1. ) ) );
 
 		final Element timePointsElement = document
 				.getRootElement()
@@ -424,9 +426,9 @@ private Element[] trackCollectionToXml()
 						public void processVertexLate( final Spot vertex, final DepthFirstSearch< Spot, Link > search )
 						{
 							/*
-							 * 1 root = 1 track, unless a track has several roots. Add
-							 * the iterated vertex to the list of root to skip if
-							 * needed.
+							 * 1 root = 1 track, unless a track has several
+							 * roots. Add the iterated vertex to the list of
+							 * root to skip if needed.
 							 */
 							if ( vertex.incomingEdges().isEmpty() )
 								toSkip.add( vertex );
@@ -520,6 +522,15 @@ private Element spotCollectionToXml()
 		return spotCollectionElement;
 	}
 
+	/**
+	 * Collection of link feature names that we want to export in the mamut
+	 * file, but computed from the link data currently set in Mastodon. We used
+	 * this collection to avoid exporting a feature with identical name in the
+	 * case a feature imported as the same name.
+	 */
+	private final static Set< String > IMPORTED_LINK_BUILTIN_FEATURES = new HashSet<>( Arrays.asList(
+			EDGE_SOURCE_ATTRIBUTE, EDGE_TARGET_ATTRIBUTE ) );
+
 	private Element edgeToXml( final Link edge, final int sourceSpotID, final int targetSpotID )
 	{
 		final Collection< Attribute > attributes = new ArrayList<>();
@@ -529,9 +540,45 @@ private Element edgeToXml( final Link edge, final int sourceSpotID, final int ta
 		attributes.add( new Attribute( EDGE_TARGET_ATTRIBUTE, Integer.toString( targetSpotID ) ) );
 
 		// Link features.
-		linkFeatureProjections.forEach( p -> attributes.add( new Attribute(
-				p.attributeName,
-				Double.toString( p.projection.value( edge ) ) ) ) );
+		for ( final ExportFeatureProjection< Link > p : linkFeatureProjections )
+		{
+			final String origName = p.attributeName;
+			/*
+			 * Do not export link features that are common TrackMate features
+			 * and that we already exported above.
+			 */
+			if ( CommonTrackMateFeatureDeclarations.redundantLinkProjectionKeys.contains( origName ) )
+				continue;
+
+			final String attName;
+			/*
+			 * If the model to export was imported from a TrackMate or a MaMuT
+			 * file, it will already contain features with the same name that
+			 * the builtin feature we added just above. Which will cause an
+			 * error.
+			 * 
+			 * To avoid this, rename these imported features.
+			 */
+			if ( IMPORTED_LINK_BUILTIN_FEATURES.contains( origName ) )
+			{
+				final String importedAttName = "IMPORTED_" + origName;
+				attName = importedAttName;
+			}
+			else if ( origName.startsWith( "IMPORTED_" ) )
+			{
+				// We skip features that have been re-imported.
+				continue;
+			}
+			else
+			{
+				// All good.
+				attName = origName;
+			}
+
+			attributes.add( new Attribute(
+					attName,
+					Double.toString( p.projection.value( edge ) ) ) );
+		}
 
 		final Element edgeElement = new Element( EDGE_TAG );
 		edgeElement.setAttributes( attributes );
@@ -556,9 +603,20 @@ private Element trackToXml( final Spot root )
 		return trackElement;
 	}
 
+	/**
+	 * Collection of spot feature names that we want to export in the mamut
+	 * file, but computed from the actual position, etc, currently set in
+	 * Mastodon. We used this collection to avoid exporting a feature with
+	 * identical name in the case a feature imported as the same name.
+	 */
+	private final static Set< String > IMPORTED_SPOT_BUILTIN_FEATURES = new HashSet<>( Arrays.asList( ID_FEATURE_NAME, LABEL_FEATURE_NAME, POSITION_X_FEATURE_NAME,
+			POSITION_Y_FEATURE_NAME, POSITION_Z_FEATURE_NAME, FRAME_FEATURE_NAME,
+			POSITION_T_FEATURE_NAME, QUALITY_FEATURE_NAME, VISIBILITY_FEATURE_NAME,
+			RADIUS_FEATURE_NAME ) );
+
 	private Element spotToXml( final Spot spot )
 	{
-		final Collection< Attribute > attributes = new ArrayList<>();
+		final List< Attribute > attributes = new ArrayList<>();
 
 		// Id.
 		attributes.add( new Attribute( ID_FEATURE_NAME, Integer.toString( spot.getInternalPoolIndex() ) ) );
@@ -583,10 +641,54 @@ private Element spotToXml( final Spot spot )
 		final double meanRadius = Arrays.stream( eig.getRealEigenvalues() ).map( Math::sqrt ).average().getAsDouble();
 		attributes.add( new Attribute( RADIUS_FEATURE_NAME, Double.toString( meanRadius ) ) );
 
-		// Spot features.
-		spotFeatureProjections.forEach( p -> attributes.add( new Attribute(
-				p.attributeName,
-				Double.toString( p.projection.value( spot ) ) ) ) );
+		for (final ExportFeatureProjection< Spot > p : spotFeatureProjections )
+		{
+			final String origName = p.attributeName;
+			/*
+			 * Do not export spot features that are common TrackMate features
+			 * and that we already exported above.
+			 */
+			if ( CommonTrackMateFeatureDeclarations.redundantSpotProjectionKeys.contains( origName ) )
+				continue;
+
+			final String attName;
+			/*
+			 * If the model to export was imported from a TrackMate or a MaMuT
+			 * file, it will already contain features with the same name that
+			 * the builtin feature we added just above. Which will cause an
+			 * error.
+			 * 
+			 * To avoid this, rename these imported features.
+			 */
+			if ( IMPORTED_SPOT_BUILTIN_FEATURES.contains( origName ) )
+			{
+				final String importedAttName = "IMPORTED_" + origName;
+				attName = importedAttName;
+			}
+			else if ( origName.startsWith( "IMPORTED_" ) )
+			{
+				// We skip features that have been re-imported.
+				continue;
+			}
+			else
+			{
+				// All good.
+				attName = origName;
+			}
+			
+			
+			String val;
+			if ( p.projection instanceof IntFeatureProjection )
+			{
+				val = Integer.toString( (int) p.projection.value( spot ) );
+			}
+			else
+			{
+				// Assume double.
+				val = Double.toString( p.projection.value( spot ) );
+			}
+			attributes.add( new Attribute( attName, val ) );
+		}
 
 		final Element spotElement = new Element( SPOT_ELEMENT_TAG );
 		spotElement.setAttributes( attributes );
@@ -596,6 +698,7 @@ private Element spotToXml( final Spot spot )
 	private Element featuresDeclarationToXml()
 	{
 		final Element featuresElement = new Element( FEATURE_DECLARATION_TAG );
+		appendBasicFeatureDeclarations( featuresElement );
 		appendFeaturesDeclarationOfClass( Spot.class, featuresElement, SPOT_FEATURE_DECLARATION_TAG );
 		appendFeaturesDeclarationOfClass( Link.class, featuresElement, EDGE_FEATURE_DECLARATION_TAG );
 		// Create an empty declaration for track features, for now.
@@ -603,21 +706,53 @@ private Element featuresDeclarationToXml()
 		return featuresElement;
 	}
 
+	private void appendBasicFeatureDeclarations( final Element featuresElement )
+	{
+		// Spots.
+		final Element spotFeaturesElement = getOrAddChild( featuresElement, SPOT_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.spotFeatureDeclarations.forEach( cf -> spotFeaturesElement.addContent( cf.toElement() ) );
+
+		// Edges.
+		final Element edgeFeaturesElement = getOrAddChild( featuresElement, EDGE_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.edgeFeatureDeclarations.forEach( cf -> edgeFeaturesElement.addContent( cf.toElement() ) );
+
+		// Tracks.
+		final Element trackFeaturesElement = getOrAddChild( featuresElement, TRACK_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.trackFeatureDeclarations.forEach( cf -> trackFeaturesElement.addContent( cf.toElement() ) );
+	}
+
 	@SuppressWarnings( { "unchecked", "rawtypes" } )
 	private < T > void appendFeaturesDeclarationOfClass( final Class< T > clazz, final Element featuresElement,
 			final String classFeatureDeclarationTag )
 	{
 		final List< ExportFeatureProjection< T > > projections;
+		List< String > redundantFeatures;
 		if ( clazz.equals( Spot.class ) )
+		{
 			projections = ( List ) spotFeatureProjections;
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantSpotProjectionKeys;
+		}
 		else if ( clazz.equals( Link.class ) )
+		{
 			projections = ( List ) linkFeatureProjections;
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantLinkProjectionKeys;
+		}
 		else
+		{
 			projections = Collections.emptyList();
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantTrackProjectionKeys;
+		}
 
-		final Element classFeaturesElement = new Element( classFeatureDeclarationTag );
+		final Element classFeaturesElement = getOrAddChild( featuresElement, classFeatureDeclarationTag );
 		for ( final ExportFeatureProjection< T > p : projections )
 		{
+			/*
+			 * Do not export features that are common TrackMate features and
+			 * that we already declared.
+			 */
+			if ( redundantFeatures.contains( p.attributeName ) )
+				continue;
+
 			final String isint = ( p.projection instanceof IntFeatureProjection )
 					? "true"
 					: "false";
@@ -633,7 +768,17 @@ else if ( clazz.equals( Link.class ) )
 			fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, isint );
 			classFeaturesElement.addContent( fel );
 		}
-		featuresElement.addContent( classFeaturesElement );
+	}
+
+	private Element getOrAddChild( final Element parent, final String childName )
+	{
+		Element child = parent.getChild( childName );
+		if ( null == child )
+		{
+			child = new Element( childName );
+			parent.addContent( child );
+		}
+		return child;
 	}
 
 	private static Document getSAXParsedDocument( final String fileName )
@@ -652,8 +797,8 @@ private static Document getSAXParsedDocument( final String fileName )
 	}
 
 	/**
-	 * Tries to recover the TrackMate dimension from the unit string and the spatial and
-	 * time units.
+	 * Tries to recover the TrackMate dimension from the unit string and the
+	 * spatial and time units.
 	 *
 	 * @param units
 	 *            the unit string.
@@ -914,4 +1059,5 @@ public static final void export( final File target, final Model model, final Mam
 		exporter.appendGuiState();
 		exporter.write( target );
 	}
+
 }
diff --git a/src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateXMLKeys.java b/src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateXMLKeys.java
index 9f5dee71f..7028b5f25 100644
--- a/src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateXMLKeys.java
+++ b/src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateXMLKeys.java
@@ -125,6 +125,8 @@ public class TrackMateXMLKeys
 
 	public static final String NFRAMES_ATTRIBUTE = "nframes";
 
+	public static final String FRAME_INTERVAL_ATTRIBUTE = "timeinterval";
+
 	public static final String PIXEL_WIDTH_ATTRIBUTE = "pixelwidth";
 
 	public static final String PIXEL_HEIGHT_ATTRIBUTE = "pixelheight";
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/DataDisplayFrameSupplier.java b/src/main/java/org/mastodon/mamut/views/grapher/DataDisplayFrameSupplier.java
deleted file mode 100644
index 8c60ed77c..000000000
--- a/src/main/java/org/mastodon/mamut/views/grapher/DataDisplayFrameSupplier.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*-
- * #%L
- * Mastodon
- * %%
- * Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package org.mastodon.mamut.views.grapher;
-
-import org.mastodon.Ref;
-import org.mastodon.graph.Edge;
-import org.mastodon.graph.Vertex;
-import org.mastodon.model.HasLabel;
-import org.mastodon.spatial.HasTimepoint;
-import org.mastodon.views.grapher.display.DataDisplayFrame;
-
-public interface DataDisplayFrameSupplier< V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > >
-{
-	DataDisplayFrame< V, E > getFrame();
-}
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java b/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
index 9d3c14663..9fd0a3bf8 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -38,10 +38,11 @@
 import org.mastodon.model.HasLabel;
 import org.mastodon.spatial.HasTimepoint;
 import org.mastodon.views.grapher.datagraph.ScreenTransform;
-import org.mastodon.views.grapher.display.DataDisplayFrame;
 import org.mastodon.views.grapher.display.FeatureGraphConfig;
 import org.mastodon.views.grapher.display.FeatureSpecPair;
 import org.mastodon.views.grapher.display.GrapherSidePanel;
+import org.mastodon.views.grapher.display.Plotable;
+import org.mastodon.views.grapher.display.ScreenTransformState;
 
 public class GrapherGuiState
 {
@@ -100,40 +101,39 @@ private GrapherGuiState()
 	 */
 	public static final String GRAPHER_SHOW_EDGES_KEY = "GrapherShowEdges";
 
-	static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > void
-			writeGuiState( final DataDisplayFrameSupplier< V, E > frameProvider, final Map< String, Object > guiState )
+	public static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > void
+			writeGuiState( final ScreenTransformState screenTransformState, final FeatureGraphConfig config,
+					final Map< String, Object > guiState )
 	{
-		DataDisplayFrame< V, E > frame = frameProvider.getFrame();
 		// Transform.
-		final ScreenTransform transform = frame.getDataDisplayPanel().getScreenTransform().get();
+		final ScreenTransform transform = screenTransformState.get();
 		guiState.put( GRAPHER_TRANSFORM_KEY, transform );
 		// Feature graph config.
-		writeFeatureGraphConfig( frame, guiState );
+		writeFeatureGraphConfig( config, guiState );
 	}
 
-	static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > void
-			loadGuiState( final DataDisplayFrameSupplier< V, E > frameSupplier, final Map< String, Object > guiState,
-					final FeatureGraphConfig defaultConfig )
+	public static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > void
+			loadGuiState( final Map< String, Object > guiState, final ScreenTransformState screenTransformState,
+					final GrapherSidePanel<V, E> sidePanel, final FeatureGraphConfig defaultConfig,
+					final Plotable plotable )
 	{
-		DataDisplayFrame< V, E > frame = frameSupplier.getFrame();
-
 		// Read Screen Transform.
 		final ScreenTransform screenTransform = ( ScreenTransform ) guiState.get( GRAPHER_TRANSFORM_KEY );
 		if ( null != screenTransform )
-			frame.getDataDisplayPanel().getScreenTransform().set( screenTransform );
+			screenTransformState.set( screenTransform );
 
 		// Read Feature graph config.
-		FeatureGraphConfig config = loadFeatureGraphConfig( frame, guiState, defaultConfig );
-		frame.getVertexSidePanel().setGraphConfig( config );
+		FeatureGraphConfig config = loadFeatureGraphConfig( sidePanel, guiState, defaultConfig );
+		sidePanel.setGraphConfig( config );
 
 		// Plot with loaded transform and config.
-		frame.plot( screenTransform );
+		if ( plotable != null )
+			plotable.plot( screenTransform );
 	}
 
 	private static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > void
-			writeFeatureGraphConfig( final DataDisplayFrame< V, E > frame, final Map< String, Object > guiState )
+			writeFeatureGraphConfig( final FeatureGraphConfig config, final Map< String, Object > guiState )
 	{
-		FeatureGraphConfig config = frame.getVertexSidePanel().getGraphConfig();
 		// X-axis feature.
 		FeatureSpecPair featureSpecPairX = config.getXFeature();
 		guiState.put( GRAPHER_X_AXIS_FEATURE_IS_EDGE_KEY, featureSpecPairX.isEdgeFeature() );
@@ -150,11 +150,12 @@ private GrapherGuiState()
 		guiState.put( GRAPHER_SHOW_EDGES_KEY, config.drawConnected() );
 	}
 
-	private static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > FeatureGraphConfig
-			loadFeatureGraphConfig( final DataDisplayFrame< V, E > frame, final Map< String, Object > guiState,
-					final FeatureGraphConfig defaultConfig )
+	public static < V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > > FeatureGraphConfig
+			loadFeatureGraphConfig(
+					final GrapherSidePanel<V, E> sidePanel, final Map< String, Object > guiState,
+					final FeatureGraphConfig defaultConfig
+			)
 	{
-		GrapherSidePanel sidePanel = frame.getVertexSidePanel();
 		FeatureSpecPair featureSpecPairX = loadFeatureSpecPair( guiState, sidePanel, GRAPHER_X_AXIS_FEATURE_IS_EDGE_KEY,
 				GRAPHER_X_AXIS_FEATURE_SPEC_KEY, GRAPHER_X_AXIS_FEATURE_PROJECTION_KEY, GRAPHER_X_AXIS_INCOMING_EDGE_KEY );
 		FeatureSpecPair featureSpecPairY = loadFeatureSpecPair( guiState, sidePanel, GRAPHER_Y_AXIS_FEATURE_IS_EDGE_KEY,
@@ -165,7 +166,7 @@ private GrapherGuiState()
 		return new FeatureGraphConfig( featureSpecPairX, featureSpecPairY, FeatureGraphConfig.GraphDataItemsSource.CONTEXT, showEdges );
 	}
 
-	private static FeatureSpecPair loadFeatureSpecPair( final Map< String, Object > guiState, final GrapherSidePanel sidePanel,
+	private static < V extends Vertex< E >,  E extends Edge< V > > FeatureSpecPair loadFeatureSpecPair( final Map< String, Object > guiState, final GrapherSidePanel<V, E> sidePanel,
 			final String edgeKey, final String featureSpecKey, final String projectionKey, final String incomingEdgeKey )
 	{
 		Boolean isEdgeFeature = ( Boolean ) guiState.get( edgeKey );
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java b/src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java
index 61ca3ce52..a32388f4b 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java
@@ -71,6 +71,7 @@
 import org.mastodon.ui.coloring.ColorBarOverlay;
 import org.mastodon.ui.coloring.ColoringModel;
 import org.mastodon.ui.coloring.GraphColorGeneratorAdapter;
+import org.mastodon.ui.commandfinder.CommandFinder;
 import org.mastodon.views.context.ContextChooser;
 import org.mastodon.views.grapher.datagraph.DataContextListener;
 import org.mastodon.views.grapher.datagraph.DataEdge;
@@ -275,6 +276,23 @@ void addSearchPanel( final Actions viewActions )
 		frame.getSettingsPanel().add( searchPanel );
 	}
 
+	void addCommandFinder(final Actions viewActions, final String[] keyConfigContexts)
+	{
+		final CommandFinder cf = CommandFinder.build()
+				.context( appModel.getContext() )
+				.inputTriggerConfig( appModel.getKeymap().getConfig() )
+				.keyConfigContexts( keyConfigContexts )
+				.descriptionProvider( appModel.getWindowManager().getViewFactories().getCommandDescriptions() )
+				.register( viewActions )
+				.register( appModel.getModelActions() )
+				.register( appModel.getProjectActions() )
+				.register( appModel.getPlugins().getPluginActions() )
+				.modificationListeners( appModel.getKeymap().updateListeners() )
+				.parent( frame )
+				.installOn( viewActions );
+		cf.getDialog().setTitle( cf.getDialog().getTitle() + " - " + frame.getTitle() );
+	}
+
 	private void
 			registerColoring(
 					final TriFunction< ViewMenuBuilder.JMenuHandle, GraphColorGeneratorAdapter< V, E, DataVertex, DataEdge >,
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapher.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapher.java
index 4ab88e809..7120e2b64 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapher.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapher.java
@@ -57,7 +57,7 @@
 import java.util.function.BiConsumer;
 
 public class MamutBranchViewGrapher extends MamutBranchView< DataGraph< BranchSpot, BranchLink >, DataVertex, DataEdge >
-		implements HasColoringModel, HasColorBarOverlay, DataDisplayFrameSupplier< BranchSpot, BranchLink >
+		implements HasColoringModel, HasColorBarOverlay
 {
 
 	private final GrapherInitializer< BranchSpot, BranchLink > grapherInitializer;
@@ -82,6 +82,7 @@ public class MamutBranchViewGrapher extends MamutBranchView< DataGraph< BranchSp
 		setFrame( grapherInitializer.getFrame() ); // this creates viewActions and viewBehaviours thus must be called before installActions
 		grapherInitializer.installActions( viewActions, viewBehaviours );
 		grapherInitializer.addSearchPanel( viewActions );
+		grapherInitializer.addCommandFinder( viewActions, keyConfigContexts );
 
 		TriFunction< JMenuHandle, GraphColorGeneratorAdapter< BranchSpot, BranchLink, DataVertex, DataEdge >,
 				DataDisplayPanel< BranchSpot, BranchLink >, ColoringModel > colorModelRegistration =
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
index db0aee0ca..b95fdfa0d 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -31,8 +31,11 @@
 import java.util.Map;
 
 import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.model.branch.BranchLink;
+import org.mastodon.mamut.model.branch.BranchSpot;
 import org.mastodon.mamut.views.AbstractMamutViewFactory;
 import org.mastodon.mamut.views.MamutViewFactory;
+import org.mastodon.views.grapher.display.DataDisplayFrame;
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
@@ -51,7 +54,9 @@ public MamutBranchViewGrapher create( final ProjectModel projectModel )
 	public Map< String, Object > getGuiState( final MamutBranchViewGrapher view )
 	{
 		final Map< String, Object > guiState = super.getGuiState( view );
-		GrapherGuiState.writeGuiState( view, guiState );
+		DataDisplayFrame< BranchSpot, BranchLink > frame = view.getFrame();
+		GrapherGuiState.writeGuiState( frame.getDataDisplayPanel().getScreenTransform(), frame.getVertexSidePanel().getGraphConfig(),
+				guiState );
 		return guiState;
 	}
 
@@ -59,7 +64,9 @@ public Map< String, Object > getGuiState( final MamutBranchViewGrapher view )
 	public void restoreGuiState( final MamutBranchViewGrapher view, final Map< String, Object > guiState )
 	{
 		super.restoreGuiState( view, guiState );
-		GrapherGuiState.loadGuiState( view, guiState, MamutBranchViewGrapher.getFeatureGraphConfig() );
+		DataDisplayFrame< BranchSpot, BranchLink > frame = view.getFrame();
+		GrapherGuiState.loadGuiState( guiState, frame.getDataDisplayPanel().getScreenTransform(), frame.getVertexSidePanel(),
+				MamutBranchViewGrapher.getFeatureGraphConfig(), view.getFrame() );
 	}
 
 	@Override
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
index 6471106a7..14b594c53 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
@@ -59,7 +59,7 @@
 import net.imglib2.loops.LoopBuilder;
 
 public class MamutViewGrapher extends MamutView< DataGraph< Spot, Link >, DataVertex, DataEdge >
-		implements HasContextChooser< Spot >, HasColoringModel, HasColorBarOverlay, DataDisplayFrameSupplier< Spot, Link >
+		implements HasContextChooser< Spot >, HasColoringModel, HasColorBarOverlay
 {
 
 	private final GrapherInitializer< Spot, Link > grapherInitializer;
@@ -83,6 +83,7 @@ public class MamutViewGrapher extends MamutView< DataGraph< Spot, Link >, DataVe
 		setFrame( grapherInitializer.getFrame() ); // this creates viewActions and viewBehaviours thus must be called before installActions
 		grapherInitializer.installActions( viewActions, viewBehaviours );
 		grapherInitializer.addSearchPanel( viewActions );
+		grapherInitializer.addCommandFinder( viewActions, keyConfigContexts );
 
 		final TriFunction< ViewMenuBuilder.JMenuHandle, GraphColorGeneratorAdapter< Spot, Link, DataVertex, DataEdge >,
 				DataDisplayPanel< Spot, Link >, ColoringModel > colorModelRegistration = ( menuHandle, coloringAdaptor,
@@ -95,20 +96,6 @@ public class MamutViewGrapher extends MamutView< DataGraph< Spot, Link >, DataVe
 		grapherInitializer.addMenusAndRegisterColors( colorModelRegistration, colorBarRegistration, tagSetMenuRegistration,
 				keyConfigContexts );
 		grapherInitializer.layout();
-
-		final CommandFinder cf = CommandFinder.build()
-				.context( appModel.getContext() )
-				.inputTriggerConfig( appModel.getKeymap().getConfig() )
-				.keyConfigContexts( keyConfigContexts )
-				.descriptionProvider( appModel.getWindowManager().getViewFactories().getCommandDescriptions() )
-				.register( viewActions )
-				.register( appModel.getModelActions() )
-				.register( appModel.getProjectActions() )
-				.register( appModel.getPlugins().getPluginActions() )
-				.modificationListeners( appModel.getKeymap().updateListeners() )
-				.parent( frame )
-				.installOn( viewActions );
-		cf.getDialog().setTitle( cf.getDialog().getTitle() + " - " + frame.getTitle() );
 	}
 
 	static FeatureGraphConfig getFeatureGraphConfig()
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
index 47a945374..e6836fba0 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -31,9 +31,12 @@
 import java.util.Map;
 
 import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.model.Link;
+import org.mastodon.mamut.model.Spot;
 import org.mastodon.mamut.views.AbstractMamutViewFactory;
 import org.mastodon.mamut.views.MamutViewFactory;
 import org.mastodon.ui.coloring.ColorBarOverlay.Position;
+import org.mastodon.views.grapher.display.DataDisplayFrame;
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
@@ -82,7 +85,9 @@ public MamutViewGrapher create( final ProjectModel projectModel )
 	public Map< String, Object > getGuiState( final MamutViewGrapher view )
 	{
 		final Map< String, Object > guiState = super.getGuiState( view );
-		GrapherGuiState.writeGuiState( view, guiState );
+		DataDisplayFrame< Spot, Link > frame = view.getFrame();
+		GrapherGuiState.writeGuiState( frame.getDataDisplayPanel().getScreenTransform(), frame.getVertexSidePanel().getGraphConfig(),
+				guiState );
 		return guiState;
 	}
 
@@ -91,7 +96,9 @@ public Map< String, Object > getGuiState( final MamutViewGrapher view )
 	public void restoreGuiState( final MamutViewGrapher view, final Map< String, Object > guiState )
 	{
 		super.restoreGuiState( view, guiState );
-		GrapherGuiState.loadGuiState( view, guiState, MamutViewGrapher.getFeatureGraphConfig() );
+		DataDisplayFrame< Spot, Link > frame = view.getFrame();
+		GrapherGuiState.loadGuiState( guiState, frame.getDataDisplayPanel().getScreenTransform(), frame.getVertexSidePanel(),
+				MamutViewGrapher.getFeatureGraphConfig(), view.getFrame() );
 	}
 
 	@Override
diff --git a/src/main/java/org/mastodon/views/bdv/overlay/OverlayNavigation.java b/src/main/java/org/mastodon/views/bdv/overlay/OverlayNavigation.java
index 073771222..ae4864614 100644
--- a/src/main/java/org/mastodon/views/bdv/overlay/OverlayNavigation.java
+++ b/src/main/java/org/mastodon/views/bdv/overlay/OverlayNavigation.java
@@ -46,6 +46,10 @@ public class OverlayNavigation< V extends OverlayVertex< V, E >, E extends Overl
 
 	private NavigationBehaviour< V, E > navigationBehaviour;
 
+	private long lastNavigationTime = 0;
+
+	private static final int ANIMATION_DURATION = 300;
+
 	public OverlayNavigation(
 			final AbstractViewerPanel panel,
 			final OverlayGraph< V, E > graph )
@@ -82,6 +86,9 @@ public void setNavigationEtiquette( final NavigationEtiquette navigationEtiquett
 	@Override
 	public void navigateToVertex( final V vertex )
 	{
+		if (shouldThrottle())
+			return; // Throttle navigation requests.
+
 		// Always move in T.
 		final int tp = vertex.getTimepoint();
 		panel.state().setCurrentTimepoint( tp );
@@ -90,17 +97,20 @@ public void navigateToVertex( final V vertex )
 		final double[] target = navigationBehaviour.navigateToVertex( vertex, currentTransform );
 		if ( target != null )
 		{
-			final TranslationAnimator animator = new TranslationAnimator( currentTransform, target, 300 );
-			animator.setTime( System.currentTimeMillis() );
+			final TranslationAnimator animator = new TranslationAnimator( currentTransform, target, ANIMATION_DURATION );
+			lastNavigationTime = System.currentTimeMillis();
+			animator.setTime( lastNavigationTime );
 			panel.setTransformAnimator( animator );
 		}
-
 		panel.requestRepaint();
 	}
 
 	@Override
 	public void navigateToEdge( final E edge )
 	{
+		if ( shouldThrottle() )
+			return; // Throttle navigation requests.
+
 		// Always move in T.
 		final V ref = graph.vertexRef();
 		final int tp = edge.getTarget( ref ).getTimepoint();
@@ -111,14 +121,21 @@ public void navigateToEdge( final E edge )
 		final double[] target = navigationBehaviour.navigateToEdge( edge, currentTransform );
 		if ( target != null )
 		{
-			final TranslationAnimator animator = new TranslationAnimator( currentTransform, target, 300 );
-			animator.setTime( System.currentTimeMillis() );
+			final TranslationAnimator animator = new TranslationAnimator( currentTransform, target, ANIMATION_DURATION );
+			lastNavigationTime = System.currentTimeMillis();
+			animator.setTime( lastNavigationTime );
 			panel.setTransformAnimator( animator );
 		}
 
 		panel.requestRepaint();
 	}
 
+	private boolean shouldThrottle()
+	{
+		final long now = System.currentTimeMillis();
+		return ( now - lastNavigationTime < ANIMATION_DURATION );
+	}
+
 	/*
 	 * Navigation behaviours
 	 */
diff --git a/src/main/java/org/mastodon/views/grapher/display/DataDisplayFrame.java b/src/main/java/org/mastodon/views/grapher/display/DataDisplayFrame.java
index 4ac5060e1..16d98ba38 100644
--- a/src/main/java/org/mastodon/views/grapher/display/DataDisplayFrame.java
+++ b/src/main/java/org/mastodon/views/grapher/display/DataDisplayFrame.java
@@ -63,13 +63,13 @@
 import org.mastodon.views.grapher.datagraph.ScreenTransform;
 import org.scijava.ui.behaviour.MouseAndKeyHandler;
 
-public class DataDisplayFrame< V extends Vertex< E > & HasTimepoint & HasLabel, E extends Edge< V > > extends ViewFrame
+public class DataDisplayFrame< V extends Vertex< E > & HasTimepoint & HasLabel, E extends Edge< V > > extends ViewFrame implements Plotable
 {
 	private static final long serialVersionUID = 1L;
 
 	private final DataDisplayPanel< V, E > dataDisplayPanel;
 
-	private final GrapherSidePanel sidePanel;
+	private final GrapherSidePanel<V, E> sidePanel;
 
 	private final FeatureModel featureModel;
 
@@ -116,7 +116,7 @@ public DataDisplayFrame(
 		 * Side panel.
 		 */
 
-		sidePanel = new GrapherSidePanel( nSources, contextChooser );
+		sidePanel = new GrapherSidePanel<>( nSources, contextChooser );
 		sidePanel.getBtnPlot().addActionListener( e -> plot( false ) );
 
 		final FeatureModelListener featureModelListener = () -> sidePanel.setFeatures(
@@ -183,7 +183,7 @@ public DataDisplayPanel< V, E > getDataDisplayPanel()
 		return dataDisplayPanel;
 	}
 
-	public GrapherSidePanel getVertexSidePanel()
+	public GrapherSidePanel<V, E> getVertexSidePanel()
 	{
 		return sidePanel;
 	}
@@ -194,8 +194,10 @@ public GrapherSidePanel getVertexSidePanel()
 	 */
 	public void plot( boolean keepCurrentScreenTransform )
 	{
-		dataDisplayPanel.plot( sidePanel.getGraphConfig(), featureModel,
-				keepCurrentScreenTransform ? dataDisplayPanel.getScreenTransform().get() : null );
+		if ( keepCurrentScreenTransform )
+			plot( dataDisplayPanel.getScreenTransform().get() );
+		else
+			plot( null );
 	}
 
 	public void plot( final ScreenTransform transform )
diff --git a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
index af6ff2f1f..5e5440aeb 100644
--- a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
+++ b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
@@ -56,6 +56,8 @@
 import org.mastodon.feature.FeatureProjectionSpec;
 import org.mastodon.feature.FeatureSpec;
 import org.mastodon.feature.Multiplicity;
+import org.mastodon.graph.Edge;
+import org.mastodon.graph.Vertex;
 import org.mastodon.graph.io.RawGraphIO.FileIdToGraphMap;
 import org.mastodon.mamut.feature.MamutRawFeatureModelIO;
 import org.mastodon.mamut.io.project.MamutProject;
@@ -68,16 +70,17 @@
 import org.mastodon.ui.util.EverythingDisablerAndReenabler;
 import org.mastodon.util.FeatureUtils;
 import org.mastodon.views.context.ContextChooser;
+import org.mastodon.views.context.HasContextChooser;
 import org.mastodon.views.grapher.display.FeatureGraphConfig.GraphDataItemsSource;
 import org.scijava.Context;
 
 /**
  * Panel that lets the user specifies what to plot. The user specifications are
  * bundled as a {@link FeatureGraphConfig} object.
- * 
+ *
  * @author Jean-Yves Tinevez
  */
-public class GrapherSidePanel extends JPanel
+public class GrapherSidePanel< V extends Vertex< E >, E extends Edge< V > > extends JPanel implements HasContextChooser< V >
 {
 
 	private static final long serialVersionUID = 1L;
@@ -102,10 +105,13 @@ public class GrapherSidePanel extends JPanel
 
 	private final JButton btnPlot;
 
-	public GrapherSidePanel( final int nSources, final ContextChooser< ? > contextChooser )
+	private final ContextChooser< V > contextChooser;
+
+	public GrapherSidePanel( final int nSources, final ContextChooser< V > contextChooser )
 	{
 		this.nSources = nSources;
 		this.specs = new ArrayList<>();
+		this.contextChooser = contextChooser;
 
 		final GridBagLayout gridBagLayout = new GridBagLayout();
 		gridBagLayout.columnWidths = new int[] { 150, 0 };
@@ -261,7 +267,7 @@ public GrapherSidePanel( final int nSources, final ContextChooser< ? > contextCh
 
 	/**
 	 * Exposes the plot button of this panel.
-	 * 
+	 *
 	 * @return the plot button.
 	 */
 	public JButton getBtnPlot()
@@ -430,6 +436,11 @@ public FeatureProjectionSpec getFeatureProjectionSpec( final String projectionKe
 		return null;
 	}
 
+	public ContextChooser< V > getContextChooser()
+	{
+		return this.contextChooser;
+	}
+
 	private static final FeatureModel demoFM()
 	{
 		final Model model = new Model();
@@ -463,7 +474,7 @@ public static void main( final String[] args ) throws ClassNotFoundException, In
 				FeatureUtils.collectFeatureMap( fm, Spot.class );
 		final Map< FeatureSpec< ?, Link >, Feature< Link > > linkFeatures =
 				FeatureUtils.collectFeatureMap( fm, Link.class );
-		final GrapherSidePanel gsp = new GrapherSidePanel( 2, new ContextChooser<>( null ) );
+		final GrapherSidePanel<Spot, Link> gsp = new GrapherSidePanel<Spot, Link>( 2, new ContextChooser<>( null ) );
 		gsp.setFeatures( spotFeatures, linkFeatures );
 
 		final JFrame frame = new JFrame( "Grapher side panel" );
diff --git a/src/main/java/org/mastodon/views/grapher/display/Plotable.java b/src/main/java/org/mastodon/views/grapher/display/Plotable.java
new file mode 100644
index 000000000..a23073969
--- /dev/null
+++ b/src/main/java/org/mastodon/views/grapher/display/Plotable.java
@@ -0,0 +1,10 @@
+package org.mastodon.views.grapher.display;
+
+import org.mastodon.views.grapher.datagraph.ScreenTransform;
+
+public interface Plotable
+{
+	void plot( final ScreenTransform screenTransform );
+
+	void plot( final boolean keepCurrentScreenTransform );
+}

From 49fe757a19af1e94508efc9d08a377675a8882fe Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:53:21 +0200
Subject: [PATCH 07/13] Update parent pom to pom-scijava v42.0.0

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 4db071598..e0662434e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>40.0.0</version>
+		<version>42.0.0</version>
 	</parent>
 
 	<groupId>org.mastodon</groupId>

From c3955a406ebf87226c66d7cd2d7528a01240008c Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:53:52 +0200
Subject: [PATCH 08/13] Fix compile errors with new N5 version.

---
 .../util/mobie/OmeZarrMultiscalesAdapter.java |  1 -
 .../mamut/launcher/NewFromUrlPanel.java       | 29 +++++++------------
 2 files changed, 11 insertions(+), 19 deletions(-)

diff --git a/src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java b/src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java
index 3cb0fcd26..91fd7b11c 100644
--- a/src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java
+++ b/src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java
@@ -45,7 +45,6 @@
 public class OmeZarrMultiscalesAdapter implements JsonDeserializer< OmeZarrMultiscales >, JsonSerializer< OmeZarrMultiscales >
 {
 
-	@SuppressWarnings( "serial" )
 	@Override
     public OmeZarrMultiscales deserialize( final JsonElement json, final Type typeOfT, final JsonDeserializationContext context ) throws JsonParseException
     {
diff --git a/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java b/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
index f99b6a26c..0a1a1f52b 100644
--- a/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
+++ b/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -66,7 +66,7 @@
 import org.janelia.saalfeldlab.n5.metadata.N5ViewerMultichannelMetadata;
 import org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
-import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
@@ -404,21 +404,14 @@ public N5Reader apply( final String n5UriOrPath )
 			String rootPath = null;
 			if ( n5UriOrPath.contains( "?" ) )
 			{
-				try
-				{
-					// need to strip off storage format for n5uri to correctly
-					// remove query;
-					final Pair< StorageFormat, URI > fmtUri = N5Factory.StorageFormat.parseUri( n5UriOrPath );
-					final StorageFormat format = fmtUri.getA();
-
-					final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
-					// add the format prefix back if it was present
-					rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
-				}
-				catch ( final URISyntaxException e )
-				{
-					messenger.accept( "The URI is not valid or credentials are missing: " + n5UriOrPath );
-				}
+				// need to strip off storage format for n5uri to correctly
+				// remove query;
+				final Pair< StorageFormat, URI > fmtUri = StorageFormat.parseUri( n5UriOrPath );
+				final StorageFormat format = fmtUri.getA();
+
+				final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
+				// add the format prefix back if it was present
+				rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
 			}
 
 			if ( rootPath == null )

From 517f0942be238197861f5dab8c2ec72c4afad1fe Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:54:23 +0200
Subject: [PATCH 09/13] Fix minor warnings.

---
 .../mamut/views/grapher/MamutViewGrapher.java     |  1 -
 .../views/grapher/display/GrapherSidePanel.java   |  7 ++++---
 .../graph/revised/CreateLargeModelExample.java    | 15 +++++----------
 3 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
index 14b594c53..9c992e3ed 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java
@@ -43,7 +43,6 @@
 import org.mastodon.ui.coloring.GraphColorGeneratorAdapter;
 import org.mastodon.ui.coloring.HasColorBarOverlay;
 import org.mastodon.ui.coloring.HasColoringModel;
-import org.mastodon.ui.commandfinder.CommandFinder;
 import org.mastodon.ui.keymap.KeyConfigContexts;
 import org.mastodon.views.context.ContextChooser;
 import org.mastodon.views.context.HasContextChooser;
diff --git a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
index 5e5440aeb..6e91e0407 100644
--- a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
+++ b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -275,7 +275,7 @@ public JButton getBtnPlot()
 		return btnPlot;
 	}
 
-	public < V, E > void setFeatures(
+	public void setFeatures(
 			final Map< FeatureSpec< ?, V >, Feature< V > > vertexFeatures,
 			final Map< FeatureSpec< ?, E >, Feature< E > > edgeFeatures )
 	{
@@ -436,6 +436,7 @@ public FeatureProjectionSpec getFeatureProjectionSpec( final String projectionKe
 		return null;
 	}
 
+	@Override
 	public ContextChooser< V > getContextChooser()
 	{
 		return this.contextChooser;
diff --git a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
index c223ad4c0..b56967942 100644
--- a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
+++ b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
@@ -30,15 +30,10 @@
 
 import java.io.IOException;
 
-import org.mastodon.mamut.ProjectModel;
-import org.mastodon.mamut.WindowManager;
 import org.mastodon.mamut.io.importer.ModelImporter;
-import org.mastodon.mamut.io.project.MamutProject;
 import org.mastodon.mamut.model.Link;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.views.bdv.SharedBigDataViewerData;
-import org.scijava.Context;
 
 public class CreateLargeModelExample
 {
@@ -184,11 +179,11 @@ public static void main( final String[] args ) throws IOException
 				( Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory() ) / 1e6d ) );
 
 
-		final Context context = new Context();
-		final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
-		final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
-		final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project  );
-		final WindowManager wm = new WindowManager( appModel  );
+//		final Context context = new Context();
+//		final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
+//		final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
+//		final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project  );
+//		final WindowManager wm = new WindowManager( appModel  );
 
 //		start = System.currentTimeMillis();
 //		wm.createBigDataViewer();

From bb861f4bfbb415bff70caab26700e39ead2ed29f Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:54:33 +0200
Subject: [PATCH 10/13] Update test drive path.

---
 .../java/org/mastodon/StartMastodonDefaultProject.java    | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/test/java/org/mastodon/StartMastodonDefaultProject.java b/src/test/java/org/mastodon/StartMastodonDefaultProject.java
index 541b7a434..971b91da0 100644
--- a/src/test/java/org/mastodon/StartMastodonDefaultProject.java
+++ b/src/test/java/org/mastodon/StartMastodonDefaultProject.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -34,8 +34,8 @@ public class StartMastodonDefaultProject
 	public static void main( final String[] args )
 	{
 //		final String projectPath = "samples/MaMuT_Parhyale_small.mastodon";
-//		final String projectPath = "/Users/tinevez/Google Drive/Mastodon/Datasets/Remote/ParhyaleHawaiensis/MaMuT_Parhyale_demo-mamut.mastodon";
-		final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
+		final String projectPath = "/Users/tinevez/Library/CloudStorage/GoogleDrive-jeanyves.tinevez@gmail.com/My Drive/Mastodon/Datasets/Remote/BDV/Tribolium/CTC_TRIF_trainingVideo02_jy-GT-done.mastodon";
+//		final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
 //		final String projectPath = "samples/drosophila_crop.mastodon";
 		StartMastodonOnProject.launch( projectPath );
 	}

From 6ed9ea6ee6f4d4b6f732c014c7cc74b2cb8b5580 Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:56:14 +0200
Subject: [PATCH 11/13] Repository to store script examples.

---
 scripts/MastodonScriptExample.py | 77 ++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100755 scripts/MastodonScriptExample.py

diff --git a/scripts/MastodonScriptExample.py b/scripts/MastodonScriptExample.py
new file mode 100755
index 000000000..93728377b
--- /dev/null
+++ b/scripts/MastodonScriptExample.py
@@ -0,0 +1,77 @@
+#@ Context context
+
+from java.io import File
+
+from org.mastodon.mamut import WindowManager
+from org.mastodon.mamut.project import MamutProject
+from org.mastodon.tracking.mamut.trackmate import TrackMate
+from org.mastodon.tracking.mamut.trackmate import Settings
+from org.mastodon.tracking.mamut.detection import DoGDetectorMamut
+from org.mastodon.tracking.mamut.linking import SimpleSparseLAPLinkerMamut
+from org.mastodon.tracking.linking import LinkingUtils
+
+bdv_file = "/Users/tinevez/Development/Mastodon/mastodon/samples/datasethdf5.xml"
+project = MamutProject( None, File( bdv_file ) );
+
+# Open the project.
+wm = WindowManager( context )
+wm.getProjectManager().open( project )
+app_model = wm.getAppModel()
+
+# Get Mastodon model.
+model = app_model.getModel()
+selection_model = app_model.getSelectionModel()
+
+# Get image data.
+image_data = app_model.getSharedBdvData()
+
+# Configure TrackMate.
+
+# Detector settings.
+detector_settings = {
+	"MIN_TIMEPOINT" : 0,
+	"MAX_TIMEPOINT" : 1000,
+	"SETUP" : 0, 				# The channel or source in the BDV data.
+	"RADIUS" : 7., 			# The cell expected radius.
+	"THRESHOLD" : 200.	 		# Threshold on quality.
+}
+
+# Linker settings. There are too many, so we take the default and edit it.
+linker_settings = LinkingUtils.getDefaultLAPSettingsMap()
+linker_settings[ "MIN_TIMEPOINT" ] = 0
+linker_settings[ "MAX_TIMEPOINT" ] = 1000
+linker_settings[ "LINKING_MAX_DISTANCE" ] = 10.
+linker_settings[ "ALLOW_GAP_CLOSING" ] = True
+linker_settings[ "MAX_FRAME_GAP" ] = 2 
+
+# Create the settings objects.
+settings = Settings() \
+		.sources( image_data.getSources() ) \
+		.detector( DoGDetectorMamut ) \
+		.detectorSettings( detector_settings ) \
+		.linker( SimpleSparseLAPLinkerMamut ) \
+		.linkerSettings( linker_settings )
+
+trackmate = TrackMate( settings, model, selection_model )
+
+# We need to give a context to TrackMate.
+trackmate.setContext( context )
+
+# Run TrackMate.
+trackmate.run()
+if trackmate.isCanceled():
+	print( "Calculation was canceled. Reason: " + trackmate.getCancelReason() )
+elif not trackmate.isSuccessful():
+	print( "Calculation failed with error message:\n" + trackmate.getErrorMessage() )
+else:
+	print( "Calculation complete." );
+
+wm.createTrackScheme()
+wm.createBigDataViewer()
+
+# Compute features.
+
+
+
+
+wm.createTable( False )

From d9bb718f0c550def6951fc732b1bb0e96e19bd4b Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:57:06 +0200
Subject: [PATCH 12/13] Update license blurbs

---
 .../CommonTrackMateFeatureDeclarations.java   | 28 +++++++++++++++++++
 .../mamut/launcher/NewFromUrlPanel.java       |  4 +--
 .../mamut/views/grapher/GrapherGuiState.java  |  4 +--
 .../MamutBranchViewGrapherFactory.java        |  4 +--
 .../grapher/MamutViewGrapherFactory.java      |  4 +--
 .../grapher/display/GrapherSidePanel.java     |  4 +--
 .../views/grapher/display/Plotable.java       | 28 +++++++++++++++++++
 .../mastodon/StartMastodonDefaultProject.java |  4 +--
 .../revised/CreateLargeModelExample.java      |  4 +--
 9 files changed, 70 insertions(+), 14 deletions(-)

diff --git a/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java b/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
index 5aac6f5cc..b2dcb5389 100644
--- a/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
+++ b/src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java
@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package org.mastodon.mamut.io.importer.trackmate;
 
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;
diff --git a/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java b/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
index 0a1a1f52b..2e265716c 100644
--- a/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
+++ b/src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java b/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
index 9fd0a3bf8..d6af79d9e 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/GrapherGuiState.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
index b95fdfa0d..591a3028f 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapherFactory.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
index e6836fba0..9aefbcc63 100644
--- a/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
+++ b/src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapherFactory.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
index 6e91e0407..5ce4158b6 100644
--- a/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
+++ b/src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/main/java/org/mastodon/views/grapher/display/Plotable.java b/src/main/java/org/mastodon/views/grapher/display/Plotable.java
index a23073969..f77780cb4 100644
--- a/src/main/java/org/mastodon/views/grapher/display/Plotable.java
+++ b/src/main/java/org/mastodon/views/grapher/display/Plotable.java
@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package org.mastodon.views.grapher.display;
 
 import org.mastodon.views.grapher.datagraph.ScreenTransform;
diff --git a/src/test/java/org/mastodon/StartMastodonDefaultProject.java b/src/test/java/org/mastodon/StartMastodonDefaultProject.java
index 971b91da0..27b92cacd 100644
--- a/src/test/java/org/mastodon/StartMastodonDefaultProject.java
+++ b/src/test/java/org/mastodon/StartMastodonDefaultProject.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
diff --git a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
index b56967942..358d35f55 100644
--- a/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
+++ b/src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java
@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

From f0b7564f26cb9fcb5ef11e8ca131fbca6c111a6b Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 8 Sep 2025 16:59:10 +0200
Subject: [PATCH 13/13] Bump to next development cycle

Signed-off-by: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index e0662434e..12f04e6bc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -10,7 +10,7 @@
 
 	<groupId>org.mastodon</groupId>
 	<artifactId>mastodon</artifactId>
-	<version>1.0.0-beta-35-SNAPSHOT</version>
+	<version>1.0.0-beta-36-SNAPSHOT</version>
 
 	<name>Mastodon</name>
 	<description>Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.</description>