Import spots from label images

.ci/settings.xml

@@ -0,0 +1,6 @@
+<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 https://maven.apache.org/xsd/settings-1.0.0.xsd">
+    <activeProfiles>
+        <activeProfile>build</activeProfile>
+    </activeProfiles>
+</settings>

.github/workflows/sonarcloud.yml

@@ -50,7 +50,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} # Generate a token on Sonarcloud.io, add it to the secrets of this repo with the name SONAR_TOKEN (Settings > Secrets > Actions > add new repository secret)
-          MAVEN_OPTS: -Xmx4096m
         run: |
           export DISPLAY=:99
           sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &

README.md

@@ -17,6 +17,8 @@
 * [Lineage Tree Classification](#lineage-tree-classification)
   * [Parameters](#parameters)
   * [Example](#example)
+* [Imports](#imports)
+  * [Import Spots from Label Image](#import-spots-from-label-image)
 * [Exports](#exports)
   * [Label Image Exporter](#label-image-exporter)
   * [GraphML Exporter](#graphml-exporter)
@@ -215,6 +217,85 @@ Tree2
 * The resulting tag set used for coloring the track scheme branch
   view. ![Trackscheme Branch View with tags](doc/deep_lineage/lineage_classification/trackscheme_branch_with_tags.png)
 
+## Imports
+
+### Import Spots from Label Image
+
+* You can use the plugin to import spots from a label image representing an instance segmentation into Mastodon. This
+  may be useful if you have an instance segmentation of cells or other objects, and you want to track them using
+  Mastodon.
+* The label image is expected to contain the spot ids as pixel values.
+* The label image is expected to have the same dimensions as the image data in Mastodon.
+* Labels are processed frame by frame.
+* Multiple blobs with the same id in the same frame are considered to belong to the same spot by this importer. It is
+  advised to use a unique ids for spots in the same frame.
+* The resulting spots are ellipsoids with the semi axes computed from the variance covariance matrix of this pixel
+  positions of each label.
+* The resulting spots may be linked using the linker plugin in Mastodon (`Plugins > Tracking > Linking...`)
+  or [Elephant](https://elephant-track.github.io/#/?id=linking-workflow).
+
+#### Parameters
+
+* Ellipsoid scaling factor: The scaling factor to apply to the ellipsoids. The default is 1.0. The scaling factor is
+  applied to the semi axes of the ellipsoids. The ellipsoid scaling factor can be used to increase (>1) or decrease (
+  <1) the size of the resulting ellipsoid. 1 is equivalent of ellipsoids drawn at 2.2σ.
+* Link spots having the same id in consecutive frames: If checked, spots with the same id in consecutive frames are
+  linked.
+
+#### Instance segmentation as active image in ImageJ
+
+* The label image can be opened in ImageJ and the plugin can be called from the
+  menu: ![Plugin Import Menu](doc/deep_lineage/import/label_image/imagej/plugin_import_imagej_menu.png)
+* Please make sure that the label image is the active image in ImageJ.
+* Please make sure that the label image has the same dimensions as the image data in Mastodon.
+  * You can use the `Image > Properties` command ImageJ to check (and) set the dimensions of the label image.
+
+##### Example
+
+* Example
+  dataset: [Fluo-C3DL-MDA231 from Cell Tracking Challenge](http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DL-MDA231.zip)
+  * Extract the file to a folder named `Fluo-C3DL-MDA231`
+  * Import the image sequence with the actual image into ImageJ contained in folder `Fluo-C3DL-MDA231/01/`
+    * `File > Import > Image Sequence...`
+  * Set the dimensions of the image sequence to 512x512x1x30x12 (XYCTZ) using `Image > Properties`
+  * ![plugin_import_example_1.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_1.png)
+  * Open Mastodon from Fiji and create a new project with the image sequence
+    * `Plugins > Mastodon > new Mastodon project > Use an image opened in ImageJ > Create`
+    * ![plugin_import_example_2.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_2.png)
+  * Import the image sequence encoding the label images into ImageJ contained in folder: `Fluo-C3DL-MDA231/01_ERR_SEG/`
+  * Set the dimensions of the label image to 512x512x1x30x12 (XYCTZ) using `Image > Properties`
+    * ![plugin_import_example_3.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_3.png)
+  * Open Import window in Mastodon: `Plugins > Imports > Import spots from label image > Import spots from ImageJ image`
+  * Click `OK` and the spots are imported into Mastodon.
+    * ![plugin_import_example_4.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_4.png)
+
+#### Instance segmentation as BDV channel
+
+* The plugin can be called from the
+  menu: ![Plugin Import Menu](doc/deep_lineage/import/label_image/imagej/plugin_import_imagej_menu.png)
+
+##### Example
+
+* Example
+  dataset: [Fluo-C3DL-MDA231 from Cell Tracking Challenge](http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DL-MDA231.zip)
+  * Extract the file to a folder named `Fluo-C3DL-MDA231`
+  * Import the image sequence with the actual image into ImageJ contained in folder `Fluo-C3DL-MDA231/01/`
+    * `File > Import > Image Sequence...`
+  * Set the dimensions of the image sequence to 512x512x1x30x12 (XYCTZ) using `Image > Properties`
+  * ![plugin_import_example_1.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_1.png)
+  * Import the image sequence encoding the label images into ImageJ contained in folder: `Fluo-C3DL-MDA231/01_ERR_SEG/`
+  * Set the dimensions of the label image to 512x512x1x30x12 (XYCTZ) using `Image > Properties`
+    * ![plugin_import_example_3.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_3.png)
+  * Merge the 2 images into a single image using the `Image > Color > Merge Channels...` command
+    * ![plugin_import_example_5.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_5.png)
+  * Open Mastodon from Fiji and create a new project with merged image
+    * `Plugins > Mastodon > new Mastodon project > Use an image opened in ImageJ > Create`
+    * ![plugin_import_example_6.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_6.png)
+  * Open Import window: `Plugins > Imports > Import spots from label image > Import spots from BDV channel`
+  * Select the BDV channel containing the label image
+  * Click `OK` and the spots are imported into Mastodon.
+    * ![plugin_import_example_7.png](doc/deep_lineage/import/label_image/imagej/plugin_import_example_7.png)
+
 ## Exports
 
 ### Label Image Exporter

pom.xml

@@ -19,7 +19,7 @@
         <license.organizationName>Mastodon authors</license.organizationName>
         <license.copyrightOwners>Stefan Hahmann</license.copyrightOwners>
 
-        <mastodon.version>1.0.0-beta-29</mastodon.version>
+        <mastodon.version>1.0.0-beta-30-SNAPSHOT</mastodon.version>
         <mastodon.group>org.mastodon</mastodon.group>
         <!-- with pom-scijava >= 37.1.0, this can be removed again -->
         <scijava-common.version>2.97.1</scijava-common.version>
@@ -201,15 +201,13 @@
             <id>build</id>
             <build>
                 <plugins>
-                    <!-- Configure the maven-surefire-plugin to use a larger heap size while running tests. -->
-                    <!-- This is necessary for the tests to run, since there is a memory leak in mastodon. -->
-                    <!-- Can be removed after https://github.com/mastodon-sc/mastodon/issues/225 has been resolved -->
+                    <!-- Configure the maven-surefire-plugin to use a heap size of 1gb while running tests. -->
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-surefire-plugin</artifactId>
                         <version>3.1.0</version>
                         <configuration>
-                            <argLine>-Xmx4096m</argLine>
+                            <argLine>-Xmx1g</argLine>
                         </configuration>
                     </plugin>
                 </plugins>
@@ -219,6 +217,15 @@
             <id>coverage</id>
             <build>
                 <plugins>
+                    <!-- Configure the maven-surefire-plugin to use a heap size of 1gb while running tests for jacoco coverage analysis. -->
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <version>3.1.0</version>
+                        <configuration>
+                            <argLine>@{argLine} -Xmx1g</argLine>
+                        </configuration>
+                    </plugin>
                     <plugin>
                         <groupId>org.jacoco</groupId>
                         <artifactId>jacoco-maven-plugin</artifactId>

src/main/java/org/mastodon/mamut/io/importer/labelimage/ImportSpotsFromLabelImagePlugin.java

@@ -0,0 +1,80 @@
+package org.mastodon.mamut.io.importer.labelimage;
+
+import org.mastodon.app.ui.ViewMenuBuilder;
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.io.importer.labelimage.ui.ImportSpotsFromImgPlusView;
+import org.mastodon.mamut.plugin.MamutPlugin;
+import org.mastodon.mamut.io.importer.labelimage.ui.ImportSpotsFromBdvChannelView;
+import org.scijava.command.CommandService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.ui.behaviour.util.AbstractNamedAction;
+import org.scijava.ui.behaviour.util.Actions;
+import org.scijava.ui.behaviour.util.RunnableAction;
+
+import java.util.Collections;
+import java.util.List;
+
+import static org.mastodon.app.ui.ViewMenuBuilder.item;
+import static org.mastodon.app.ui.ViewMenuBuilder.menu;
+
+@SuppressWarnings( "unused" )
+@Plugin( type = MamutPlugin.class )
+public class ImportSpotsFromLabelImagePlugin implements MamutPlugin
+{
+	private static final String IMPORT_SPOTS_FROM_IMAGEJ = "Import spots from ImageJ image";
+
+	private static final String IMPORT_SPOTS_FROM_BDV_CHANNEL = "Import spots from BDV channel";
+
+	private static final String[] SHORT_CUTS = { "not mapped" };
+
+	private final AbstractNamedAction imageJImport;
+
+	private final AbstractNamedAction bdvChannelImport;
+
+	private ProjectModel appModel;
+
+	@SuppressWarnings( "unused" )
+	@Parameter
+	private CommandService commandService;
+
+	@SuppressWarnings( "unused" )
+	public ImportSpotsFromLabelImagePlugin()
+	{
+		imageJImport = new RunnableAction( IMPORT_SPOTS_FROM_IMAGEJ, this::importSpotsFromImageJ );
+		bdvChannelImport = new RunnableAction( IMPORT_SPOTS_FROM_BDV_CHANNEL, this::importSpotsFromBdvChannel );
+	}
+
+	@Override
+	public void setAppPluginModel( final ProjectModel appPluginModel )
+	{
+		this.appModel = appPluginModel;
+	}
+
+	@Override
+	public List< ViewMenuBuilder.MenuItem > getMenuItems()
+	{
+		return Collections.singletonList(
+				menu( "Plugins", menu( "Imports",
+						menu( "Import spots from label image", item( IMPORT_SPOTS_FROM_IMAGEJ ),
+								item( IMPORT_SPOTS_FROM_BDV_CHANNEL ) ) ) ) );
+	}
+
+	@Override
+	public void installGlobalActions( Actions actions )
+	{
+		actions.namedAction( imageJImport, SHORT_CUTS );
+		actions.namedAction( bdvChannelImport, SHORT_CUTS );
+	}
+
+	private void importSpotsFromImageJ()
+	{
+		commandService.run( ImportSpotsFromImgPlusView.class, true, "projectModel", appModel );
+	}
+
+	private void importSpotsFromBdvChannel()
+	{
+		commandService.run( ImportSpotsFromBdvChannelView.class, true, "projectModel", appModel );
+	}
+
+}