initial version

.gitignore

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+## Maven ##
+/target/
+
+## Eclipse ##
+/.classpath
+/.project
+/.settings/
+
+## Interactive tests ##
+/samples/
+
+## IntelliJ
+/.idea/
+*.iml

README.md

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+TrackMate-clij2
+===============
+
+A [clij2](https://clij.github.io) plugin for [TrackMate](https://imagej.net/plugins/trackmate/).
+
+![img.png](docs/trackmate_clij2_screenhot.png)
+
+This plugin was inspired by [TrackMate-Examples](https://github.com/fiji/TrackMate-examples), [TrackMate-MorpholibJ](https://github.com/tinevez/TrackMate-MorphoLibJ) and [TrackMate-StarDist](https://github.com/tinevez/TrackMate-StarDist) 
+and this [preprint by Dimitry Ershov](https://www.biorxiv.org/content/10.1101/2021.09.03.458852v1.full).
+
+# Installation
+
+* Download and install [Fiji](https://fiji.sc/Downloads)
+* Install [clij](https://clij.github.io/clij2-docs/installationInFiji)
+
+# Usage
+
+* Open a dataset and start TrackMate from the `Plugins > Tracking` menu.
+* In the 2nd step (Select Detector), choose `CLIJ2 Voronoi Otsu Labeling`.
+
+![img.png](docs/choose_clij2.png)
+
+* When configuring the detector, enter `spot-sigma` to fine-tune how close objects can be and `outline_sigma` to control how precise outlines are. 
+  Read more in the [Voronoi-Otsu-Labeling tutorial]
+
+![img.png](docs/config_detector.png)
+
+* Wait a moment :-)
+
+![img.png](docs/wait_detection.png)
+
+* In further processing, it is recommended to filter detected spots by their area.
+
+![img.png](docs/filter_spots_by_area.png)
+
+* Therefore, it might be helpful to change the visualization by adapting the maximum shown area. This makes objects better visible that stick to each other.
+
+![img.png](docs/visualize_area.png)
+
+* For tracking, the overlap tracker is recommended.
+
+![img.png](docs/choose_overlap_tracker.png)
+
+* For visualization, select 'Show tracks local in time'.
+![img_1.png](docs/visualize_spots_int_time.png)
+
+## Feedback and support
+CLIJ is developed in the open because we believe in the open source community. 
+See our [community guidelines](https://clij.github.io/clij2-docs/community_guidelines). 
+Feel free to drop feedback or ask questions via [image.sc](https://image.sc). 
+
+[Imprint](https://clij.github.io/imprint)

install.bat

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+mvn clean -DskipTests=true install -Dgpg.skip

pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+		http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>net.haesleinhuepf</groupId>
+		<artifactId>clij-parent-pom</artifactId>
+		<version>2.5.1.1</version>
+		<relativePath />
+	</parent>
+
+	<groupId>net.haesleinhuepf</groupId>
+	<artifactId>TrackMate_clij2</artifactId>
+	<version>2.5.1.1</version>
+
+	<name>TrackMate clij2 bridge</name>
+	<description>A clij2 detector plugin for TrackMate</description>
+	<url>https://imagej.net/TrackMate_examples</url>
+	<inceptionYear>2014</inceptionYear>
+	<organization>
+		<name>Fiji</name>
+		<url>https://fiji.sc/</url>
+	</organization>
+	<licenses>
+		<license>
+			<name>GNU General Public License v3+</name>
+			<url>https://www.gnu.org/licenses/gpl.html</url>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<developers>
+		<developer>
+			<id>haesleinhuepf</id>
+			<name>Robert Haase</name>
+			<url>https://haesleinhuepf.net</url>
+			<organization>DFG Cluster of Excellence Physics of Life, TU Dresden</organization>
+			<roles>
+				<role>founder</role>
+				<role>lead</role>
+				<role>developer</role>
+				<role>debugger</role>
+				<role>reviewer</role>
+				<role>support</role>
+				<role>maintainer</role>
+			</roles>
+		</developer>
+	</developers>
+	<contributors>
+		<contributor>
+			<name>none</name>
+		</contributor>
+	</contributors>
+
+	<mailingLists>
+		<mailingList>
+			<name>Image.sc Forum</name>
+			<archive>https://forum.image.sc/tags/fiji</archive>
+		</mailingList>
+	</mailingLists>
+
+	<scm>
+		<connection>scm:git:git://github.com/clij/TrackMate-clij2</connection>
+		<developerConnection>scm:git:git@github.com:clij/TrackMate-clij2</developerConnection>
+		<tag>HEAD</tag>
+		<url>scm:git:git@github.com:clij/TrackMate-clij2</url>
+	</scm>
+	<issueManagement>
+		<system>GitHub Issues</system>
+		<url>scm:git:git@github.com:clij/TrackMate-clij2/issues</url>
+	</issueManagement>
+	<ciManagement>
+		<system>GitHub Actions</system>
+		<url>https://github.com/clij/TrackMate-clij2/actions</url>
+	</ciManagement>
+
+	<properties>
+		<package-name>net.haesleinhuepf</package-name>
+		<license.licenseName>bsd_3</license.licenseName>
+		<license.copyrightOwners>Robert Haase, MPI CBG</license.copyrightOwners>
+		<scijava.app.directory>C:/programs/fiji-win64/Fiji.app/</scijava.app.directory>
+	</properties>
+
+	<repositories>
+		<repository>
+			<id>scijava.public</id>
+			<url>https://maven.scijava.org/content/groups/public</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<!-- Fiji dependencies -->
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>TrackMate</artifactId>
+			<version>7.0.3</version>
+		</dependency>
+
+		<!-- ImageJ dependencies -->
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>ij</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej-common</artifactId>
+		</dependency>
+
+		<!-- ImgLib2 dependencies -->
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2</artifactId>
+		</dependency>
+
+		<!-- SciJava dependencies -->
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-common</artifactId>
+		</dependency>
+
+		<!-- CLIJ dependencies -->
+		<dependency>
+			<groupId>net.haesleinhuepf</groupId>
+			<artifactId>clij2_</artifactId>
+		</dependency>
+	</dependencies>
+</project>

src/main/java/plugin/trackmate/clij2/CLIJ2VoronoiOtsuLabelingDetector.java

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+package plugin.trackmate.clij2;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import fiji.plugin.trackmate.util.TMUtils;
+import ij.ImagePlus;
+import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
+import net.haesleinhuepf.clij2.CLIJ2;
+import net.imagej.ImgPlus;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.detection.SpotDetector;
+import fiji.plugin.trackmate.detection.LabelImageDetector;
+
+
+public class CLIJ2VoronoiOtsuLabelingDetector< T extends RealType< T > & NativeType< T >> implements SpotDetector< T >
+{
+	private final static String BASE_ERROR_MESSAGE = "CLIJ2 Voronoi-Otsu-Labeling Detector: ";
+
+	protected final Interval interval;
+
+	/** The frame we operate in. */
+	private final int frame;
+	private final double outline_sigma;
+	private final double spot_sigma;
+	private final ImgPlus<T> img;
+
+	/** Holder for the results of detection. */
+	private List< Spot > spots;
+
+	/** Error message holder. */
+	private String errorMessage;
+
+	/** Holder for the processing time. */
+	private long processingTime;
+
+	/*
+	 * CONSTRUCTOR
+	 */
+
+	public CLIJ2VoronoiOtsuLabelingDetector(final ImgPlus< T > img, final Interval interval, double spot_sigma, double outline_sigma, final int frame )
+	{
+		this.img = img;
+
+		// Take the ROI box from the interval parameter.
+		this.interval = interval;
+
+		this.spot_sigma = spot_sigma;
+		this.outline_sigma = outline_sigma;
+
+		// We need to know what frame we are in.
+		this.frame = frame;
+	}
+
+	/*
+	 * METHODS
+	 */
+
+	@Override
+	public List< Spot > getResult()
+	{
+		return spots;
+	}
+
+	@Override
+	public boolean checkInput()
+	{
+		if ( null == img )
+		{
+			errorMessage = BASE_ERROR_MESSAGE + "Image is null.";
+			return false;
+		}
+		return true;
+	}
+
+	@Override
+	public boolean process()
+	{
+		final long start = System.currentTimeMillis();
+
+		final ImagePlus tmp = ImageJFunctions.wrap( img, "tmpwrapped" );
+
+		CLIJ2 clij2 = CLIJ2.getInstance();
+
+		ClearCLBuffer input_image = clij2.push(tmp);
+		ClearCLBuffer output_labels = clij2.create_like(input_image);
+
+		clij2.voronoiOtsuLabeling(input_image, output_labels, spot_sigma, outline_sigma);
+
+		RandomAccessibleInterval labelImage = clij2.pullRAI(output_labels);
+
+		output_labels.close();
+		input_image.close();
+
+		final double[] calibration = TMUtils.getSpatialCalibration( img );
+		boolean simplify = false;
+
+		final LabelImageDetector< T > lbldetector = new LabelImageDetector<T>( labelImage, interval, calibration, simplify );
+		if ( !lbldetector.checkInput() || !lbldetector.process() )
+		{
+			errorMessage = BASE_ERROR_MESSAGE + lbldetector.getErrorMessage();
+			return false;
+		}
+		spots = lbldetector.getResult();
+
+		final long end = System.currentTimeMillis();
+		this.processingTime = end - start;
+		return true;
+	}
+
+
+
+	@Override
+	public String getErrorMessage()
+	{
+		/*
+		 * If something wrong happens while you #checkInput() or #process(),
+		 * state it in the errorMessage field.
+		 */
+		return errorMessage;
+	}
+
+	@Override
+	public long getProcessingTime()
+	{
+		return processingTime;
+	}
+
+}