Merge branch 'develop' into main

.classpath

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path=".apt_generated">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path=".apt_generated_tests">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.gitignore

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+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+.idea/
+
+/target/
+
+linux32/target/
+
+linux64/target/
+
+core/target/
+
+mac64/target/
+
+win32/target/
+
+win64/target/
+
+.project
+.settings/
+
+*/.classpath
+*/.factorypath
+*/.project
+*/.settings

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "automatic"
+}

README.md

@@ -0,0 +1,22 @@
+About MIA_DeepLearning
+------------------
+MIA_DeepLearning is a [MIA](https://github.com/mianalysis/MIA) plugin, which adds additional modules that rely on the [CSBDeep](https://imagej.net/plugins/csbdeep) Fiji plugin for deep learning.  The latest release includes the following modules:
+- "StarDist detection" will apply [StarDist](https://imagej.net/plugins/stardist) to each slice of an input image and output the detected objects.
+
+Installation
+------------
+1. Download the version of MIA_DeepLearning, corresponding to your copy of MIA, from the [Releases](https://github.com/mianalysis/mia_deeplearning/releases) page
+2. Place this .jar file into the /plugins directory of the your Fiji installation
+3. Install CSBDeep and StarDist from the Fiji [Updater](https://imagej.net/Updater) tool 
+
+Usage
+-----
+MIA_DeepLearning will add various modules to MIA.  These can be accessed in the same way as other modules.
+
+Acknowledgements
+----------------
+This plugin currently relies on the [CSBDeep](https://imagej.net/plugins/csbdeep) and [StarDist](https://imagej.net/plugins/stardist) plugins for Fiji.
+
+Note
+----
+This plugin is still in development and test coverage is currently incomplete.  Please keep an eye on results and add an [issue](https://github.com/mianalysis/mia_deeplearning/issues) if any problems are encountered.

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>
+
+    <artifactId>MIA_DeepLearning</artifactId>
+    <groupId>io.github.mianalysis</groupId>
+    <version>1.0.0</version>
+    <packaging>jar</packaging>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <dependency.locations.selected>false</dependency.locations.selected>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+        <scp>compile</scp>
+        <license.licenseName>GNU General Public License v3+</license.licenseName>
+        <license.copyrightOwners>Stephen Cross</license.copyrightOwners>
+    </properties>
+
+    <repositories>
+        <repository>
+            <id>jitpack.io</id>
+            <url>https://jitpack.io</url>
+        </repository>
+
+        <repository>
+            <id>scijava.public</id>
+            <url>https://maven.scijava.org/content/groups/public</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.github.stardist</groupId>
+            <artifactId>stardist-imagej</artifactId>
+            <version>master</version>
+            <scope>${scp}</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>de.csbdresden</groupId>
+            <artifactId>csbdeep</artifactId>
+            <version>0.6.0</version>
+            <scope>${scp}</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.github.mianalysis</groupId>
+            <artifactId>mia</artifactId>
+            <version>v0.21.3</version>
+            <scope>${scp}</scope>
+            <!-- <groupId>io.github.mianalysis</groupId>
+            <artifactId>mia</artifactId>
+            <version>0.21.3</version>
+            <scope>${scp}</scope> -->
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.5.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                    <compilerArgument>-proc:none</compilerArgument>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>