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Merge NJ3 modifications and code cleanup
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‎.github/workflows/maven.yml‎

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@@ -7,24 +7,24 @@ jobs:
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runs-on : ubuntu-latest
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steps :
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Checkout NJ-image-test
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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repository: GReD-Clermont/NucleusJ2-tests-images
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repository: GReD-Clermont/NucleusJ-tests-images
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ref: 'v1'
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path: test-images
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- name: Set up JDK 11
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uses: actions/setup-java@v3
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uses: actions/setup-java@v4
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with:
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java-version: '11'
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distribution: 'adopt'
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server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
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settings-path: ${{ github.workspace }} # location for the settings.xml file
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- name: Cache Maven packages
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/.m2
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key: ${{ runner.os }}-m2-${{ secrets.CACHE_VERSION }}-${{ hashFiles('**/pom.xml') }}
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- name : Package and test
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run: mvn clean package
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- name: Upload Artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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path: target
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deploy:
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runs-on : ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up JDK 11
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uses: actions/setup-java@v3
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uses: actions/setup-java@v4
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with:
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java-version: '11'
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distribution: 'adopt'
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server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
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settings-path: ${{ github.workspace }} # location for the settings.xml file
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- name: Cache Maven packages
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/.m2
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key: ${{ runner.os }}-m2-${{ secrets.CACHE_VERSION }}-${{ hashFiles('**/pom.xml') }}

‎.gitlab-ci.yml‎

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@@ -3,7 +3,7 @@ image: maven:3-jdk-8
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variables:
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CI_PROJECT_PATH: "ReightI/test-nucleusj-ci-cd"
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API_IMAGE_NAME: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME
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VERSION: "2.0.1"
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VERSION: "3.0.0-SNAPSHOT"
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stages:
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- compile

‎README.md‎

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# NucleusJ2.0
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# NucleusJ 3.0
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NucleusJ 2.0 is a new release of [NucleusJ](https://github.com/PouletAxel/NucleusJ_), in which image processing is achieved more quickly using a command-line user interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unmarked nucleoli.
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NucleusJ 3.0 is a new release of [NucleusJ](https://github.com/PouletAxel/NucleusJ_), in which image processing is achieved more quickly using a command-line user interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unmarked nucleoli.
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A discrete geometric method was introduced to improve the surface area calculation, a key parameter when studying nuclear morphology, replacing an imageJ default tool by a new one that includes pixel context information.
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# Download and manual user links
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Download the latest version: [jar](https://github.com/GReD-Clermont/NucleusJ2/releases/latest)
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Download the latest version: [jar](https://github.com/GReD-Clermont/NucleusJ/releases/latest)
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Manual user and examples: [wiki](https://github.com/GReD-Clermont/NucleusJ2/wiki)
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Manual user and examples: [wiki](https://github.com/GReD-Clermont/NucleusJ/wiki)
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# Authors & contact
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‎pom.xml‎

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http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>fr.igred</groupId>
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<artifactId>nucleusj_2</artifactId>
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<version>2.2.0-SNAPSHOT</version>
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<artifactId>nucleusj</artifactId>
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<version>3.0.0-SNAPSHOT</version>
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<name>NucleusJ</name>
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<description>Ensemble of ImageJ plugins for nuclear analysis</description>
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<dependency>
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<groupId>fr.inra.ijpb</groupId>
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<artifactId>MorphoLibJ_</artifactId>
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<version>1.4.0</version>
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<version>1.6.4</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-codec/commons-codec -->
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<dependency>
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<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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<version>1.11</version>
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<version>1.18.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.6</version>
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<version>2.19.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
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<dependency>
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<groupId>commons-cli</groupId>
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<artifactId>commons-cli</artifactId>
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<version>1.4</version>
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<version>1.9.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-lang/commons-lang -->
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<dependency>
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<groupId>commons-lang</groupId>
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<artifactId>commons-lang</artifactId>
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<version>2.6</version>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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<version>3.17.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<version>1.7.30</version>
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<version>2.0.17</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-classic -->
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<dependency>
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
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<version>1.2.3</version>
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<version>1.3.15</version>
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<scope>runtime</scope>
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<optional>true</optional>
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</dependency>
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<!-- https://mvnrepository.com/artifact/ome/bioformats_plugins -->
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<!-- https://mvnrepository.com/artifact/ome/bio-formats_plugins -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>bio-formats_plugins</artifactId>
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<version>6.6.0</version>
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<version>8.2.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/ome/formats-api -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>formats-api</artifactId>
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<version>6.6.0</version>
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<version>8.2.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/sc.fiji/imagescience -->
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>imagescience</artifactId>
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<version>2.4.1</version>
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<version>3.0.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/net.imagej/ij -->
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>ij</artifactId>
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<version>1.53i</version>
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<version>1.54p</version>
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</dependency>
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<dependency>
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<groupId>fr.igred</groupId>
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<artifactId>simple-omero-client</artifactId>
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<version>5.14.1</version>
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<version>5.19.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
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<version>5.7.1</version>
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<version>5.13.3</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<target>8</target>
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</configuration>
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</plugin>
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<!--plugin>
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<artifactId>maven-deploy-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>deploy-file</goal>
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</goals>
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<phase>deploy</phase>
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<configuration>
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<repositoryId>gitlab-maven</repositoryId>
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<url>https://gitlab.com/api/v4/projects/19044962/packages/maven</url>
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<file>target/NucleusJ_2-1.0.2-jar-with-dependencies.jar</file>
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<generatePom>false</generatePom>
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<uniqueVersion>false</uniqueVersion>
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<groupId>burp</groupId>
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<artifactId>NucleusJ_2</artifactId>
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<version>1.0.2</version>
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</configuration>
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</execution>
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</executions>
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</plugin-->
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</plugins>
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</pluginManagement>
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<plugins>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<developers>
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<repository>
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<id>github</id>
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<name>GitHub GReD-Clermont Apache Maven Packages</name>
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<url>https://maven.pkg.github.com/GReD-Clermont/NucleusJ2</url>
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<url>https://maven.pkg.github.com/GReD-Clermont/NucleusJ</url>
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</repository>
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</distributionManagement>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
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<maven.compiler.source>7</maven.compiler.source>
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<maven.compiler.target>7</maven.compiler.target>
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<maven.compiler.source>8</maven.compiler.source>
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<maven.compiler.target>8</maven.compiler.target>
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</properties>
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</project>

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