diff --git a/mia-algorithms/pom.xml b/mia-algorithms/pom.xml index 029bd883d..8b5b7e2a2 100644 --- a/mia-algorithms/pom.xml +++ b/mia-algorithms/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-algorithms - 1.6.8 + 1.6.9 jar mia-algorithms https://github.com/mianalysis/mia diff --git a/mia-bonej/pom.xml b/mia-bonej/pom.xml index 822f6f11a..46792ff95 100644 --- a/mia-bonej/pom.xml +++ b/mia-bonej/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-bonej - 1.6.8 + 1.6.9 jar mia-bonej https://github.com/mianalysis/mia diff --git a/mia-coordinates/pom.xml b/mia-coordinates/pom.xml index fb44860c4..8df771503 100644 --- a/mia-coordinates/pom.xml +++ b/mia-coordinates/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-coordinates - 1.6.8 + 1.6.9 jar mia-coordinates https://github.com/mianalysis/mia diff --git a/mia-core/pom.xml b/mia-core/pom.xml index bf5fb049b..169b99a24 100644 --- a/mia-core/pom.xml +++ b/mia-core/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-core - 1.6.8 + 1.6.9 jar mia-core https://github.com/mianalysis/mia diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java index a1354800a..7155d6dec 100644 --- a/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java +++ b/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java @@ -274,23 +274,6 @@ public boolean is2D() { return spatCal.nSlices == 1; } - @Deprecated - public ArrayList getXCoords() { - return getPoints().stream().map(Point::getX).collect(Collectors.toCollection(ArrayList::new)); - - } - - @Deprecated - public ArrayList getYCoords() { - return getPoints().stream().map(Point::getY).collect(Collectors.toCollection(ArrayList::new)); - } - - @Deprecated - public ArrayList getZCoords() { - return getPoints().stream().map(Point::getZ).collect(Collectors.toCollection(ArrayList::new)); - - } - @Deprecated public double[] getX(boolean pixelDistances) { if (pixelDistances) diff --git a/mia-deepimagej/pom.xml b/mia-deepimagej/pom.xml index 0d9279cf8..e8090927d 100644 --- a/mia-deepimagej/pom.xml +++ b/mia-deepimagej/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-deepimagej - 1.6.8 + 1.6.9 jar mia-deepimagej https://github.com/mianalysis/mia diff --git a/mia-macros/pom.xml b/mia-macros/pom.xml index c3559e67d..812834b5a 100644 --- a/mia-macros/pom.xml +++ b/mia-macros/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-macros - 1.6.8 + 1.6.9 jar mia-macros https://github.com/mianalysis/mia @@ -127,13 +127,13 @@ io.github.mianalysis mia-core - 1.6.8 + 1.6.9 io.github.mianalysis mia-modules - 1.6.8 + 1.6.9 diff --git a/mia-modules/pom.xml b/mia-modules/pom.xml index 44529f683..69eb3da38 100644 --- a/mia-modules/pom.xml +++ b/mia-modules/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-modules - 1.6.8 + 1.6.9 jar mia-modules https://github.com/mianalysis/mia @@ -127,7 +127,7 @@ io.github.mianalysis mia-core - 1.6.8 + 1.6.9 diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java index 3d6684170..521337775 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java @@ -32,6 +32,7 @@ import io.github.mianalysis.mia.object.Obj; import io.github.mianalysis.mia.object.Objs; import io.github.mianalysis.mia.object.Workspace; +import io.github.mianalysis.mia.object.coordinates.Point; import io.github.mianalysis.mia.object.image.Image; import io.github.mianalysis.mia.object.parameters.BooleanP; import io.github.mianalysis.mia.object.parameters.ChildObjectsP; @@ -291,19 +292,16 @@ public void filterObjectsOnImageEdge(Objs inputObjects, @Nullable Objs outputObj while (iterator.hasNext()) { Obj inputObject = iterator.next(); - ArrayList x = inputObject.getXCoords(); - ArrayList y = inputObject.getYCoords(); - ArrayList z = inputObject.getZCoords(); - - for (int i = 0; i < x.size(); i++) { - if (x.get(i) == minX | x.get(i) == maxX | y.get(i) == minY | y.get(i) == maxY) { + for (Point pt:inputObject.getCoordinateSet()) { + // for (int i = 0; i < x.size(); i++) { + if (pt.x == minX || pt.x == maxX || pt.y == minY || pt.y == maxY) { if (remove) processRemoval(inputObject, outputObjects, iterator); break; } // Only consider Z if the user requested this - if (includeZ && (z.get(i) == minZ | z.get(i) == maxZ)) { + if (includeZ && (pt.z == minZ || pt.z == maxZ)) { if (remove) processRemoval(inputObject, outputObjects, iterator); break; diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java index 8aad2b041..31a67a4c4 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java @@ -3,20 +3,22 @@ import java.util.ArrayList; import java.util.Iterator; -import com.drew.lang.annotations.Nullable; - -import io.github.mianalysis.mia.module.Modules; -import io.github.mianalysis.mia.module.Module; import org.scijava.Priority; import org.scijava.plugin.Plugin; -import io.github.mianalysis.mia.module.Category; + +import com.drew.lang.annotations.Nullable; + import io.github.mianalysis.mia.module.Categories; +import io.github.mianalysis.mia.module.Category; +import io.github.mianalysis.mia.module.Module; +import io.github.mianalysis.mia.module.Modules; import io.github.mianalysis.mia.object.Obj; import io.github.mianalysis.mia.object.Objs; import io.github.mianalysis.mia.object.Workspace; +import io.github.mianalysis.mia.object.coordinates.Point; import io.github.mianalysis.mia.object.parameters.BooleanP; -import io.github.mianalysis.mia.object.parameters.SeparatorP; import io.github.mianalysis.mia.object.parameters.Parameters; +import io.github.mianalysis.mia.object.parameters.SeparatorP; import io.github.mianalysis.mia.object.parameters.text.IntegerP; import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs; import io.github.mianalysis.mia.object.refs.collections.MetadataRefs; @@ -158,18 +160,14 @@ public static boolean hasContactWithEdge(Obj obj, int maxContact, boolean[] remo maxY = Integer.MAX_VALUE; if (!removalEdges[3]) maxX = Integer.MAX_VALUE; - - ArrayList x = obj.getXCoords(); - ArrayList y = obj.getYCoords(); - ArrayList z = obj.getZCoords(); - + int count = 0; - for (int i = 0; i < x.size(); i++) { - if (x.get(i) == minX | x.get(i) == maxX | y.get(i) == minY | y.get(i) == maxY) + for (Point pt:obj.getCoordinateSet()) { + if (pt.x == minX || pt.x == maxX || pt.y == minY || pt.y == maxY) count++; // Only consider Z if the user requested this - if (includeZ && (z.get(i) == minZ | z.get(i) == maxZ)) + if (includeZ && (pt.z == minZ | pt.z == maxZ)) count++; // Check if the maximum number of contacts with the edge has been made diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java index 1923366ad..f237d622e 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java @@ -183,20 +183,15 @@ public static CumStat[] measureWeightedCentre(Obj object, Image image, boolean a CumStat csY = new CumStat(); CumStat csZ = new CumStat(); - // Getting pixel coordinates - ArrayList x = object.getXCoords(); - ArrayList y = object.getYCoords(); - ArrayList z = object.getZCoords(); int tPos = object.getT(); // Running through all pixels in this object and adding the intensity to the // MultiCumStat object - for (int i = 0; i < x.size(); i++) { - ipl.setPosition(1, z.get(i) + 1, tPos + 1); - csX.addMeasure(x.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i))); - csY.addMeasure(y.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i))); - csZ.addMeasure(z.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i))); - + for (Point pt:object.getCoordinateSet()) { + ipl.setPosition(1, pt.z + 1, tPos + 1); + csX.addMeasure(pt.x, ipl.getProcessor().getPixelValue(pt.x, pt.y)); + csY.addMeasure(pt.y, ipl.getProcessor().getPixelValue(pt.x, pt.y)); + csZ.addMeasure(pt.z, ipl.getProcessor().getPixelValue(pt.x, pt.y)); } if (addMeasurements) { diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCentroid.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCentroid.java index bb3099515..053d19dce 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCentroid.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCentroid.java @@ -1,18 +1,20 @@ -// TODO: Add measurements - package io.github.mianalysis.mia.module.objects.measure.spatial; -import io.github.mianalysis.mia.module.Module; -import io.github.mianalysis.mia.module.Modules; -import io.github.mianalysis.mia.module.Module; import org.scijava.Priority; import org.scijava.plugin.Plugin; -import io.github.mianalysis.mia.module.Category; + import io.github.mianalysis.mia.module.Categories; -import io.github.mianalysis.mia.object.*; +import io.github.mianalysis.mia.module.Category; +import io.github.mianalysis.mia.module.Module; +import io.github.mianalysis.mia.module.Modules; +import io.github.mianalysis.mia.object.Measurement; +import io.github.mianalysis.mia.object.Obj; +import io.github.mianalysis.mia.object.Objs; +import io.github.mianalysis.mia.object.Workspace; import io.github.mianalysis.mia.object.parameters.InputObjectsP; +import io.github.mianalysis.mia.object.parameters.Parameters; import io.github.mianalysis.mia.object.parameters.SeparatorP; -import io.github.mianalysis.mia.object.refs.*; +import io.github.mianalysis.mia.object.refs.ObjMeasurementRef; import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs; import io.github.mianalysis.mia.object.refs.collections.MetadataRefs; import io.github.mianalysis.mia.object.refs.collections.ObjMeasurementRefs; @@ -20,33 +22,33 @@ import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs; import io.github.mianalysis.mia.object.refs.collections.PartnerRefs; import io.github.mianalysis.mia.object.system.Status; -import io.github.mianalysis.mia.object.parameters.Parameters; import io.github.mianalysis.mia.object.units.SpatialUnit; -import java.util.ArrayList; - /** * Created by sc13967 on 11/05/2017. */ /** -* Measure mean XYZ centroid for all objects in an object collection.

Note: Z-coordinates are specified in terms of slices (not pixels). -*/ -@Plugin(type = Module.class, priority=Priority.LOW, visible=true) + * Measure mean XYZ centroid for all objects in an object collection.
+ *
+ * Note: Z-coordinates are specified in terms of slices (not pixels). + */ +@Plugin(type = Module.class, priority = Priority.LOW, visible = true) public class MeasureObjectCentroid extends Module { - /** - * - */ + /** + * + */ public static final String INPUT_SEPARATOR = "Object input"; - /** - * Objects to measure mean XYZ centroid for. Measurements will be associated with each object. - */ + /** + * Objects to measure mean XYZ centroid for. Measurements will be associated + * with each object. + */ public static final String INPUT_OBJECTS = "Input objects"; public MeasureObjectCentroid(Modules modules) { - super("Measure object centroid",modules); + super("Measure object centroid", modules); } public interface Measurements { @@ -59,8 +61,6 @@ public interface Measurements { } - - @Override public Category getCategory() { return Categories.OBJECTS_MEASURE_SPATIAL; @@ -79,30 +79,26 @@ public String getDescription() { @Override public Status process(Workspace workspace) { // Getting current objects - String inputObjectName = parameters.getValue(INPUT_OBJECTS,workspace); + String inputObjectName = parameters.getValue(INPUT_OBJECTS, workspace); Objs inputObjects = workspace.getObjects().get(inputObjectName); // Getting the centroids of each and saving them to the objects - for (Obj object:inputObjects.values()) { - ArrayList x = object.getXCoords(); - ArrayList y = object.getYCoords(); - ArrayList z = object.getZCoords(); - - if (x != null) { - object.addMeasurement(new Measurement(Measurements.MEAN_X_PX,object.getXMean(true))); - object.addMeasurement(new Measurement(Measurements.MEAN_X_CAL,object.getXMean(false))); - } - if (y!= null) { - object.addMeasurement(new Measurement(Measurements.MEAN_Y_PX,object.getYMean(true))); - object.addMeasurement(new Measurement(Measurements.MEAN_Y_CAL,object.getYMean(false))); - } - if (z!= null) { - object.addMeasurement(new Measurement(Measurements.MEAN_Z_SLICE,object.getZMean(true,false))); - object.addMeasurement(new Measurement(Measurements.MEAN_Z_CAL,object.getZMean(false,false))); - } + int count = 0; + int total = inputObjects.size(); + for (Obj object : inputObjects.values()) { + object.addMeasurement(new Measurement(Measurements.MEAN_X_PX, object.getXMean(true))); + object.addMeasurement(new Measurement(Measurements.MEAN_X_CAL, object.getXMean(false))); + object.addMeasurement(new Measurement(Measurements.MEAN_Y_PX, object.getYMean(true))); + object.addMeasurement(new Measurement(Measurements.MEAN_Y_CAL, object.getYMean(false))); + object.addMeasurement(new Measurement(Measurements.MEAN_Z_SLICE, object.getZMean(true, false))); + object.addMeasurement(new Measurement(Measurements.MEAN_Z_CAL, object.getZMean(false, false))); + + writeProgressStatus(++count, total, "objects"); + } - if (showOutput) inputObjects.showMeasurements(this,modules); + if (showOutput) + inputObjects.showMeasurements(this, modules); return Status.PASS; @@ -110,7 +106,7 @@ public Status process(Workspace workspace) { @Override protected void initialiseParameters() { - parameters.add(new SeparatorP(INPUT_SEPARATOR,this)); + parameters.add(new SeparatorP(INPUT_SEPARATOR, this)); parameters.add(new InputObjectsP(INPUT_OBJECTS, this)); addParameterDescriptions(); @@ -119,55 +115,54 @@ protected void initialiseParameters() { @Override public Parameters updateAndGetParameters() { -Workspace workspace = null; return parameters; } @Override public ImageMeasurementRefs updateAndGetImageMeasurementRefs() { -return null; + return null; } @Override -public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() { -Workspace workspace = null; + public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() { + Workspace workspace = null; ObjMeasurementRefs returnedRefs = new ObjMeasurementRefs(); - String inputObjectsName = parameters.getValue(INPUT_OBJECTS,workspace); + String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace); ObjMeasurementRef reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_X_PX); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean x-position of all pixels in the object, \""+inputObjectsName+"\"." + + reference.setDescription("Mean x-position of all pixels in the object, \"" + inputObjectsName + "\"." + " Measured in pixel units."); returnedRefs.add(reference); reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_Y_PX); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean y-position of all pixels in the object, \""+inputObjectsName+"\"." + + reference.setDescription("Mean y-position of all pixels in the object, \"" + inputObjectsName + "\"." + " Measured in pixel units."); returnedRefs.add(reference); reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_Z_SLICE); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean z-position of all pixels in the object, \""+inputObjectsName+"\"." + + reference.setDescription("Mean z-position of all pixels in the object, \"" + inputObjectsName + "\"." + " Measured in slice units."); returnedRefs.add(reference); reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_X_CAL); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean x-position of all pixels in the object, \""+inputObjectsName+"\"." + - " Measured in calibrated ("+SpatialUnit.getOMEUnit().getSymbol()+") units."); + reference.setDescription("Mean x-position of all pixels in the object, \"" + inputObjectsName + "\"." + + " Measured in calibrated (" + SpatialUnit.getOMEUnit().getSymbol() + ") units."); returnedRefs.add(reference); reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_Y_CAL); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean y-position of all pixels in the object, \""+inputObjectsName+"\"." + - " Measured in calibrated ("+SpatialUnit.getOMEUnit().getSymbol()+") units."); + reference.setDescription("Mean y-position of all pixels in the object, \"" + inputObjectsName + "\"." + + " Measured in calibrated (" + SpatialUnit.getOMEUnit().getSymbol() + ") units."); returnedRefs.add(reference); reference = objectMeasurementRefs.getOrPut(Measurements.MEAN_Z_CAL); reference.setObjectsName(inputObjectsName); - reference.setDescription("Mean z-position of all pixels in the object, \""+inputObjectsName+"\"." + - " Measured in calibrated ("+SpatialUnit.getOMEUnit().getSymbol()+") units."); + reference.setDescription("Mean z-position of all pixels in the object, \"" + inputObjectsName + "\"." + + " Measured in calibrated (" + SpatialUnit.getOMEUnit().getSymbol() + ") units."); returnedRefs.add(reference); return returnedRefs; @@ -175,23 +170,23 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() { } @Override - public ObjMetadataRefs updateAndGetObjectMetadataRefs() { - return null; + public ObjMetadataRefs updateAndGetObjectMetadataRefs() { + return null; } @Override public MetadataRefs updateAndGetMetadataReferences() { -return null; + return null; } @Override public ParentChildRefs updateAndGetParentChildRefs() { -return null; + return null; } @Override public PartnerRefs updateAndGetPartnerRefs() { -return null; + return null; } @Override @@ -200,6 +195,7 @@ public boolean verify() { } void addParameterDescriptions() { - parameters.get(INPUT_OBJECTS).setDescription("Objects to measure mean XYZ centroid for. Measurements will be associated with each object."); + parameters.get(INPUT_OBJECTS).setDescription( + "Objects to measure mean XYZ centroid for. Measurements will be associated with each object."); } } diff --git a/mia-plugin/pom.xml b/mia-plugin/pom.xml index 32ddfbef7..cbdd4fc8b 100644 --- a/mia-plugin/pom.xml +++ b/mia-plugin/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-plugin - 1.6.8 + 1.6.9 jar mia-plugin https://github.com/mianalysis/mia diff --git a/mia-ptbiop/pom.xml b/mia-ptbiop/pom.xml index 08aea2643..438a21966 100644 --- a/mia-ptbiop/pom.xml +++ b/mia-ptbiop/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-ptbiop - 1.6.8 + 1.6.9 jar mia-ptbiop https://github.com/mianalysis/mia diff --git a/mia-stardist/pom.xml b/mia-stardist/pom.xml index b2ad9f749..4f9ab8715 100644 --- a/mia-stardist/pom.xml +++ b/mia-stardist/pom.xml @@ -6,12 +6,12 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 io.github.mianalysis mia-stardist - 1.6.8 + 1.6.9 jar mia-stardist https://github.com/mianalysis/mia diff --git a/pom.xml b/pom.xml index afa928b07..9cf4eb7c7 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ io.github.mianalysis pom-mia - 1.6.8 + 1.6.9 pom pom-mia https://github.com/mianalysis/mia diff --git a/target/site/dependencies.html b/target/site/dependencies.html deleted file mode 100644 index 58e72d8da..000000000 --- a/target/site/dependencies.html +++ /dev/null @@ -1,5876 +0,0 @@ - - - - - - pom-mia – Project Dependencies - - - - - - - - -
- -
-
-
- -
-

Project Dependencies

-
-

compile

-

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

- - - - - - - - - - - - - - - - - - - - - - - - -
GroupIdArtifactIdVersionTypeLicenses
net.objecthunterexp4j0.4.8jarApache License 2.0
org.apache.logging.log4jlog4j-to-slf4j2.18.0jarApache License, Version 2.0
org.commonmarkcommonmark0.17.0jarBSD 2-Clause License
-
-

test

-

The following is a list of test dependencies for this project. These dependencies are only required to compile and run unit tests for the application:

- - - - - - - - - - - - - - - - - - -
GroupIdArtifactIdVersionTypeLicenses
org.junit.jupiterjunit-jupiter-engine5.10.2jarEclipse Public License v2.0
org.junit.jupiterjunit-jupiter-params5.10.2jarEclipse Public License v2.0
-
-

provided

-

The following is a list of provided dependencies for this project. These dependencies are required to compile the application, but should be provided by default when using the library:

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
GroupIdArtifactIdVersionTypeLicenses
io.scifscifio0.46.0jarSimplified BSD License
io.scifscifio-bf-compat4.1.1jarSimplified BSD License
net.imagejimagej2.15.0jarSimplified BSD License
net.imagejimagej-ops2.0.0jarSimplified BSD License
net.imagejimagej-ui-swing1.0.1jarSimplified BSD License
omebio-formats_plugins7.3.0jarGNU General Public License v2+
omeformats-bsd7.3.0jarSimplified BSD License
omeformats-gpl7.3.0jarGNU General Public License v2+
org.apache.maven.pluginsmaven-project-info-reports-plugin3.2.1maven-pluginApache License, Version 2.0
org.scijavascript-editor0.7.6jarSimplified BSD License
-
-

Project Transitive Dependencies

-

The following is a list of transitive dependencies for this project. Transitive dependencies are the dependencies of the project dependencies.

-
-

compile

-

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

- - - - - - - - - - - - - - - - - - -
GroupIdArtifactIdVersionTypeLicenses
org.apache.logging.log4jlog4j-api2.20.0jarApache License, Version 2.0
org.slf4jslf4j-api1.7.36jarMIT License
-
-

test

-

The following is a list of test dependencies for this project. These dependencies are only required to compile and run unit tests for the application:

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
GroupIdArtifactIdVersionTypeLicenses
org.apiguardianapiguardian-api1.1.2jarThe Apache License, Version 2.0
org.junit.jupiterjunit-jupiter-api5.10.2jarEclipse Public License v2.0
org.junit.platformjunit-platform-commons1.10.2jarEclipse Public License v2.0
org.junit.platformjunit-platform-engine1.10.2jarEclipse Public License v2.0
org.opentest4jopentest4j1.3.0jarThe Apache License, Version 2.0
-
-

provided

-

The following is a list of provided dependencies for this project. These dependencies are required to compile the application, but should be provided by default when using the library:

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GroupIdArtifactIdVersionClassifierTypeLicenses
args4jargs4j2.33-jarMIT License
ch.ethz.ganymedganymed-ssh2build210-jarBSD style license
cisdbase18.09.0-jarApache 2
cisdjhdf519.04.1-jarApache 2
com.adobe.xmpxmpcore6.1.11-jarThe BSD 3-Clause License (BSD3)
com.carrotsearchjava-sizeof0.0.5-jarThe Apache Software License, Version 2.0
com.drewnoakesmetadata-extractor2.18.0-jarThe Apache Software License, Version 2.0
com.esotericsoftwarekryo5.6.0-jar3-Clause BSD License
com.esotericsoftwareminlog1.3.1-jar3-Clause BSD License
com.esotericsoftwarereflectasm1.11.9-jar3-Clause BSD License
com.fasterxml.jackson.corejackson-annotations2.16.1-jarThe Apache Software License, Version 2.0
com.fasterxml.jackson.corejackson-core2.16.1-jarThe Apache Software License, Version 2.0
com.fasterxml.jackson.corejackson-databind2.16.1-jarThe Apache Software License, Version 2.0
com.fifesoftautocomplete3.3.1-jarBSD-3-Clause
com.fifesoftlanguagesupport3.3.0-jarBSD-3-Clause
com.fifesoftrsyntaxtextarea3.4.0-jarBSD-3-Clause
com.formdevflatlaf3.4-jarThe Apache License, Version 2.0
com.github.ben-manes.caffeinecaffeine2.9.3-jarApache License, Version 2.0
com.github.jnrjffi1.3.13-jarThe Apache Software License, Version 2.0GNU Lesser General Public License version 3
com.github.jnrjffi1.3.13nativejarThe Apache Software License, Version 2.0GNU Lesser General Public License version 3
com.github.jnrjnr-a64asm1.0.0-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-constants0.10.4-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-enxio0.16-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-ffi2.2.16-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-netdb1.2.0-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-posix3.1.19-jarEclipse Public License - v 2.0GNU General Public License Version 2GNU Lesser General Public License Version 2.1
com.github.jnrjnr-unixsocket0.17-jarThe Apache Software License, Version 2.0
com.github.jnrjnr-x86asm1.0.2-jarMIT License
com.github.sbridges.object-inspectorobject-inspector0.1-jar-
com.google.code.findbugsjsr3053.0.2-jarThe Apache Software License, Version 2.0
com.google.code.gsongson2.10.1-jarApache-2.0
com.google.errorproneerror_prone_annotations2.25.0-jarApache 2.0
com.google.guavafailureaccess1.0.2-jarThe Apache Software License, Version 2.0
com.google.guavaguava33.0.0-jre-jarApache License, Version 2.0
com.google.guavalistenablefuture9999.0-empty-to-avoid-conflict-with-guava-jarThe Apache Software License, Version 2.0
com.google.http-clientgoogle-http-client1.44.1-jarThe Apache Software License, Version 2.0
com.google.http-clientgoogle-http-client-xml1.44.1-jarThe Apache Software License, Version 2.0
com.google.j2objcj2objc-annotations2.8-jarApache License, Version 2.0
com.google.protobufprotobuf-java3.2.0-jarNew BSD license
com.google.re2jre2j1.7-jarGo License
com.headiusinvokebinder1.10-jarThe Apache Software License, Version 2.0
com.headiusmodulator1.0-jarThe Apache Software License, Version 2.0
com.headiusoptions1.4-jarThe Apache Software License, Version 2.0
com.headiusunsafe-fences1.0-jarApache License, Version 2.0
com.ibm.icuicu4j74.2-jarUnicode/ICU License
com.jcraftjsch0.1.55-jarRevised BSD
com.jcraftjzlib1.1.3-jarBSD
com.jgoodiesjgoodies-common1.7.0-jarThe BSD License
com.jgoodiesjgoodies-forms1.7.2-jarThe BSD License
com.martiansoftwarenailgun-server0.9.1-jarThe Apache Software License, Version 2.0
com.miglayoutmiglayout-core5.3-jarBSD
com.miglayoutmiglayout-swing5.3-jarBSD
com.squareup.okhttp3okhttp4.12.0-jarThe Apache Software License, Version 2.0
com.squareup.okiookio3.8.0-jarThe Apache Software License, Version 2.0
com.squareup.okiookio-jvm3.8.0-jarThe Apache Software License, Version 2.0
com.sun.codemodelcodemodel2.6-jarCDDL v1.1 / GPL v2 dual license
commons-beanutilscommons-beanutils1.9.4-jarApache License, Version 2.0
commons-chaincommons-chain1.1-jar-
commons-codeccommons-codec1.16.1-jarApache-2.0
commons-collectionscommons-collections3.2.2-jarApache License, Version 2.0
commons-digestercommons-digester2.1-jarThe Apache Software License, Version 2.0
commons-iocommons-io2.15.1-jarApache-2.0
commons-langcommons-lang2.6-jarThe Apache Software License, Version 2.0
commons-loggingcommons-logging1.3.0-jarApache-2.0
commons-validatorcommons-validator1.7-jarApache License, Version 2.0
de.erichseifert.vectorgraphics2dVectorGraphics2D0.13-jarGNU Library or Lesser General Public License (LGPL)
dom4jdom4j1.1-jar-
edu.emory.mathcsjtransforms2.4-jar-
edu.minesmines-jtk20151125-jar-
edu.ucarcdm-core5.3.3-jar-
edu.ucarhttpservices5.3.3-jar-
edu.ucarudunits4.3.18-jar-
gov.nist.mathjama1.0.3-jarPublic Domain
io.airliftaircompressor0.21-jarApache License 2.0
io.grpcgrpc-api1.62.2-jarApache 2.0
io.grpcgrpc-context1.62.2-jarApache 2.0
io.miniominio5.0.2-jarThe Apache License, Version 2.0
io.nettynetty-buffer4.1.73.Final-jarApache License, Version 2.0
io.nettynetty-codec4.1.73.Final-jarApache License, Version 2.0
io.nettynetty-common4.1.73.Final-jarApache License, Version 2.0
io.nettynetty-handler4.1.73.Final-jarApache License, Version 2.0
io.nettynetty-resolver4.1.73.Final-jarApache License, Version 2.0
io.nettynetty-tcnative-classes2.0.46.Final-jar-
io.nettynetty-transport4.1.73.Final-jarApache License, Version 2.0
io.opencensusopencensus-api0.31.1-jarThe Apache License, Version 2.0
io.opencensusopencensus-contrib-http-util0.31.1-jarThe Apache License, Version 2.0
io.scifscifio-cli0.6.1-jarSimplified BSD License
io.scifscifio-jai-imageio1.1.1-jarSimplified BSD License
io.scifscifio-labeling0.3.1-jarSimplified BSD License
io.scifscifio-ome-xml0.17.1-jarSimplified BSD License
javax.eljavax.el-api3.0.0-jarCDDL + GPLv2 with classpath exception
javax.enterprisecdi-api2.0.SP1-jarApache License 2.0
javax.injectjavax.inject1-jarThe Apache Software License, Version 2.0
javax.interceptorjavax.interceptor-api1.2-jarCDDL + GPLv2 with classpath exception
javax.servletjavax.servlet-api3.1.0-jarCDDL + GPLv2 with classpath exception
jitkjitk-tps3.0.4-jarApache Software License, Version 2.0
jlinejline2.14.6-jarThe BSD License
joda-timejoda-time2.12.7-jarApache License, Version 2.0
net.iharderbase642.3.8-jarPublic domain
net.imagejij1.54g-jarPublic domain
net.imagejimagej-common2.1.0-jarSimplified BSD License
net.imagejimagej-deprecated0.2.0-jarSimplified BSD License
net.imagejimagej-launcher6.0.2-jarSimplified BSD License
net.imagejimagej-mesh0.8.1-jarSimplified BSD License
net.imagejimagej-mesh-io0.1.2-jarSimplified BSD License
net.imagejimagej-notebook0.7.1-jarSimplified BSD License
net.imagejimagej-plugins-batch0.1.1-jarSimplified BSD License
net.imagejimagej-plugins-commands0.8.1-jarSimplified BSD License
net.imagejimagej-plugins-tools0.3.1-jarSimplified BSD License
net.imagejimagej-plugins-uploader-ssh0.3.2-jarSimplified BSD License
net.imagejimagej-plugins-uploader-webdav0.3.3-jarSimplified BSD License
net.imagejimagej-scripting0.8.4-jarSimplified BSD License
net.imagejimagej-ui-awt0.3.1-jarSimplified BSD License
net.imagejimagej-updater1.0.1-jarSimplified BSD License
net.imglib2imglib26.3.0-jarSimplified BSD License
net.imglib2imglib2-algorithm0.14.0-jarSimplified BSD License
net.imglib2imglib2-algorithm-fft0.2.1-jarSimplified BSD License
net.imglib2imglib2-cache1.0.0-beta-17-jarSimplified BSD License
net.imglib2imglib2-realtransform4.0.2-jarSimplified BSD License
net.imglib2imglib2-roi0.14.1-jarSimplified BSD License
net.java.dev.jnajna5.11.0-jarLGPL-2.1-or-laterApache-2.0
net.sf.jungjung-api2.0.1-jarThe BSD License
net.sf.jungjung-graph-impl2.0.1-jarThe BSD License
net.sf.trove4jtrove4j3.0.3-jarGNU Lesser General Public License 2.1
net.sourceforge.collectionscollections-generic4.01-jarApache License V2.0
net.sourceforge.jdatepickerjdatepicker1.3.2-jarSimplified BSD License
omeformats-api7.3.0-jarSimplified BSD License
omejxrlib-all0.2.4-jarSimplified BSD License
ometurbojpeg7.3.0-jarSimplified BSD License
org.antlrST44.3.4-jarThe BSD License
org.antlrantlr3.5.3-jarBSD licence
org.antlrantlr-runtime3.5.3-jarBSD licence
org.apache-extras.beanshellbsh2.1.0-jarApache License, Version 2.0
org.apache.antant1.10.14-jarThe Apache Software License, Version 2.0
org.apache.antant-launcher1.10.14-jarThe Apache Software License, Version 2.0
org.apache.bcelbcel6.2-jarApache License, Version 2.0
org.apache.commonscommons-compress1.26.0-jarApache-2.0
org.apache.commonscommons-lang33.14.0-jarApache-2.0
org.apache.commonscommons-math2.2-jarThe Apache Software License, Version 2.0
org.apache.commonscommons-math33.6.1-jarApache License, Version 2.0
org.apache.commonscommons-text1.11.0-jarApache-2.0
org.apache.commonscommons-vfs22.0-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy4.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-dateutil4.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-json4.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-jsr2234.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-swing4.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-templates4.0.18-jarThe Apache Software License, Version 2.0
org.apache.groovygroovy-xml4.0.18-jarThe Apache Software License, Version 2.0
org.apache.httpcomponentshttpclient4.5.14-jarApache License, Version 2.0
org.apache.httpcomponentshttpcore4.4.16-jarApache License, Version 2.0
org.apache.httpcomponentshttpmime4.5.14-jarApache License, Version 2.0
org.apache.ivyivy2.5.2-jarThe Apache Software License, Version 2.0
org.apache.jackrabbitjackrabbit-webdav2.21.22-jarApache-2.0
org.apache.mavenmaven-artifact3.0-jarThe Apache Software License, Version 2.0
org.apache.mavenmaven-model3.0-jarThe Apache Software License, Version 2.0
org.apache.mavenmaven-plugin-api3.0-jarThe Apache Software License, Version 2.0
org.apache.mavenmaven-repository-metadata3.0-jarThe Apache Software License, Version 2.0
org.apache.mavenmaven-settings3.0-jarThe Apache Software License, Version 2.0
org.apache.maven.doxiadoxia-core1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-decoration-model1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-integration-tools1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-logging-api1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-module-xhtml1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-module-xhtml51.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-sink-api1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-site-renderer1.11.1-jarApache License, Version 2.0
org.apache.maven.doxiadoxia-skin-model1.11.1-jarApache License, Version 2.0
org.apache.maven.reportingmaven-reporting-impl3.0.0-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-api1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-manager-plexus1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-cvs-commons1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-cvsexe1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-cvsjava1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-git-commons1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-gitexe1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-hg1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-perforce1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-starteam1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-svn-commons1.12.2-jarApache License, Version 2.0
org.apache.maven.scmmaven-scm-provider-svnexe1.12.2-jarApache License, Version 2.0
org.apache.maven.sharedmaven-artifact-transfer0.13.1-jarApache License, Version 2.0
org.apache.maven.sharedmaven-common-artifact-filters3.3.2-jarApache License, Version 2.0
org.apache.maven.sharedmaven-dependency-tree2.2-jarApache License, Version 2.0
org.apache.maven.sharedmaven-shared-jar1.2-jarApache License, Version 2.0
org.apache.maven.sharedmaven-shared-utils3.3.3-jarApache License, Version 2.0
org.apache.velocityvelocity1.7-jarThe Apache Software License, Version 2.0
org.apache.velocityvelocity-tools2.0-jarThe Apache Software License, Version 2.0
org.bouncycastlebcpkix-jdk18on1.71-jarBouncy Castle Licence
org.bouncycastlebcprov-jdk18on1.71-jarBouncy Castle Licence
org.bouncycastlebcutil-jdk18on1.71-jarBouncy Castle Licence
org.checkerframeworkchecker-qual3.42.0-jarThe MIT License
org.clojureclojure1.8.0-jarEclipse Public License 1.0
org.codehaus.gparsgpars1.2.1-jarThe Apache Software License, Version 2.0
org.codehaus.jsr166-mirrorjsr166y1.7.0-jar-
org.codehaus.plexusplexus-classworlds2.5.2-jarThe Apache Software License, Version 2.0
org.codehaus.plexusplexus-component-annotations2.2.0-jarApache License, Version 2.0
org.codehaus.plexusplexus-container-default1.0-alpha-8-jar-
org.codehaus.plexusplexus-digest1.0-jar-
org.codehaus.plexusplexus-i18n1.0-beta-10-jar-
org.codehaus.plexusplexus-interpolation1.26-jarApache License, Version 2.0
org.codehaus.plexusplexus-utils4.0.0-jarApache License, Version 2.0
org.codehaus.plexusplexus-velocity1.2-jarApache License, Version 2.0
org.eclipse.aetheraether-util0.9.0.M2-jarEclipse Public License, Version 1.0
org.eclipse.sisuorg.eclipse.sisu.inject0.3.0-jarEclipse Public License, Version 1.0
org.ejmlejml-all0.41-jarThe Apache License, Version 2.0
org.ejmlejml-cdense0.41-jarThe Apache License, Version 2.0
org.ejmlejml-core0.41-jarThe Apache License, Version 2.0
org.ejmlejml-ddense0.41-jarThe Apache License, Version 2.0
org.ejmlejml-dsparse0.41-jarThe Apache License, Version 2.0
org.ejmlejml-fdense0.41-jarThe Apache License, Version 2.0
org.ejmlejml-fsparse0.41-jarThe Apache License, Version 2.0
org.ejmlejml-simple0.41-jarThe Apache License, Version 2.0
org.ejmlejml-zdense0.41-jarThe Apache License, Version 2.0
org.jetbrainsannotations13.0-jarThe Apache Software License, Version 2.0
org.jetbrains.kotlinkotlin-stdlib1.9.22-jarThe Apache License, Version 2.0
org.jetbrains.kotlinkotlin-stdlib-jdk71.9.22-jarThe Apache License, Version 2.0
org.jetbrains.kotlinkotlin-stdlib-jdk81.9.22-jarThe Apache License, Version 2.0
org.jfreejfreechart1.5.4-jarGNU Lesser General Public Licence
org.jfreejfreesvg3.4.3-jarGNU General Public License (GPL)
org.jhotdrawjhotdraw7.6.0-jar-
org.jlinejline-native3.25.1-jarThe BSD License
org.jlinejline-reader3.25.1-jarThe BSD License
org.jlinejline-terminal3.25.1-jarThe BSD License
org.jlinejline-terminal-jna3.25.1-jarThe BSD License
org.jomljoml1.10.5-jarMIT License
org.jrubydirgra0.3-jarEPL
org.jrubyjruby-core9.1.17.0-jarGPL-2.0LGPL-2.1EPL-2.0
org.jrubyjruby-stdlib9.1.17.0-jarGPL-2.0LGPL-2.1EPL-2.0
org.jruby.extrasbytelist1.0.15-jarMIT License
org.jruby.jcodingsjcodings1.0.58-jarMIT License
org.jruby.jonijoni2.2.1-jarMIT License
org.jsonjson20240205-jarPublic Domain
org.knowm.xchartxchart3.5.4-jarThe Apache Software License, Version 2.0
org.markdownjmarkdownj0.3.0-1.0.2b4-jarBSD license
org.mozillarhino1.7.14-jarMozilla Public License, Version 2.0
org.multiversemultiverse-core0.7.0-jar-
org.netbeans.libcvsclient20060125-jarSun Public License
org.netlibblas0.8-jar-
org.netlibf2jutil0.8-jar-
org.netliblapack0.8-jar-
org.netlibnetlib-java0.9.3-renjin-patched-2-jar-
org.netlibxerbla0.8-jar-
org.objenesisobjenesis3.3-jarApache License, Version 2.0
org.ocpsoft.prettytimeprettytime4.0.1.Final-jarApache License
org.ojalgoojalgo45.1.1-jarMIT
org.openmicroscopymetakit5.3.6-jarGNU General Public License v2+
org.openmicroscopyome-codecs1.0.1-jarSimplified BSD License
org.openmicroscopyome-common6.0.21-jarSimplified BSD License
org.openmicroscopyome-jai0.1.3-jarSimplified BSD License
org.openmicroscopyome-mdbtools5.3.3-jarGNU Lesser General Public License v2.1+
org.openmicroscopyome-poi5.3.8-jarApache License, Version 2.0
org.openmicroscopyome-xml6.3.6-jarSimplified BSD License
org.openmicroscopyspecification6.3.6-jarSimplified BSD LicenseCreative Commons Attribution 3.0 Unported License
org.ow2.asmasm9.6-jarBSD-3-Clause
org.ow2.asmasm-analysis9.6-jarBSD-3-Clause
org.ow2.asmasm-commons9.6-jarBSD-3-Clause
org.ow2.asmasm-tree9.6-jarBSD-3-Clause
org.ow2.asmasm-util9.6-jarBSD-3-Clause
org.perf4jperf4j0.9.16-jarApache 2
org.pythonjython-slim2.7.3-jarJython Software License
org.renjindatasets0.8.1906-jarPart of R 2.14.2
org.renjingcc-runtime0.8.1906-jar-
org.renjingrDevices0.8.1906-jarPart of R 2.14.2
org.renjingraphics0.8.1906-jarPart of R 2.14.2
org.renjinmethods0.8.1906-jarPart of R 2.14.2
org.renjinrenjin-appl0.8.1906-jar-
org.renjinrenjin-core0.8.1906-jar-
org.renjinrenjin-gnur-runtime0.8.1906-jar-
org.renjinrenjin-script-engine0.8.1906-jar-
org.renjinstats0.8.1906-jarPart of R 2.14.2
org.renjinutils0.8.1906-jarPart of R 2.14.2
org.scala-langscala-library2.13.10-jarApache-2.0
org.scala-langscala3-compiler_33.3.0-jarApache-2.0
org.scala-langscala3-interfaces3.3.0-jarApache-2.0
org.scala-langscala3-library_33.3.0-jarApache-2.0
org.scala-langtasty-core_33.3.0-jarApache-2.0
org.scala-lang.modulesscala-asm9.4.0-scala-1-jar-
org.scala-sbtcompiler-interface1.3.5-jarApache-2.0
org.scala-sbtutil-interface1.3.0-jarBSD New
org.scijavabatch-processor0.4.2-jarSimplified BSD License
org.scijavaminimaven2.2.2-jarSimplified BSD License
org.scijavanative-lib-loader2.5.0-jarSimplified BSD License
org.scijavaparsington3.1.0-jarSimplified BSD License
org.scijavascijava-common2.98.0-jarSimplified BSD License
org.scijavascijava-io-http0.3.0-jarSimplified BSD License
org.scijavascijava-optional1.0.1-jarSimplified BSD License
org.scijavascijava-plot0.2.0-jarSimplified BSD License
org.scijavascijava-plugins-commands0.2.5-jarSimplified BSD License
org.scijavascijava-plugins-platforms0.3.1-jarSimplified BSD License
org.scijavascijava-plugins-text-markdown0.1.3-jarSimplified BSD License
org.scijavascijava-plugins-text-plain0.1.4-jarSimplified BSD License
org.scijavascijava-search2.0.4-jarSimplified BSD License
org.scijavascijava-table1.0.2-jarSimplified BSD License
org.scijavascijava-ui-awt0.1.7-jarSimplified BSD License
org.scijavascijava-ui-swing1.0.1-jarSimplified BSD License
org.scijavascript-editor-jython1.1.0-jarSimplified BSD License
org.scijavascript-editor-scala0.2.1-jarSimplified BSD License
org.scijavascripting-beanshell0.4.1-jarSimplified BSD License
org.scijavascripting-clojure0.1.6-jarSimplified BSD License
org.scijavascripting-groovy1.0.0-jarSimplified BSD License
org.scijavascripting-java0.4.1-jarSimplified BSD License
org.scijavascripting-javascript1.0.0-jarSimplified BSD License
org.scijavascripting-jruby0.3.1-jarSimplified BSD License
org.scijavascripting-jython1.0.1-jarSimplified BSD License
org.scijavascripting-renjin0.2.3-jarGNU General Public License v2+
org.scijavascripting-scala0.3.2-jarSimplified BSD License
org.scijavaswing-checkbox-tree1.0.2-jarSimplified BSD License
org.smurnjply0.2.1-jarThe Apache Software License, Version 2.0
org.sonatype.sisusisu-guice3.2.5no_aopjarThe Apache Software License, Version 2.0
org.sonatype.sisusisu-inject-bean2.6.0-jarEclipse Public License, Version 1.0
org.sonatype.sisusisu-inject-plexus2.6.0-jarEclipse Public License, Version 1.0
org.xerialsqlite-jdbc3.28.0-jarThe Apache Software License, Version 2.0
org.yamlsnakeyaml2.2-jarApache License, Version 2.0
orooro2.0.8-jar-
xercesxercesImpl2.12.2-jarThe Apache Software License, Version 2.0
xml-apisxml-apis1.4.01-jarThe Apache Software License, Version 2.0The SAX LicenseThe W3C License
xpp3xpp31.1.4c-jarIndiana University Extreme! Lab Software License, vesion 1.1.1Public DomainApache Software License, version 1.1
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system

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The following is a list of system dependencies for this project. These dependencies are required to compile the application:

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GroupIdArtifactIdVersionTypeLicenses
com.suntools1.8.0jar-
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Project Dependency Graph

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Dependency Tree

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Licenses

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EPL: Dirgra

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3-Clause BSD License: Kryo, MinLog, ReflectASM

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GNU General Public License v2+: Bio-Formats Plugins for ImageJ, Bio-Formats library, Metakit, SciJava Scripting: Renjin

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The BSD License: JGoodies Common, JGoodies Forms, JLine, JLine JNA Terminal, JLine Native Library, JLine Reader, JLine Terminal, StringTemplate 4, jung-api, jung-graph-impl

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Eclipse Public License 1.0: clojure

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GPL-2.0: JRuby Core, JRuby Lib Setup

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BSD 2-Clause License: commonmark-java core

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Apache 2: ETH SIS Base Library, JHDF5 (HDF5 for Java), Perf4J

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BSD: JZlib, MiGLayout Core, MiGLayout Swing

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Unknown: Netty/TomcatNative [OpenSSL - Classes], Plexus I18N Component, Renjin Core, Renjin GCC Runtime, Renjin GNU-R Runtime, Renjin Script Engine, The Multiverse Code (so API and implementation), blas, cdm-core, dom4j, f2jutil, httpservices, jhotdraw, jsr166y, jtransforms, lapack, mines-jtk, netlib-java, object-inspector, oro, renjin-appl, udunits, xerbla

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New BSD license: Protocol Buffers [Core]

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LGPL-2.1-or-later: Java Native Access

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The MIT License: Checker Qual

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Apache-2.0: Apache Commons Codec, Apache Commons Compress, Apache Commons IO, Apache Commons Lang, Apache Commons Logging, Apache Commons Text, Compiler Interface, Gson, Jackrabbit WebDAV Library, Java Native Access, Scala Library, scala3-compiler-bootstrapped, scala3-interfaces, scala3-library-bootstrapped, tasty-core-bootstrapped

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BSD style license: Ganymed SSH2 for Java

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CDDL v1.1 / GPL v2 dual license: Codemodel Core

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GNU General Public License v3+: pom-mia

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LGPL-2.1: JRuby Core, JRuby Lib Setup

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The BSD 3-Clause License (BSD3): Adobe XMPCore

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BSD-3-Clause: LanguageSupport, asm, asm-analysis, asm-commons, asm-tree, asm-util, autocomplete, rsyntaxtextarea

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The W3C License: XML Commons External Components XML APIs

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Jython Software License: Jython

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Indiana University Extreme! Lab Software License, vesion 1.1.1: MXP1: Xml Pull Parser 3rd Edition (XPP3)

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Public Domain: JAMA, JSON in Java, MXP1: Xml Pull Parser 3rd Edition (XPP3)

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Apache License V2.0: larvalabs collections

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Bouncy Castle Licence: Bouncy Castle ASN.1 Extension and Utility APIs, Bouncy Castle PKIX, CMS, EAC, TSP, PKCS, OCSP, CMP, and CRMF APIs, Bouncy Castle Provider

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Public domain: ImageJ, base64

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BSD New: Util Interface

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MIT: ojAlgo

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CDDL + GPLv2 with classpath exception: Expression Language 3.0 API, Java Servlet API, javax.interceptor API

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Eclipse Public License - v 2.0: jnr-posix

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BSD license: markdownj

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The Apache Software License, Version 2.0: Apache Ant Core, Apache Ant Launcher, Apache Groovy, Apache Ivy, Apache Velocity, Commons Digester, Commons Lang, Commons Math, Commons VFS Core, FindBugs-jsr305, GPars, Google HTTP Client Library for Java, Guava InternalFutureFailureAccess and InternalFutures, Guava ListenableFuture only, IntelliJ IDEA Annotations, Jackson-annotations, Jackson-core, Maven Artifact, Maven Model, Maven Plugin API, Maven Repository Metadata Model, Maven Settings, Plexus Classworlds, SQLite JDBC, Sisu Guice - Core Library, VelocityTools, XChart, XML Commons External Components XML APIs, XML extensions to the Google HTTP Client Library for Java., Xerces2-j, com.drewnoakes:metadata-extractor, invokebinder, jPLY, jackson-databind, java-sizeof, javax.inject, jffi, jnr-a64asm, jnr-constants, jnr-enxio, jnr-ffi, jnr-netdb, jnr-unixsocket, modulator, nailgun-server, okhttp, okio, options

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GNU General Public License Version 2: jnr-posix

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GNU Lesser General Public License v2.1+: MDB Tools (Java port)

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The Apache License, Version 2.0: EJML, FlatLaf, Kotlin Stdlib, Kotlin Stdlib Jdk7, Kotlin Stdlib Jdk8, OpenCensus, minio, org.apiguardian:apiguardian-api, org.opentest4j:opentest4j

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Apache 2.0: error-prone annotations, io.grpc:grpc-api, io.grpc:grpc-context

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MIT License: ByteList, JCodings, JOML, Joni, SLF4J API Module, args4j, jnr-x86asm

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Revised BSD: JSch

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Mozilla Public License, Version 2.0: rhino

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Eclipse Public License v2.0: JUnit Jupiter API, JUnit Jupiter Engine, JUnit Jupiter Params, JUnit Platform Commons, JUnit Platform Engine API

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Unicode/ICU License: icu4j

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BSD licence: ANTLR 3 Runtime, ANTLR 3 Tool

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Go License: RE2/J

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Eclipse Public License, Version 1.0: Aether Utilities, Sisu-Inject-Bean : legacy wrapper, Sisu-Inject-Plexus : legacy wrapper, org.eclipse.sisu.inject

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GNU Library or Lesser General Public License (LGPL): VectorGraphics2D

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Apache License 2.0: CDI APIs, aircompressor, exp4j

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Apache License, Version 2.0: Apache Commons BCEL, Apache Commons BeanUtils, Apache Commons Collections, Apache Commons Math, Apache Commons Validator, Apache HttpClient, Apache HttpClient Mime, Apache HttpCore, Apache Log4j API, Apache Log4j to SLF4J Adapter, Apache Maven Artifact Transfer, Apache Maven Common Artifact Filters, Apache Maven Dependency Tree, Apache Maven JAR Utilities, Apache Maven Project Info Reports Plugin, Apache Maven Reporting Implementation, Apache Maven Shared Utils, BeanShell, Caffeine cache, Doxia :: Core, Doxia :: Logging API, Doxia :: Sink API, Doxia :: XHTML Module, Doxia :: XHTML5 Module, Doxia Sitetools :: Decoration Model, Doxia Sitetools :: Integration Tools, Doxia Sitetools :: Site Renderer, Doxia Sitetools :: Skin Model, Guava: Google Core Libraries for Java, J2ObjC Annotations, Joda-Time, Maven SCM API, Maven SCM CVS Provider - CVS Executable Impl., Maven SCM CVS Provider - CVS Java Impl., Maven SCM CVS Provider - Common library, Maven SCM Git Provider - Common library, Maven SCM Git Provider - Git Executable Impl., Maven SCM Manager for Plexus, Maven SCM Mercurial (Hg) Provider, Maven SCM Perforce Provider, Maven SCM Starteam Provider, Maven SCM Subversion Provider - Common library, Maven SCM Subversion Provider - SVN Executable Impl., Netty/Buffer, Netty/Codec, Netty/Common, Netty/Handler, Netty/Resolver, Netty/Transport, OME POI, Objenesis, Plexus :: Component Annotations (deprecated), Plexus Common Utilities, Plexus Interpolation API, Plexus Velocity Component, SnakeYAML, unsafe-fences

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GNU Lesser General Public License Version 2.1: jnr-posix

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Creative Commons Attribution 3.0 Unported License: Metadata model specification

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GNU Lesser General Public License version 3: jffi

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Sun Public License: cvsclient

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The SAX License: XML Commons External Components XML APIs

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Apache License: PrettyTime - Core

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Simplified BSD License: BSD Bio-Formats readers and writers, Batch Processor, Bio-Formats API, ImageJ Common, ImageJ Deprecated, ImageJ Launcher, ImageJ Mesh, ImageJ Mesh I/O plugins, ImageJ Notebook, ImageJ Ops, ImageJ Plugins Batch, ImageJ Plugins: Commands, ImageJ Plugins: Tools, ImageJ Plugins: Uploader: SSH, ImageJ Plugins: Uploader: WebDAV, ImageJ Scripting, ImageJ UI: AWT, ImageJ UI: Swing, ImageJ Updater, ImageJ2, ImgLib2 Algorithms, ImgLib2 Algorithms: FFT, ImgLib2 Cache Library, ImgLib2 Core Library, ImgLib2 ROI, ImgLib2 Real Transform, JAI Image I/O Tools, JXRLib Java Bindings, Jython Script Editor plugin, Metadata model specification, Minimal support for Maven projects, Native Library Loader, OME Codecs, OME Common Java, OME JAI, OME XML library, Parsington: The SciJava Expression Parser, SCIFIO Command Line Tools, SCIFIO Core, SCIFIO Labeling, SCIFIO OME-XML Extension, SCIFIO-Bio-Formats Compatibility Format, Scala Script Editor plugin, SciJava Common, SciJava I/O: HTTP, SciJava Optional, SciJava Plot, SciJava Plugins: Commands, SciJava Plugins: Platforms, SciJava Plugins: Text: Markdown, SciJava Plugins: Text: Plain, SciJava Script Editor, SciJava Scripting: BeanShell, SciJava Scripting: Clojure, SciJava Scripting: Groovy, SciJava Scripting: JRuby, SciJava Scripting: Java, SciJava Scripting: JavaScript, SciJava Scripting: Jython, SciJava Scripting: Scala, SciJava Search, SciJava Table, SciJava UI: AWT, SciJava UI: Swing, Swing Check Box Tree, jdatepicker, libjpeg-turbo Java bindings

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GNU General Public License (GPL): JFreeSVG

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Part of R 2.14.2: datasets, grDevices, graphics, methods, stats, utils

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GNU Lesser General Public License 2.1: GNU Trove

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Apache Software License, Version 2.0: JavaITK thin plate spline

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GNU Lesser General Public Licence: JFreeChart

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EPL-2.0: JRuby Core, JRuby Lib Setup

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Apache Software License, version 1.1: MXP1: Xml Pull Parser 3rd Edition (XPP3)

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