diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..3d47f986c41db29ec6dc0d5036bf760b3a1cf366
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+.idea/
+target/
+.settings/
+*.iml
+.project
+.classpath
\ No newline at end of file
diff --git a/export.jardesc b/export.jardesc
new file mode 100644
index 0000000000000000000000000000000000000000..e77c24867e74d71b8eb75983f47d5bcdb8072367
--- /dev/null
+++ b/export.jardesc
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+ <jar path="sphereVTK/drawSphereVTK.jar"/>
+ <options buildIfNeeded="true" compress="true" descriptionLocation="/sphereVTK/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+ <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+ <selectedProjects/>
+ <manifest generateManifest="true" manifestLocation="/Icy-Kernel/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+ <sealing sealJar="false">
+ <packagesToSeal/>
+ <packagesToUnSeal/>
+ </sealing>
+ </manifest>
+ <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+ <javaElement handleIdentifier="=sphereVTK/src"/>
+ </selectedElements>
+</jardesc>
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b80d4c1341c5aa0c515f2c4e6ffcbac15139dd8b
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,101 @@
+<?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>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.3</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>3d-spheres-vtk</artifactId>
+ <version>1.0.0</version>
+
+ <packaging>jar</packaging>
+
+ <name>Draw 3D Spheres with VTK.</name>
+ <description>
+ This protocol’s block draws 3D spheres with VTK from a list of cartesian coordinates (x,y,z). It is used by SODA-STORM protocol to
+ visualize SODA results obtained with single localizations microscopy (STORM).
+ Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics:
+ https://www.nature.com/articles/s41467-018-03053-x
+ </description>
+ <url>http://icy.bioimageanalysis.org/plugin/draw-3d-spheres-with-vtk/</url>
+ <inceptionYear>2020</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>lagache</id>
+ <name>Thibault Lagache</name>
+ <url>https://research.pasteur.fr/fr/member/thibault-lagache/</url>
+ <roles>
+ <role>founder</role>
+ <role>developer</role>
+ </roles>
+ </developer>
+ <developer>
+ <id>sdallongeville</id>
+ <name>Stéphane Dallongeville</name>
+ <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url>
+ <roles>
+ <role>founder</role>
+ <role>lead</role>
+ <role>architect</role>
+ <role>developer</role>
+ <role>debugger</role>
+ <role>tester</role>
+ <role>maintainer</role>
+ <role>support</role>
+ </roles>
+ </developer>
+ </developers>
+
+ <!-- Project properties -->
+ <properties>
+
+ </properties>
+
+ <!-- Project build configuration -->
+ <build>
+
+ </build>
+
+ <!-- List of project's dependencies -->
+ <dependencies>
+ <!-- The core of Icy -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>protocols</artifactId>
+ </dependency>
+ </dependencies>
+
+ <!-- Icy Maven repository (to find parent POM) -->
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <name>Icy's Nexus</name>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
diff --git a/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java b/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java
new file mode 100644
index 0000000000000000000000000000000000000000..5347509d4b748190c25b60c880b1528ce03c7b1d
--- /dev/null
+++ b/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java
@@ -0,0 +1,60 @@
+package plugins.lagache.spherevtk;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.BooleanMask2D;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarColor;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarDoubleArrayNative;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.VarString;
+import plugins.kernel.roi.roi2d.ROI2DPoint;
+
+// Colocalisation with Ripley function K
+// Significant
+
+public class DrawSpheresVTK extends Plugin implements Block {
+
+ VarSequence input_sequence = new VarSequence("Input sequence", null);
+ VarDoubleArrayNative x= new VarDoubleArrayNative("x", null);
+ VarDoubleArrayNative y= new VarDoubleArrayNative("y", null);
+ VarDoubleArrayNative z= new VarDoubleArrayNative("z", null);
+ VarString name = new VarString("Name of the overlay", "detections");
+ VarColor color = new VarColor("Color", Color.blue);
+ VarDouble size = new VarDouble("Size", 1.0);
+ @Override
+ public void declareInput(VarList inputMap) {
+
+ inputMap.add("Input Sequence", input_sequence);
+ inputMap.add("x",x);
+ inputMap.add("y",y);
+ inputMap.add("z",z);
+ inputMap.add("Size",size);
+ inputMap.add("Color",color);
+ inputMap.add("Name of the overlay",name);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap) {
+ }
+
+ @Override
+ public void run() {
+
+ // Add the cross overlay, it becomes active after being added.
+ input_sequence.getValue().addOverlay(new SphereVTK(x.getValue(),y.getValue(),z.getValue(),size.getValue(),color.getValue(),name.getValue()));
+ }
+
+ }
+
+
+
+
\ No newline at end of file
diff --git a/src/main/java/plugins/lagache/spherevtk/SphereVTK.java b/src/main/java/plugins/lagache/spherevtk/SphereVTK.java
new file mode 100644
index 0000000000000000000000000000000000000000..1f038980d4c36d1dfedd41268da1da62b3f7ed60
--- /dev/null
+++ b/src/main/java/plugins/lagache/spherevtk/SphereVTK.java
@@ -0,0 +1,224 @@
+/*
+ * Copyright 2010, 2011 Institut Pasteur.
+ *
+ * This file is part of ICY.
+ *
+ * ICY is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ICY is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with ICY. If not, see <http://www.gnu.org/licenses/>.
+ */
+package plugins.lagache.spherevtk;
+
+import icy.canvas.IcyCanvas;
+import icy.painter.Overlay;
+import icy.painter.VtkPainter;
+import icy.sequence.Sequence;
+import icy.vtk.VtkUtil;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+
+import plugins.kernel.canvas.VtkCanvas;
+import vtk.vtkActor;
+import vtk.vtkFloatArray;
+import vtk.vtkGlyph3D;
+import vtk.vtkLookupTable;
+import vtk.vtkMolecule;
+import vtk.vtkMoleculeMapper;
+import vtk.vtkPoints;
+import vtk.vtkPolyDataMapper;
+import vtk.vtkProp;
+import vtk.vtkSphereSource;
+import vtk.vtkUnsignedShortArray;
+import vtk.vtkUnstructuredGrid;
+
+/**
+ * @author stephane
+ */
+public class SphereVTK extends Overlay implements VtkPainter
+{
+ double[] x, y, z;
+ double size;
+ Color color;
+
+ private vtkActor[] sphere_ens;
+
+ public SphereVTK(double[] x, double[] y, double[] z, double size, Color color, String name)
+ {
+ super(name);
+
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ this.size = size;
+ this.color = color;
+
+ init();
+ }
+
+ private void init()
+ {
+ // create points
+ final vtkPoints points = new vtkPoints();
+ // setup scales
+ final vtkFloatArray scales = new vtkFloatArray();
+ scales.SetName("scales");
+ // setup color label
+ final vtkFloatArray col = new vtkFloatArray();
+ col.SetName("col");
+
+ // setup lookupTable and add some colors
+ final vtkLookupTable colors = new vtkLookupTable();
+ colors.SetNumberOfTableValues(1);
+ // index, R, G, B, A
+ colors.SetTableValue(0, color.getRed() / 255f, color.getGreen() / 255f, color.getBlue() / 255f, 1.0);
+
+ for (int i = 0; i < x.length; i++)
+ {
+ points.InsertNextPoint(x[i], y[i], z[i]);
+ scales.InsertNextValue(1);
+ col.InsertNextValue(0); // first color
+ }
+
+ // grid structured to append center, radius and color label
+ final vtkUnstructuredGrid grid = new vtkUnstructuredGrid();
+
+ grid.SetPoints(points);
+ grid.GetPointData().AddArray(scales);
+ grid.GetPointData().SetActiveScalars("scales"); // !!!to set radius first
+ grid.GetPointData().AddArray(col);
+
+ points.Delete();
+ scales.Delete();
+ col.Delete();
+
+ // create anything you want here, we will use a sphere for the demo
+ final vtkSphereSource sphere = new vtkSphereSource();
+
+ sphere.SetRadius(size);
+ sphere.SetThetaResolution(6);
+ sphere.SetPhiResolution(6);
+
+ // object to group sphere and grid and keep smooth interaction
+ final vtkGlyph3D glyph3D = new vtkGlyph3D();
+
+ glyph3D.SetInputData(grid);
+ glyph3D.SetSourceConnection(sphere.GetOutputPort());
+
+ // create a mapper and actor
+ final vtkPolyDataMapper mapper = new vtkPolyDataMapper();
+ mapper.SetInputConnection(glyph3D.GetOutputPort());
+
+ mapper.SetScalarModeToUsePointFieldData(); // without, color are displayed regarding radius and not color label
+ // mapper.SetScalarRange(0, 3); // to scale color label (without, col should be between 0 and 1)
+ mapper.SelectColorArray("col"); // !!!to set color (nevertheless you will have nothing)
+ mapper.SetLookupTable(colors);
+
+ final vtkActor actor = new vtkActor();
+ actor.SetMapper(mapper);
+
+ sphere_ens = new vtkActor[1];
+ sphere_ens[0] = actor;
+ }
+
+ // init vtk objects
+ private void init_2()
+ {
+ final double[] pts = new double[x.length * 3];
+
+ // convert to single array
+ for (int i = 0; i < x.length; i++)
+ {
+ pts[(i * 3) + 0] = x[i];
+ pts[(i * 3) + 1] = y[i];
+ pts[(i * 3) + 2] = z[i];
+ }
+
+ final vtkPoints vtkPts = VtkUtil.getPoints(pts);
+
+ sphere_ens = new vtkActor[1];
+ final vtkMolecule mol = new vtkMolecule();
+
+ mol.SetPoints(vtkPts);
+ vtkPts.Delete();
+
+ final vtkUnsignedShortArray atomicNums = (vtkUnsignedShortArray) mol.GetVertexData().GetScalars();
+
+ // set atomic num
+ for (int i = 0; i < x.length; i++)
+ atomicNums.InsertValue(i, 0);
+
+ // mapper
+ final vtkMoleculeMapper molMapper = new vtkMoleculeMapper();
+
+ molMapper.SetInputData(mol);
+ molMapper.UseFastSettings();
+
+ // molMapper.SetRenderAtoms(true);
+ // molMapper.SetRenderBonds(false);
+
+ // actor
+ final vtkActor molActor = new vtkActor();
+ molActor.SetMapper(molMapper);
+
+ sphere_ens[0] = molActor;
+ }
+
+ // init vtk objects
+ private void init_old()
+ {
+ sphere_ens = new vtkActor[x.length];
+ for (int i = 0; i < x.length; i++)
+ {
+ // source
+ final vtkSphereSource sphere = new vtkSphereSource();
+ sphere.SetRadius(size);
+ sphere.SetThetaResolution(6);
+ sphere.SetPhiResolution(6);
+
+ sphere.SetCenter(x[i], y[i], z[i]);
+
+ // mapper
+ final vtkPolyDataMapper map = new vtkPolyDataMapper();
+ map.SetInputConnection(sphere.GetOutputPort());
+
+ // actor
+ vtkActor aSphere = new vtkActor();
+ aSphere.SetMapper(map);
+ // double total = color.getRed()+ color.getGreen()+ color.getBlue();
+ double red = color.getRed() / 255.;
+ double green = color.getGreen() / 255.;
+ double blue = color.getBlue() / 255.;
+
+ aSphere.GetProperty().SetColor(red, green, blue);
+ sphere_ens[i] = aSphere;
+ }
+ }
+
+ @Override
+ public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
+ {
+ super.paint(g, sequence, canvas);
+
+ if (canvas instanceof VtkCanvas)
+ {
+ // disable picking by using this property
+ ((VtkCanvas) canvas).getPicker().PickFromListOn();
+ }
+ }
+
+ @Override
+ public vtkProp[] getProps()
+ {
+ return sphere_ens;
+ }
+}
\ No newline at end of file