diff --git a/pom.xml b/pom.xml
index 550cad5..b0dfa83 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>27.0.1</version>
+		<version>28.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>de.csbdresden</groupId>
 	<artifactId>StarDist_</artifactId>
-	<version>0.1.0</version>
+	<version>0.2.0</version>
 
 	<name>StarDist</name>
 	<description>StarDist - Object Detection with Star-convex Shapes</description>
@@ -69,6 +69,16 @@
 			<url>https://github.com/frauzufall</url>
 			<roles><role>reviewer</role></roles>
 		</contributor>
+		<contributor>
+			<name>Olivier Burri</name>
+			<url>https://github.com/lacan</url>
+			<roles><role>developer</role></roles>
+		</contributor>
+		<contributor>
+			<name>Romain Guiet</name>
+			<url>https://github.com/romainGuiet</url>
+			<roles><role>developer</role></roles>
+		</contributor>
 	</contributors>
 
 	<mailingLists>
@@ -79,14 +89,14 @@
 	</mailingLists>
 
 	<scm>
-		<connection>scm:git:git://github.com/uschmidt83/stardist-imagej</connection>
-		<developerConnection>scm:git:git://github.com/uschmidt83/stardist-imagej</developerConnection>
+		<connection>scm:git:git://github.com/mpicbg-csbd/stardist-imagej</connection>
+		<developerConnection>scm:git:git://github.com/mpicbg-csbd/stardist-imagej</developerConnection>
 		<tag>HEAD</tag>
-		<url>https://github.com/uschmidt83/stardist-imagej</url>
+		<url>https://github.com/mpicbg-csbd/stardist-imagej</url>
 	</scm>
 	<issueManagement>
 		<system>GitHub Issues</system>
-		<url>https://github.com/uschmidt83/stardist-imagej/issues</url>
+		<url>https://github.com/mpicbg-csbd/stardist-imagej/issues</url>
 	</issueManagement>
 	<ciManagement>
 		<system>None</system>
diff --git a/src/main/java/de/csbdresden/stardist/Candidates.java b/src/main/java/de/csbdresden/stardist/Candidates.java
index 97eacc5..951656c 100644
--- a/src/main/java/de/csbdresden/stardist/Candidates.java
+++ b/src/main/java/de/csbdresden/stardist/Candidates.java
@@ -12,6 +12,9 @@
 import de.lighti.clipper.Path;
 import de.lighti.clipper.Paths;
 import de.lighti.clipper.Point.LongPoint;
+import ij.gui.PointRoi;
+import ij.gui.PolygonRoi;
+import ij.gui.Roi;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.real.FloatType;
@@ -29,6 +32,9 @@ public class Candidates {
     private final boolean[] suppressed;
     private final boolean verbose;
     private final LogService log;
+
+    // scale all coordinates by this value and divide later to get subpixel resolution
+    private static final long S = 100;
     
     public Candidates(RandomAccessibleInterval<FloatType> prob, RandomAccessibleInterval<FloatType> dist) {
         this(prob, dist, 0.4);
@@ -65,8 +71,8 @@ public Candidates(RandomAccessibleInterval<FloatType> prob, RandomAccessibleInte
                     for (int k = 0; k < nrays; k++) {
                         s.setPosition(k, 2);
                         FloatType d = s.get();
-                        long x = Math.round(i + d.getRealDouble() * Math.cos(phis[k]));
-                        long y = Math.round(j + d.getRealDouble() * Math.sin(phis[k]));
+                        long x = Math.round(S * (i + d.getRealDouble() * Math.cos(phis[k])));
+                        long y = Math.round(S * (j + d.getRealDouble() * Math.sin(phis[k])));
                         xmin = Math.min(xmin,x);
                         ymin = Math.min(ymin,y);
                         xmax = Math.max(xmax,x);
@@ -75,7 +81,7 @@ public Candidates(RandomAccessibleInterval<FloatType> prob, RandomAccessibleInte
                     }
                     polygons.add(poly);
                     bboxes.add(new Box2D(xmin,xmax,ymin,ymax));
-                    origins.add(new Point2D(i,j));
+                    origins.add(new Point2D(S*i,S*j));
                     scores.add(score);
                     areas.add(poly.area());
                 }
@@ -165,24 +171,36 @@ public List<Integer> getSorted() {
         return score_indices;
     }
     
-    public Point2D getOrigin(int i) {
-        return origins.get(i);
-    }
+//    public Point2D getOrigin(int i) {
+//        return origins.get(i);
+//    }
     
-    public Path getPolygon(int i) {
-        return polygons.get(i);
-    }
+//    public Path getPolygon(int i) {
+//        return polygons.get(i);
+//    }
 
-    public Box2D getBbox(int i) {
-        return bboxes.get(i);
-    }
+//    public Box2D getBbox(int i) {
+//        return bboxes.get(i);
+//    }
 
-    public float getScore(int i) {
-        return scores.get(i);
-    }
+//    public float getScore(int i) {
+//        return scores.get(i);
+//    }
 
-    public double getArea(int i) {
-        return areas.get(i);
+//    public double getArea(int i) {
+//        return areas.get(i);
+//    }
+    
+    public PolygonRoi getPolygonRoi(int i) {
+        return Utils.toPolygonRoi(polygons.get(i), S);
+    }
+    
+    public PointRoi getOriginRoi(int i) {
+        return Utils.toPointRoi(origins.get(i), S);
+    }
+    
+    public Roi getBboxRoi(int i) {
+        return Utils.toBoxRoi(bboxes.get(i), S);
     }
 
 
diff --git a/src/main/java/de/csbdresden/stardist/Opt.java b/src/main/java/de/csbdresden/stardist/Opt.java
index 69864d9..7e061dd 100644
--- a/src/main/java/de/csbdresden/stardist/Opt.java
+++ b/src/main/java/de/csbdresden/stardist/Opt.java
@@ -29,6 +29,10 @@ public class Opt {
     
     static final String NUM_TILES = "Number of Tiles";
     static final String EXCLUDE_BNDRY = "Boundary Exclusion";
+    static final String ROI_POSITION = "ROI Position";
+    static final String ROI_POSITION_AUTO = "Automatic";
+    static final String ROI_POSITION_STACK = "Stack";
+    static final String ROI_POSITION_HYPERSTACK = "Hyperstack";
     static final String VERBOSE = "Verbose";
     static final String CSBDEEP_PROGRESS_WINDOW = "Show CNN Progress";
     static final String SHOW_PROB_DIST = "Show CNN Output";
@@ -48,6 +52,7 @@ public class Opt {
         DEFAULTS.put(OUTPUT_TYPE, OUTPUT_BOTH);
         DEFAULTS.put(NUM_TILES, 1);
         DEFAULTS.put(EXCLUDE_BNDRY, 2);
+        DEFAULTS.put(ROI_POSITION, ROI_POSITION_AUTO);
         DEFAULTS.put(VERBOSE, false);
         DEFAULTS.put(CSBDEEP_PROGRESS_WINDOW, false);
         DEFAULTS.put(SHOW_PROB_DIST, false);
diff --git a/src/main/java/de/csbdresden/stardist/StarDist2D.java b/src/main/java/de/csbdresden/stardist/StarDist2D.java
index d076778..35289a5 100644
--- a/src/main/java/de/csbdresden/stardist/StarDist2D.java
+++ b/src/main/java/de/csbdresden/stardist/StarDist2D.java
@@ -3,6 +3,7 @@
 import static de.csbdresden.stardist.StarDist2DModel.MODELS;
 import static de.csbdresden.stardist.StarDist2DModel.MODEL_DSB2018_HEAVY_AUGMENTATION;
 import static de.csbdresden.stardist.StarDist2DModel.MODEL_DSB2018_PAPER;
+import static de.csbdresden.stardist.StarDist2DModel.MODEL_HE_HEAVY_AUGMENTATION;
 
 import java.io.File;
 import java.io.IOException;
@@ -54,7 +55,7 @@ public class StarDist2D extends StarDist2DBase implements Command {
     private final String msgTitle = "<html>" +
             "<table><tr valign='top'><td>" +
             "<h2>Object Detection with Star-convex Shapes</h2>" +
-            "<a href='https://github.com/mpicbg-csbd/stardist'>https://github.com/mpicbg-csbd/stardist</a>" +
+            "<a href='https://imagej.net/StarDist'>https://imagej.net/StarDist</a>" +
             "<br/><br/><small>Please cite our paper if StarDist was helpful for your research. Thanks!</small>" +
             "</td><td>&nbsp;&nbsp;<img src='"+getResource("images/logo.png")+"' width='100' height='100'></img><td>" +
             "</tr></table>" +
@@ -70,6 +71,7 @@ public class StarDist2D extends StarDist2DBase implements Command {
 
     @Parameter(label=Opt.MODEL,
                choices={MODEL_DSB2018_HEAVY_AUGMENTATION,
+                        MODEL_HE_HEAVY_AUGMENTATION,
                         MODEL_DSB2018_PAPER,
                         Opt.MODEL_FILE,
                         Opt.MODEL_URL}, style=ChoiceWidget.LIST_BOX_STYLE)
@@ -83,7 +85,7 @@ public class StarDist2D extends StarDist2DBase implements Command {
 
     @Parameter(label=Opt.PERCENTILE_HIGH, stepSize="0.1", min="0", max="100", style=NumberWidget.SLIDER_STYLE, callback="percentileTopChanged")
     private double percentileTop = (double) Opt.getDefault(Opt.PERCENTILE_HIGH);
-    
+
     @Parameter(label=Opt.PROB_IMAGE, type=ItemIO.OUTPUT)
     private Dataset prob;
 
@@ -123,16 +125,20 @@ public class StarDist2D extends StarDist2DBase implements Command {
 
     @Parameter(label=Opt.EXCLUDE_BNDRY, min="0", stepSize="1")
     private int excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);
+    
+    @Parameter(label=Opt.ROI_POSITION, choices={Opt.ROI_POSITION_AUTO, Opt.ROI_POSITION_STACK, Opt.ROI_POSITION_HYPERSTACK}, style=ChoiceWidget.RADIO_BUTTON_HORIZONTAL_STYLE)
+    private String roiPosition = (String) Opt.getDefault(Opt.ROI_POSITION);
+    private String roiPositionActive = null;
 
     @Parameter(label=Opt.VERBOSE)
     private boolean verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
-    
+
     @Parameter(label=Opt.CSBDEEP_PROGRESS_WINDOW)
     private boolean showCsbdeepProgress = (boolean) Opt.getDefault(Opt.CSBDEEP_PROGRESS_WINDOW);
-    
+
     @Parameter(label=Opt.SHOW_PROB_DIST)
     private boolean showProbAndDist = (boolean) Opt.getDefault(Opt.SHOW_PROB_DIST);
-    
+
     // TODO: values for block multiple and overlap
 
     @Parameter(label=Opt.SET_THRESHOLDS, callback="setThresholds")
@@ -153,6 +159,7 @@ private void restoreDefaults() {
         outputType = (String) Opt.getDefault(Opt.OUTPUT_TYPE);
         nTiles = (int) Opt.getDefault(Opt.NUM_TILES);
         excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);
+        roiPosition = (String) Opt.getDefault(Opt.ROI_POSITION);
         verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
         showCsbdeepProgress = (boolean) Opt.getDefault(Opt.CSBDEEP_PROGRESS_WINDOW);
         showProbAndDist = (boolean) Opt.getDefault(Opt.SHOW_PROB_DIST);
@@ -165,7 +172,7 @@ private void percentileBottomChanged() {
     private void percentileTopChanged() {
         percentileBottom = Math.min(percentileBottom, percentileTop);
     }
-    
+
     private void setThresholds() {
         switch (modelChoice) {
         case Opt.MODEL_FILE:
@@ -203,7 +210,12 @@ private void checkForCSBDeep() {
     public void run() {
         checkForCSBDeep();
         if (!checkInputs()) return;
-        
+
+        if (roiPosition.equals(Opt.ROI_POSITION_AUTO))
+            roiPositionActive = input.numDimensions() > 3 ? Opt.ROI_POSITION_HYPERSTACK : Opt.ROI_POSITION_STACK;
+        else
+            roiPositionActive = roiPosition;
+
         File tmpModelFile = null;
         try {
             final HashMap<String, Object> paramsCNN = new HashMap<>();
@@ -238,13 +250,14 @@ public void run() {
                 paramsCNN.put("blockMultiple", pretrainedModel.sizeDivBy);
                 paramsCNN.put("overlap", pretrainedModel.tileOverlap);
             }
-            
+
             final HashMap<String, Object> paramsNMS = new HashMap<>();
             paramsNMS.put("probThresh", probThresh);
             paramsNMS.put("nmsThresh", nmsThresh);
             paramsNMS.put("excludeBoundary", excludeBoundary);
-            paramsNMS.put("verbose", verbose);            
-            
+            paramsNMS.put("roiPosition", roiPositionActive);
+            paramsNMS.put("verbose", verbose);
+
             final LinkedHashSet<AxisType> inputAxes = Utils.orderedAxesSet(input);
             final boolean isTimelapse = inputAxes.contains(Axes.TIME);
 
@@ -276,11 +289,12 @@ public void run() {
 
                     final Future<CommandModule> futureNMS = command.run(StarDist2DNMS.class, false, paramsNMS);
                     final Candidates polygons = (Candidates) futureNMS.get().getOutput("polygons");
-                    export(outputType, polygons, 1+t);
-                    
+                    export(outputType, polygons, 1+t, numFrames, roiPositionActive);
+
                     status.showProgress(1+t, (int)numFrames);
                 }
-                label = labelImageToDataset(outputType);
+                label = labelImageToDataset(outputType);                
+                // if (roiManager != null) OverlayCommands.listRois(roiManager.getRoisAsArray());
 
             } else {
                 // note: the code below supports timelapse data too. differences to above:
@@ -289,7 +303,7 @@ public void run() {
                 //       - allows showing prob and dist easily
                 final Future<CommandModule> futureCNN = command.run(de.csbdresden.csbdeep.commands.GenericNetwork.class, false, paramsCNN);
                 final Dataset prediction = (Dataset) futureCNN.get().getOutput("output");
-                
+
                 final Pair<Dataset, Dataset> probAndDist = splitPrediction(prediction);
                 final Dataset probDS = probAndDist.getA();
                 final Dataset distDS = probAndDist.getB();
@@ -318,7 +332,7 @@ public void run() {
             }
         }
     }
-    
+
     // this function is very cumbersome... is there a better way to do this?
     private Pair<Dataset, Dataset> splitPrediction(final Dataset prediction) {
         final RandomAccessibleInterval<FloatType> predictionRAI = (RandomAccessibleInterval<FloatType>) prediction.getImgPlus();
@@ -331,7 +345,7 @@ private Pair<Dataset, Dataset> splitPrediction(final Dataset prediction) {
         final long[] predSize = predAxes.stream().mapToLong(axis -> {
             return axis == Axes.CHANNEL ? prediction.dimension(axis)-1 : prediction.dimension(axis);
         }).toArray();
-        
+
         final RandomAccessibleInterval<FloatType> probRAI = Views.hyperSlice(predictionRAI, predChannelDim, 0);
         final RandomAccessibleInterval<FloatType> distRAI = Views.offsetInterval(predictionRAI, predStart, predSize);
 
@@ -349,23 +363,23 @@ private boolean checkInputs() {
                (input.numDimensions() == 3 && axes.containsAll(Arrays.asList(Axes.X, Axes.Y, Axes.CHANNEL))) ||
                (input.numDimensions() == 4 && axes.containsAll(Arrays.asList(Axes.X, Axes.Y, Axes.CHANNEL, Axes.TIME))) ))
             return showError("Input must be a 2D image or timelapse (with or without channels).");
-        
-        if (!( modelChoice.equals(Opt.MODEL_FILE) || modelChoice.equals(Opt.MODEL_URL) || MODELS.containsKey(modelChoice) )) 
+
+        if (!( modelChoice.equals(Opt.MODEL_FILE) || modelChoice.equals(Opt.MODEL_URL) || MODELS.containsKey(modelChoice) ))
             return showError(String.format("Unsupported Model \"%s\".", modelChoice));
-        
+
         return true;
     }
-    
-    
+
+
     @Override
     protected void exportPolygons(Candidates polygons) {}
-    
+
 
     @Override
     protected ImagePlus createLabelImage() {
-        return IJ.createImage("Labeling", "16-bit black", (int)input.getWidth(), (int)input.getHeight(), 1, 1, (int)input.getFrames());
+        return IJ.createImage(Opt.LABEL_IMAGE, "16-bit black", (int)input.getWidth(), (int)input.getHeight(), 1, 1, (int)input.getFrames());
     }
-    
+
 
     public static void main(final String... args) throws Exception {
         final ImageJ ij = new ImageJ();
diff --git a/src/main/java/de/csbdresden/stardist/StarDist2DBase.java b/src/main/java/de/csbdresden/stardist/StarDist2DBase.java
index 3b805f8..21d5cc7 100644
--- a/src/main/java/de/csbdresden/stardist/StarDist2DBase.java
+++ b/src/main/java/de/csbdresden/stardist/StarDist2DBase.java
@@ -24,7 +24,7 @@
 import net.imglib2.img.display.imagej.ImageJFunctions;
 
 public abstract class StarDist2DBase {
-    
+
     @Parameter
     protected LogService log;
 
@@ -36,12 +36,12 @@ public abstract class StarDist2DBase {
 
     @Parameter
     protected DatasetService dataset;
-    
+
     @Parameter
     protected StatusService status;
-    
+
     // ---------
-    
+
     protected boolean exportPointRois = false;
     protected boolean exportBboxRois = false;
 
@@ -50,77 +50,85 @@ public abstract class StarDist2DBase {
     protected int labelId = 0;
     protected long labelCount = 0;
     protected static final int MAX_LABEL_ID = 65535;
-    
+
     // ---------
-    
+
     protected URL getResource(final String name) {
         return StarDist2DBase.class.getClassLoader().getResource(name);
-    }        
-    
+    }
+
     protected boolean showError(String msg) {
         ui.showDialog(msg, MessageType.ERROR_MESSAGE);
         // log.error(msg);
         return false;
     }
-    
+
     // ---------
-    
-    protected void export(String outputType, Candidates polygons, int framePosition) {
+
+    protected void export(String outputType, Candidates polygons, int framePosition, long numFrames, String roiPosition) {
         switch (outputType) {
         case Opt.OUTPUT_ROI_MANAGER:
-            exportROIs(polygons, framePosition);
+            exportROIs(polygons, framePosition, numFrames, roiPosition);
             break;
         case Opt.OUTPUT_LABEL_IMAGE:
             exportLabelImage(polygons, framePosition);
             break;
         case Opt.OUTPUT_BOTH:
-            exportROIs(polygons, framePosition);
+            exportROIs(polygons, framePosition, numFrames, roiPosition);
             exportLabelImage(polygons, framePosition);
             break;
         case Opt.OUTPUT_POLYGONS:
             exportPolygons(polygons);
             break;
         default:
-            showError(String.format("Unknown output type \"%s\"", outputType));
+            showError(String.format("Invalid %s \"%s\"", Opt.OUTPUT_TYPE, outputType));
         }
     }
-    
-    protected void exportROIs(Candidates polygons, int framePosition) {
+
+    protected void exportROIs(Candidates polygons, int framePosition, long numFrames, String roiPosition) {
         if (roiManager == null) {
             roiManager = RoiManager.getRoiManager();
             roiManager.reset(); // clear all rois
+            // https://github.com/mpicbg-csbd/stardist-imagej/pull/5:
+            // when setting the RoiManager to invisible, the position of the ROI will be properly saved
+            // -> the issue is in RoiManager.addRoi(), https://github.com/imagej/imagej1/blob/c4950ee1f19a25828e5ac915ef3f74e5aa13a6e2/ij/plugin/frame/RoiManager.java#L419
+            roiManager.setVisible(false);            
         }
 
-        // Setting the RoiManager to invisible, the position of the ROI will be properly saved.
-        // The issue is in RoiManager.addRoi(), https://github.com/imagej/imagej1/blob/c4950ee1f19a25828e5ac915ef3f74e5aa13a6e2/ij/plugin/frame/RoiManager.java#L419
-        roiManager.setVisible(false);
-
         for (final int i : polygons.getWinner()) {
-            final PolygonRoi polyRoi = Utils.toPolygonRoi(polygons.getPolygon(i));
-            if (framePosition > 0) polyRoi.setPosition(1, 1, framePosition);
-            //if (framePosition > 0) polyRoi.setPosition(framePosition);
-            roiManager.addRoi(polyRoi);
+            final PolygonRoi polyRoi = polygons.getPolygonRoi(i);
+            if (framePosition > 0) setRoiPosition(polyRoi, framePosition, roiPosition);
+            roiManager.add(polyRoi, -1);
             if (exportPointRois) {
-                final Point2D o = polygons.getOrigin(i);
-                final PointRoi pointRoi = new PointRoi(o.x, o.y);
-                if (framePosition > 0) pointRoi.setPosition(1, 1, framePosition);
-                //if (framePosition > 0) pointRoi.setPosition(framePosition);
-                roiManager.addRoi(pointRoi);
+                final PointRoi pointRoi = polygons.getOriginRoi(i);
+                if (framePosition > 0) setRoiPosition(pointRoi, framePosition, roiPosition);
+                roiManager.add(pointRoi, -1);
             }
             if (exportBboxRois) {
-                final Box2D bbox = polygons.getBbox(i);
-                final Roi bboxRoi = new Roi(bbox.xmin, bbox.ymin, bbox.xmax - bbox.xmin, bbox.ymax - bbox.ymin);
-                if (framePosition > 0) bboxRoi.setPosition(1, 1, framePosition);
-                //if (framePosition > 0) bboxRoi.setPosition(framePosition);
-                roiManager.addRoi(bboxRoi);
+                final Roi bboxRoi = polygons.getBboxRoi(i);
+                if (framePosition > 0) setRoiPosition(bboxRoi, framePosition, roiPosition);
+                roiManager.add(bboxRoi, -1);
             }
         }
 
-        //Setting the RoiManager back to visible at the end of the processing
-        roiManager.setVisible(true);
-
+        // make the RoiManager visible after adding the ROIs
+        if (framePosition == 0 || framePosition == numFrames)
+            roiManager.setVisible(true);
+    }
+    
+    protected void setRoiPosition(Roi roi, int framePosition, String roiPosition) {
+        switch (roiPosition) {
+        case Opt.ROI_POSITION_STACK:
+            roi.setPosition(framePosition);
+            break;
+        case Opt.ROI_POSITION_HYPERSTACK:
+            roi.setPosition(1, 1, framePosition);
+            break;
+        default:
+            showError(String.format("Invalid %s \"%s\"", Opt.ROI_POSITION, roiPosition));
+        }
     }
-   
+
     protected void exportLabelImage(Candidates polygons, int framePosition) {
         if (labelImage == null)
             labelImage = createLabelImage();
@@ -131,18 +139,18 @@ protected void exportLabelImage(Candidates polygons, int framePosition) {
         final int numWinners = winner.size();
         // winners are ordered by score -> draw from last to first to give priority to higher scores in case of overlaps
         for (int i = numWinners-1; i >= 0; i--) {
-            final PolygonRoi polyRoi = Utils.toPolygonRoi(polygons.getPolygon(winner.get(i)));
+            final PolygonRoi polyRoi = polygons.getPolygonRoi(winner.get(i));
             ip.setColor(1 + ((labelId + i) % MAX_LABEL_ID));
             ip.fill(polyRoi);
         }
         labelCount += numWinners;
         labelId = (labelId + numWinners) % MAX_LABEL_ID;
-    }    
-    
-    abstract protected void exportPolygons(Candidates polygons);    
-    
+    }
+
+    abstract protected void exportPolygons(Candidates polygons);
+
     abstract protected ImagePlus createLabelImage();
-    
+
     protected Dataset labelImageToDataset(String outputType) {
         if (outputType.equals(Opt.OUTPUT_LABEL_IMAGE) || outputType.equals(Opt.OUTPUT_BOTH)) {
             if (labelCount > MAX_LABEL_ID) {
diff --git a/src/main/java/de/csbdresden/stardist/StarDist2DModel.java b/src/main/java/de/csbdresden/stardist/StarDist2DModel.java
index 81b8b25..0a84ec9 100644
--- a/src/main/java/de/csbdresden/stardist/StarDist2DModel.java
+++ b/src/main/java/de/csbdresden/stardist/StarDist2DModel.java
@@ -14,12 +14,14 @@ public class StarDist2DModel {
     
     static final String MODEL_DSB2018_HEAVY_AUGMENTATION = "Versatile (fluorescent nuclei)";
     static final String MODEL_DSB2018_PAPER = "DSB 2018 (from StarDist 2D paper)";
-    static final String MODEL_DEFAULT = MODEL_DSB2018_HEAVY_AUGMENTATION;    
+    static final String MODEL_HE_HEAVY_AUGMENTATION = "Versatile (H&E nuclei)";
+    static final String MODEL_DEFAULT = MODEL_DSB2018_HEAVY_AUGMENTATION;
     
     static final Map<String, StarDist2DModel> MODELS = new LinkedHashMap<String, StarDist2DModel>();
     static {
-        MODELS.put(MODEL_DSB2018_PAPER, new StarDist2DModel(StarDist2DModel.class.getClassLoader().getResource("models/2D/dsb2018_paper.zip"), 0.417819, 0.5, 8, 47));
-        MODELS.put(MODEL_DSB2018_HEAVY_AUGMENTATION, new StarDist2DModel(StarDist2DModel.class.getClassLoader().getResource("models/2D/dsb2018_heavy_augment.zip"), 0.479071, 0.3, 16, 94));
+        MODELS.put(MODEL_DSB2018_PAPER, new StarDist2DModel(StarDist2DModel.class.getClassLoader().getResource("models/2D/dsb2018_paper.zip"), 0.417819, 0.5, 8, 48));
+        MODELS.put(MODEL_DSB2018_HEAVY_AUGMENTATION, new StarDist2DModel(StarDist2DModel.class.getClassLoader().getResource("models/2D/dsb2018_heavy_augment.zip"), 0.479071, 0.3, 16, 96));
+        MODELS.put(MODEL_HE_HEAVY_AUGMENTATION, new StarDist2DModel(StarDist2DModel.class.getClassLoader().getResource("models/2D/he_heavy_augment.zip"), 0.692478, 0.3, 16, 96));
     }
     
     // -----------
diff --git a/src/main/java/de/csbdresden/stardist/StarDist2DNMS.java b/src/main/java/de/csbdresden/stardist/StarDist2DNMS.java
index 525cbb5..f50bec0 100644
--- a/src/main/java/de/csbdresden/stardist/StarDist2DNMS.java
+++ b/src/main/java/de/csbdresden/stardist/StarDist2DNMS.java
@@ -32,9 +32,9 @@
         @Menu(label = "StarDist"),
         @Menu(label = "Other"),
         @Menu(label = "StarDist 2D NMS (postprocessing only)", weight = 2)
-}) 
+})
 public class StarDist2DNMS extends StarDist2DBase implements Command {
-    
+
     @Parameter(label=Opt.PROB_IMAGE)
     private Dataset prob;
 
@@ -55,7 +55,7 @@ public class StarDist2DNMS extends StarDist2DBase implements Command {
 
     @Parameter(label=Opt.OUTPUT_TYPE, choices={Opt.OUTPUT_ROI_MANAGER, Opt.OUTPUT_LABEL_IMAGE, Opt.OUTPUT_BOTH}, style=ChoiceWidget.RADIO_BUTTON_HORIZONTAL_STYLE)
     private String outputType = (String) Opt.getDefault(Opt.OUTPUT_TYPE);
-    
+
     // ---------
 
     @Parameter(visibility=ItemVisibility.MESSAGE)
@@ -63,13 +63,16 @@ public class StarDist2DNMS extends StarDist2DBase implements Command {
 
     @Parameter(label=Opt.EXCLUDE_BNDRY, min="0", stepSize="1")
     private int excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);
+    
+    @Parameter(label=Opt.ROI_POSITION, choices={Opt.ROI_POSITION_STACK, Opt.ROI_POSITION_HYPERSTACK}, style=ChoiceWidget.RADIO_BUTTON_HORIZONTAL_STYLE)
+    private String roiPosition = (String) Opt.getDefault(Opt.ROI_POSITION);
 
     @Parameter(label=Opt.VERBOSE)
     private boolean verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
 
     @Parameter(label=Opt.RESTORE_DEFAULTS, callback="restoreDefaults")
     private Button restoreDefaults;
-    
+
     // ---------
 
     private void restoreDefaults() {
@@ -77,6 +80,7 @@ private void restoreDefaults() {
         nmsThresh = (double) Opt.getDefault(Opt.NMS_THRESH);
         outputType = (String) Opt.getDefault(Opt.OUTPUT_TYPE);
         excludeBoundary = (int) Opt.getDefault(Opt.EXCLUDE_BNDRY);
+        roiPosition = (String) Opt.ROI_POSITION_STACK;
         verbose = (boolean) Opt.getDefault(Opt.VERBOSE);
     }
 
@@ -88,7 +92,7 @@ public void run() {
 
         final RandomAccessibleInterval<FloatType> probRAI = (RandomAccessibleInterval<FloatType>) prob.getImgPlus();
         final RandomAccessibleInterval<FloatType> distRAI = (RandomAccessibleInterval<FloatType>) dist.getImgPlus();
-        
+
         final LinkedHashSet<AxisType> probAxes = Utils.orderedAxesSet(prob);
         final LinkedHashSet<AxisType> distAxes = Utils.orderedAxesSet(dist);
         final boolean isTimelapse = probAxes.contains(Axes.TIME);
@@ -103,78 +107,81 @@ public void run() {
                 polygons.nms(nmsThresh);
                 if (verbose)
                     log.info(String.format("frame %03d: %d polygon candidates, %d remain after non-maximum suppression", t, polygons.getSorted().size(), polygons.getWinner().size()));
-                export(outputType, polygons, 1+t);
+                export(outputType, polygons, 1+t, numFrames, roiPosition);
             }
         } else {
             final Candidates polygons = new Candidates(probRAI, distRAI, probThresh, excludeBoundary, verbose ? log : null);
             polygons.nms(nmsThresh);
             if (verbose)
                 log.info(String.format("%d polygon candidates, %d remain after non-maximum suppression", polygons.getSorted().size(), polygons.getWinner().size()));
-            export(outputType, polygons, 0);
+            export(outputType, polygons, 0, 0, roiPosition);
         }
-        
+
         label = labelImageToDataset(outputType);
 
         // call at the end of the run() method
         CommandFromMacro.record(this, this.command);
     }
-    
+
 
     private boolean checkInputs() {
         final LinkedHashSet<AxisType> probAxes = Utils.orderedAxesSet(prob);
         final LinkedHashSet<AxisType> distAxes = Utils.orderedAxesSet(dist);
-        
+
         if (!( (prob.numDimensions() == 2 && probAxes.containsAll(Arrays.asList(Axes.X, Axes.Y))) ||
                (prob.numDimensions() == 3 && probAxes.containsAll(Arrays.asList(Axes.X, Axes.Y, Axes.TIME))) ))
-            return showError("Probability/Score must be a 2D image or timelapse.");
+            return showError(String.format("%s must be a 2D image or timelapse.", Opt.PROB_IMAGE));
 
         if (!( (dist.numDimensions() == 3 && distAxes.containsAll(Arrays.asList(Axes.X, Axes.Y, Axes.CHANNEL))            && dist.getChannels() >= 3) ||
                (dist.numDimensions() == 4 && distAxes.containsAll(Arrays.asList(Axes.X, Axes.Y, Axes.CHANNEL, Axes.TIME)) && dist.getChannels() >= 3) ))
-            return showError("Distance must be a 2D image or timelapse with at least three channels.");
+            return showError(String.format("%s must be a 2D image or timelapse with at least three channels.", Opt.DIST_IMAGE));
 
         if ((prob.numDimensions() + 1) != dist.numDimensions())
-            return showError("Axes of Probability/Score and Distance not compatible.");
+            return showError(String.format("Axes of %s and %s not compatible.", Opt.PROB_IMAGE, Opt.DIST_IMAGE));
 
         if (prob.getWidth() != dist.getWidth() || prob.getHeight() != dist.getHeight())
-            return showError("Width or height of Probability/Score and Distance differ.");
+            return showError(String.format("Width or height of %s and %s differ.", Opt.PROB_IMAGE, Opt.DIST_IMAGE));
 
         if (prob.getFrames() != dist.getFrames())
-            return showError("Number of frames of Probability/Score and Distance differ.");
-        
+            return showError(String.format("Number of frames of %s and %s differ.", Opt.PROB_IMAGE, Opt.DIST_IMAGE));
+
         final AxisType[] probAxesArray = probAxes.stream().toArray(AxisType[]::new);
         final AxisType[] distAxesArray = distAxes.stream().toArray(AxisType[]::new);
         if (!( probAxesArray[0] == Axes.X && probAxesArray[1] == Axes.Y ))
-            return showError("First two axes of Probability/Score must be a X and Y.");
+            return showError(String.format("First two axes of %s must be a X and Y.", Opt.PROB_IMAGE));
         if (!( distAxesArray[0] == Axes.X && distAxesArray[1] == Axes.Y ))
-            return showError("First two axes of Distance must be a X and Y.");        
+            return showError(String.format("First two axes of %s must be a X and Y.", Opt.DIST_IMAGE));
 
         if (!(0 <= nmsThresh && nmsThresh <= 1))
-            return showError("NMS Threshold must be between 0 and 1.");
+            return showError(String.format("%s must be between 0 and 1.", Opt.NMS_THRESH));
 
         if (excludeBoundary < 0)
-            return showError("Boundary Exclusion must be >= 0");
+            return showError(String.format("%s must be >= 0", Opt.EXCLUDE_BNDRY));
 
         if (!(outputType.equals(Opt.OUTPUT_ROI_MANAGER) || outputType.equals(Opt.OUTPUT_LABEL_IMAGE) || outputType.equals(Opt.OUTPUT_BOTH) || outputType.equals(Opt.OUTPUT_POLYGONS)))
-            return showError(String.format("Output Type must be one of {\"%s\", \"%s\", \"%s\"}.", Opt.OUTPUT_ROI_MANAGER, Opt.OUTPUT_LABEL_IMAGE, Opt.OUTPUT_BOTH));
-        
+            return showError(String.format("%s must be one of {\"%s\", \"%s\", \"%s\"}.", Opt.OUTPUT_TYPE, Opt.OUTPUT_ROI_MANAGER, Opt.OUTPUT_LABEL_IMAGE, Opt.OUTPUT_BOTH));
+
         if (outputType.equals(Opt.OUTPUT_POLYGONS) && probAxes.contains(Axes.TIME))
-            return showError(String.format("Timelapse not supported for output type \"%s\"", Opt.OUTPUT_POLYGONS));        
+            return showError(String.format("Timelapse not supported for output type \"%s\"", Opt.OUTPUT_POLYGONS));
+
+        if (!(roiPosition.equals(Opt.ROI_POSITION_STACK) || roiPosition.equals(Opt.ROI_POSITION_HYPERSTACK)))
+            return showError(String.format("%s must be one of {\"%s\", \"%s\"}.", Opt.ROI_POSITION, Opt.ROI_POSITION_STACK, Opt.ROI_POSITION_HYPERSTACK));        
         
         return true;
     }
 
-    
+
     @Override
     protected void exportPolygons(Candidates polygons) {
         this.polygons = polygons;
     }
-    
+
     @Override
     protected ImagePlus createLabelImage() {
-        return IJ.createImage("Labeling", "16-bit black", (int)prob.getWidth(), (int)prob.getHeight(), 1, 1, (int)prob.getFrames());
+        return IJ.createImage(Opt.LABEL_IMAGE, "16-bit black", (int)prob.getWidth(), (int)prob.getHeight(), 1, 1, (int)prob.getFrames());
     }
 
-    
+
     public static void main(final String... args) throws Exception {
         final ImageJ ij = new ImageJ();
         ij.launch(args);
diff --git a/src/main/java/de/csbdresden/stardist/Utils.java b/src/main/java/de/csbdresden/stardist/Utils.java
index 372da97..51eef2b 100644
--- a/src/main/java/de/csbdresden/stardist/Utils.java
+++ b/src/main/java/de/csbdresden/stardist/Utils.java
@@ -9,6 +9,7 @@
 
 import de.lighti.clipper.Path;
 import de.lighti.clipper.Point.LongPoint;
+import ij.gui.PointRoi;
 import ij.gui.PolygonRoi;
 import ij.gui.Roi;
 import net.imagej.Dataset;
@@ -19,16 +20,28 @@
 
 public class Utils {
 
-    public static PolygonRoi toPolygonRoi(Path poly) {
+    public static PolygonRoi toPolygonRoi(Path poly, float S) {
         int n = poly.size();
-        int[] x = new int[n];
-        int[] y = new int[n];
+        float[] x = new float[n];
+        float[] y = new float[n];
         for (int i = 0; i < n; i++) {
             LongPoint p = poly.get(i);
-            x[i] = (int) p.getX();
-            y[i] = (int) p.getY();
+            x[i] = 0.5f + p.getX() / S;
+            y[i] = 0.5f + p.getY() / S;
         }
-        return new PolygonRoi(x,y,n,Roi.POLYGON);
+        return new PolygonRoi(x, y, n, Roi.POLYGON);
+    }
+    
+    public static PointRoi toPointRoi(Point2D o, float S) {
+        return new PointRoi(0.5f + o.x / S, 0.5f + o.y / S);
+    }
+
+    public static Roi toBoxRoi(Box2D bbox, float S) {
+        double xmin = 0.5 + bbox.xmin / S;
+        double xmax = 0.5 + bbox.xmax / S;
+        double ymin = 0.5 + bbox.ymin / S;
+        double ymax = 0.5 + bbox.ymax / S;
+        return new Roi(xmin, ymin, xmax - xmin, ymax - ymin);
     }
 
     public static double[] rayAngles(int n) {
diff --git a/src/main/resources/models/2D/he_heavy_augment.zip b/src/main/resources/models/2D/he_heavy_augment.zip
new file mode 100644
index 0000000..f745bf8
Binary files /dev/null and b/src/main/resources/models/2D/he_heavy_augment.zip differ