Multi channel omezarr

modules/AdministrationGUI/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>AdministrationGUI</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>adminstration</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/ColorDepthSearch/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>ColorDepthSearch</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>colordepth</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/CommonGUI/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>CommonGUI</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>common-gui</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/CommonLibraries/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>CommonLibraries</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>libraries</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <properties>

modules/Core/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>Core</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>core</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/DarculaLAF/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>DarculaLAF</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>darcula</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/DataBrowser/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>DataBrowser</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>browser</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/GLViewerTools/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>GLViewerTools</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>gltools</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/Geometry3d/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>Geometry3d</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>geometry3d</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>

modules/HortaTracer/pom.xml

@@ -5,14 +5,14 @@
     <parent>
         <groupId>org.janelia</groupId>
         <artifactId>workstation</artifactId>
-        <version>9.24.1</version>
+        <version>9.25.1</version>
         <relativePath>../..</relativePath>
     </parent>
 
     <name>HortaTracer</name>
     <groupId>org.janelia.workstation</groupId>
     <artifactId>horta</artifactId>
-    <version>9.24.1</version>
+    <version>9.25.1</version>
     <packaging>nbm</packaging>
 
     <dependencies>
@@ -78,7 +78,7 @@
         <dependency>
             <groupId>org.aind</groupId>
             <artifactId>jomezarr</artifactId>
-            <version>1.4.3</version>
+            <version>1.4.4</version>
         </dependency>
         <dependency>
             <groupId>dev.zarr</groupId>

modules/HortaTracer/src/main/java/org/janelia/horta/NeuronTracerTopComponent.java

@@ -1123,6 +1123,17 @@ public boolean loadDroppedOmeZarr(String sourceName) {
                             if (!haveSetBoundingBox[0] && !source.getResolutions().isEmpty()) {
                                 haveSetBoundingBox[0] = true;
 
+                                // Metadata is loaded, so the channel count is known: size the
+                                // shared color model to match, plus one extra slot for the
+                                // synthetic tracing/unmix channel (mirrors the legacy 2-channel
+                                // TetVolumeActor convention), and rebuild the slider UI.
+                                if (getImageColorModel().getChannelCount() != source.getChannelCount() + 1) {
+                                    getImageColorModel().reset(65535, source.getChannelCount() + 1);
+                                    getImageColorModel().getChannel(source.getChannelCount())
+                                            .setColor(new Color(0f, 0.5f, 1.0f)); // unmixed channel in Economo blue
+                                    initColorModel();
+                                }
+
                                 TmModelManager.getInstance().setSampleBoundingBox(source.getBoundingBox3d());
                                 TmModelManager.getInstance().setVoxelCenter(source.getVoxelCenter());
 
@@ -2370,6 +2381,13 @@ void setKtxSource(KtxOctreeBlockTileSource ktxSource) {
         if (ktxSource != null) {
             omeZarrSource = null;
             setVolumeSource(null);
+            // TetVolumeActor only supports exactly 3 channels; reset the shared color
+            // model in case a previous OME-Zarr multichannel session resized it larger,
+            // otherwise TetVolumeActor.display() throws UnsupportedOperationException.
+            if (getImageColorModel().getChannelCount() != 3) {
+                getImageColorModel().reset(65535, 3);
+                initColorModel();
+            }
         }
     }
 

modules/HortaTracer/src/main/java/org/janelia/horta/ViewLoader.java

@@ -1,5 +1,6 @@
 package org.janelia.horta;
 
+import java.awt.Color;
 import java.io.IOException;
 import java.net.URL;
 
@@ -138,6 +139,18 @@ private OmeZarrBlockTileSource createOmeZarrSource(URL renderedOmeZarrUrl, TmSam
                     if (!haveFirstDataset[0] && !source.getResolutions().isEmpty()) {
                         haveFirstDataset[0] = true;
                         try {
+                            // OME-Zarr metadata is now loaded, so the channel count is known.
+                            // Size the shared color model to match, plus one extra slot for the
+                            // synthetic tracing/unmix channel (mirrors the legacy 2-channel
+                            // TetVolumeActor convention of a dedicated slider for that channel),
+                            // then re-apply the persisted/workspace color model at the correct
+                            // channel count (this also rebuilds the slider UI via ColorModelUpdateEvent).
+                            if (nttc.getImageColorModel().getChannelCount() != source.getChannelCount() + 1) {
+                                nttc.getImageColorModel().reset(65535, source.getChannelCount() + 1);
+                                nttc.getImageColorModel().getChannel(source.getChannelCount())
+                                        .setColor(new Color(0f, 0.5f, 1.0f)); // unmixed channel in Economo blue
+                                nttc.initColorModel();
+                            }
                             if (nttc.doesUpdateVolumeCache()) {
                                 loader.loadTransientOmeZarrTileAtCurrentFocus(nttc.getOmeZarrSource());
                             } else {

modules/HortaTracer/src/main/java/org/janelia/horta/actors/OmeZarrVolumeMeshActor.java

@@ -13,6 +13,7 @@
 import org.janelia.horta.blocks.OmeZarrBlockResolution;
 import org.janelia.horta.blocks.OmeZarrBlockTileKey;
 import org.janelia.horta.blocks.OmeZarrBlockTileSource;
+import org.janelia.horta.volume.OmeZarrVolumeMipMaterial;
 import org.janelia.horta.volume.VolumeMipMaterial;
 import org.janelia.workstation.controller.model.color.ImageColorModel;
 
@@ -36,8 +37,8 @@ public class OmeZarrVolumeMeshActor extends MeshActor implements SortableBlockAc
 
     private double distance;
 
-    public OmeZarrVolumeMeshActor(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile, VolumeMipMaterial.VolumeState volumeState, int colorChannel) throws IOException {
-        super(new OmeZarrMesh(tile), new OmeZarrVolumeMeshActor.MeshMaterial(source, tile, source.getColorModel(), volumeState, colorChannel), null);
+    public OmeZarrVolumeMeshActor(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile, VolumeMipMaterial.VolumeState volumeState) throws IOException {
+        super(new OmeZarrMesh(tile), new OmeZarrVolumeMeshActor.MeshMaterial(source, tile, source.getColorModel(), volumeState), null);
 
         this.meshMaterial = (OmeZarrVolumeMeshActor.MeshMaterial) getMaterial();
 
@@ -99,18 +100,25 @@ public BlockTileResolution getResolution() {
         return resolution;
     }
 
-    private static class MeshMaterial extends VolumeMipMaterial {
-        private MeshMaterial(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile, ImageColorModel imageColorModel, VolumeState volumeState, int colorChannel) throws IOException {
-            super(safeLoadData(source, tile, colorChannel), imageColorModel);
+    private static class MeshMaterial extends OmeZarrVolumeMipMaterial {
+        private MeshMaterial(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile, ImageColorModel imageColorModel, VolumeMipMaterial.VolumeState volumeState) throws IOException {
+            super(safeLoadData(source, tile), imageColorModel);
             setVolumeState(volumeState);
         }
 
-        private static Texture3d safeLoadData(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile, int colorChannel) throws IOException {
-            Texture3d brick = source.loadBrick(tile, colorChannel);
-            if (brick == null) {
-                throw new IOException("Load was interrupted");
+        // Load every channel of the block into its own single-component texture, preserving
+        // OME-Zarr's per-channel separation; the shader combines them at render time.
+        private static Texture3d[] safeLoadData(OmeZarrBlockTileSource source, OmeZarrBlockTileKey tile) throws IOException {
+            int channelCount = Math.max(1, Math.min(source.getChannelCount(), OmeZarrVolumeMipMaterial.MAX_CHANNELS));
+            Texture3d[] textures = new Texture3d[channelCount];
+            for (int c = 0; c < channelCount; ++c) {
+                Texture3d brick = source.loadBrick(tile, c);
+                if (brick == null) {
+                    throw new IOException("Load was interrupted");
+                }
+                textures[c] = brick;
             }
-            return brick;
+            return textures;
         }
     }
 }

modules/HortaTracer/src/main/java/org/janelia/horta/blocks/OmeZarrBlockLoadRunner.java

@@ -44,7 +44,7 @@ private void loadFromBlockSource() {
         try {
             state = OmeZarrBlockLoadRunner.State.LOADING;
             OmeZarrVolumeActor parentActor = OmeZarrVolumeActor.getInstance();
-            blockActor = new OmeZarrVolumeMeshActor(omeZarrBlockTileSource, omeZarrOctreeBlockTileKey, parentActor.getVolumeState(), 0);
+            blockActor = new OmeZarrVolumeMeshActor(omeZarrBlockTileSource, omeZarrOctreeBlockTileKey, parentActor.getVolumeState());
             state = OmeZarrBlockLoadRunner.State.LOADED;
             setChanged();
             long endTime = System.currentTimeMillis();

modules/HortaTracer/src/main/java/org/janelia/horta/blocks/OmeZarrBlockTileKey.java

@@ -167,10 +167,19 @@ public double getResolutionMicrometers() {
     private static final ColorModel colorModel = new ComponentColorModel(ColorSpace.getInstance(ColorSpace.CS_GRAY), false, true, Transparency.OPAQUE, DataBuffer.TYPE_USHORT);
 
     public Texture3d loadBrick(AutoContrastParameters parameters) {
+        return loadBrick(parameters, 0);
+    }
+
+    public Texture3d loadBrick(AutoContrastParameters parameters, int channel) {
         Texture3d texture = new Texture3d();
 
         try {
-            WritableRaster[] slices = TCZYXRasterZStack.fromDataset(dataset, readShape, readOffset, 1, parameters != null, parameters, null);
+            // readShape/readOffset are TCZYX; index 1 is the channel. Read one channel at a time
+            // into a single-component texture, leaving the key itself channel-agnostic.
+            int[] channelOffset = readOffset.clone();
+            channelOffset[1] = channel;
+
+            WritableRaster[] slices = TCZYXRasterZStack.fromDataset(dataset, readShape, channelOffset, 1, parameters != null, parameters, null);
 
             texture.loadRasterSlices(slices, colorModel);
 

modules/HortaTracer/src/main/java/org/janelia/horta/blocks/OmeZarrBlockTileSource.java

@@ -41,6 +41,8 @@ public class OmeZarrBlockTileSource implements BlockTileSource<OmeZarrBlockTileK
     private final ArrayList<OmeZarrBlockResolution> resolutions = new ArrayList<>();
     private OmeZarrBlockResolution maximumResolution = null;
 
+    private int channelCount = 1;
+
     private final ImageColorModel imageColorModel;
 
     private final boolean useAutoContrast;
@@ -128,6 +130,9 @@ private OmeZarrBlockTileSource init(OmeZarrReaderProgressObserver progressObserv
                         boundingBox3d = new BoundingBox3d(new Vec3(origin.getX(), origin.getY(), origin.getZ()), new Vec3(outerCorner.getX(), outerCorner.getY(), outerCorner.getZ()));
                         voxelCenter = boundingBox3d.getCenter();
 
+                        // TCZYX: channel count is the C dimension; constant across resolution levels.
+                        channelCount = Math.max(1, shapeIndex.getC());
+
                         haveExtents = true;
                     }
 
@@ -239,13 +244,16 @@ ConstVector3 getBlockSize(OmeZarrBlockResolution resolution) {
                 resolution.getChunkSize()[2] * resolution.getResolutionMicrometers());
     }
 
+    public int getChannelCount() {
+        return channelCount;
+    }
+
     public Texture3d loadBrick(OmeZarrBlockTileKey tile, int colorChannel) {
-        // setColorChannelIndex(colorChannel);
-        return loadBrick(tile);
+        return tile.loadBrick(useAutoContrast ? autoContrastParameters : null, colorChannel);
     }
 
     public Texture3d loadBrick(OmeZarrBlockTileKey tile) {
-        return tile.loadBrick(useAutoContrast ? autoContrastParameters : null);
+        return loadBrick(tile, 0);
     }
 /*
     private void createTileKeysForDataset(OmeZarrDataset dataset, OmeZarrReaderProgressObserver progressReceiver) {