Add OME-Zarr support (#66)

* Add ngff-rfc5 coordinate transformation examples as submodule
  at 8eb63f3

* add ome testdata for v0.5 and v0.4

* add ome v0.4 and v0.5 implementation

* add ome v0.4 and v0.5 tests

* add omero, bioformats2raw, labels, hcs

* add tests for omero, bioformats2raw, labels, and hcs

* add ome v1.0 and v0.6

* reduce code duplication and better unified interface between versions (via MultiscalesEntry)

* allow unknown parameters for MultiscalesEntry

* add zstd codec for v2

* version to SNAPSHOT for compability with ome-zarr-fiji-java PR

* update user guide to include OME-Zarr section and create dedicated OME-Zarr guide

* rename tests

* add zstd to ZarrPythonTests.testWriteV2

* add OmeZarrUserGuideExamplesTest

* hardened OME metadata deserialization by ignoring unknown fields

* add test to read ome sample data from s3

* add hint to stores in USERGUIDE-OME-ZARR.md

* warn on unknown metadata fields

* add v0.4zarr3

* add optional omero fields id, version, name

* add omero to v0.6

* typing of Omero Metadata

* better representation of transformations

* better representation of transformations

* test object mappers

* remove ome versions v0.4-zarr and v1.0

* add scene, plate, well, and bioformats2raw to v0.6

* refactor scene to use existing transformations

* test scene

* move the namespace of ome to dev.zarr.zarrjava.experimental.ome

* fix openSceneExample2TwoAffineLinksViaInstrument2

* refactor transformation inheritance across versions to allow for better type checks

Author: brokkoli71

.github/workflows/ci.yml

@@ -28,6 +28,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
+        with:
+          submodules: true
 
       - name: Set up JDK
         uses: actions/setup-java@v4

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "testdata/ome/v0.6/examples"]
+	path = testdata/ome/v0.6/examples
+	url = https://github.com/jo-mueller/ngff-rfc5-coordinate-transformation-examples

USERGUIDE-OME-ZARR.md

@@ -0,0 +1,151 @@
+# OME-Zarr Guide for zarr-java
+
+## Scope and supported versions
+
+`dev.zarr.zarrjava.experimental.ome` supports:
+
+- v0.4 (Zarr v2 layout)
+- v0.5 (Zarr v3 layout)
+- v0.6 / RFC-5
+
+## Primary entry points
+
+Use these static open methods:
+
+- `MultiscaleImage.open(StoreHandle)` for multiscale images (auto-detects v0.4/v0.5/v0.6 image nodes)
+- `Plate.open(StoreHandle)` for HCS plates (v0.4/v0.5)
+- `Well.open(StoreHandle)` for HCS wells (v0.4/v0.5)
+
+### StoreHandle and stores
+
+OME-Zarr APIs are store-agnostic: pass any `StoreHandle` (filesystem, S3, HTTP, ZIP, memory) to `open(...)`.  
+See storage backend setup in [`USERGUIDE.md#storage-backends`](USERGUIDE.md#storage-backends).
+
+```java
+StoreHandle s3 = new S3Store(client, "idr", "zarr/v0.5/idr0083").resolve("9822152.zarr");
+MultiscaleImage image = MultiscaleImage.open(s3);
+```
+
+## Essential methods
+
+### MultiscaleImage
+
+Metadata:
+
+- `getMultiscaleNode(int i)` → normalized `ome.metadata.MultiscalesEntry`
+- `getAxisNames()` → axis names from multiscale `0`
+- `getScaleLevelCount()` → number of datasets/levels in multiscale `0`
+- `getLabels()` / `openLabel(String)` → labels subgroup helpers
+
+Array access:
+
+- `openScaleLevel(int i)` → `dev.zarr.zarrjava.core.Array`
+- then call `read()` or `read(offset, shape)` on that array
+- typical viewer flow: read axes + scale count first, then select a level by `i`
+
+### Plate and Well (HCS)
+
+Metadata:
+
+- `Plate.getPlateMetadata()`
+- `Well.getWellMetadata()`
+
+Navigation:
+
+- `Plate.openWell(String rowColPath)` (for example `"A/1"`)
+- `Well.openImage(String path)` (for example `"0"`)
+
+## Version-specific typed metadata
+
+If you need the raw version-specific metadata model instead of normalized `MultiscalesEntry`:
+
+- Cast to `MultiscalesMetadataImage<?>` and call `getMultiscalesEntry(i)`
+
+
+## v0.6 Scene metadata
+
+Scene roots (groups with `ome.scene`) are supported via `dev.zarr.zarrjava.experimental.ome.v0_6.Scene`:
+
+- `Scene.openScene(StoreHandle)` / `Scene.open(StoreHandle)`
+- `Scene.createScene(StoreHandle, SceneMetadata)` / `Scene.create(...)`
+- `listImageNodes()` and `openImageNode(String)` for sibling multiscale images
+- `getCoordinateTransformationGraph()` for lightweight metadata graph inspection
+
+Notes:
+- Parsing is permissive and explicit (no strict full-spec validation).
+- Scene-level references (`input`/`output`) are resolved against scene-root coordinate systems and child image coordinate systems for graph inspection.
+- Path-based transform assets can be normalized with `Scene.normalizeCoordinateTransformPath(...)` and grouped under `coordinateTransformations/` via `createCoordinateTransformationsGroup()`.
+
+## Read example
+
+```java
+import dev.zarr.zarrjava.experimental.ome.MultiscaleImage;
+import dev.zarr.zarrjava.experimental.ome.Plate;
+import dev.zarr.zarrjava.experimental.ome.Well;
+import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.StoreHandle;
+
+StoreHandle imageHandle = new FilesystemStore("/data/ome/image.zarr").resolve();
+MultiscaleImage image = MultiscaleImage.open(imageHandle);
+
+int scaleCount = image.getScaleLevelCount();
+java.util.List<String> axisNames = image.getAxisNames();
+dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry entry0 = image.getMultiscaleNode(0);
+
+dev.zarr.zarrjava.core.Array s0 = image.openScaleLevel(0);
+ucar.ma2.Array full = s0.read();
+ucar.ma2.Array subset = s0.read(new long[]{0, 0, 0, 0, 0}, new long[]{1, 1, 4, 8, 8});
+
+java.util.List<String> labels = image.getLabels();
+if (!labels.isEmpty()) {
+    MultiscaleImage label = image.openLabel(labels.get(0));
+}
+
+StoreHandle plateHandle = new FilesystemStore("/data/ome/plate.zarr").resolve();
+Plate plate = Plate.open(plateHandle);
+Well well = plate.openWell("A/1");
+MultiscaleImage wellImage = well.openImage("0");
+```
+
+## Write example
+
+Creation is version-specific, but the pattern is the same: create node with version metadata, then append levels/datasets with scale transforms. For example, for v0.5:
+
+```java
+import dev.zarr.zarrjava.experimental.ome.metadata.Axis;
+import dev.zarr.zarrjava.experimental.ome.metadata.CoordinateTransformation;
+import dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry;
+import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.StoreHandle;
+import dev.zarr.zarrjava.v3.Array;
+import dev.zarr.zarrjava.v3.DataType;
+
+import java.util.Arrays;
+import java.util.Collections;
+
+StoreHandle out = new FilesystemStore("/tmp/ome_v05.zarr").resolve();
+MultiscalesEntry ms = new MultiscalesEntry(
+    Arrays.asList(new Axis("y", "space", "micrometer"), new Axis("x", "space", "micrometer")),
+    Collections.<Dataset>emptyList());
+);
+dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage.create(out, ms);
+
+written.createScaleLevel(
+    "s0",
+    Array.metadataBuilder().withShape(1024, 1024).withChunkShape(256, 256).withDataType(DataType.UINT16).build(),
+    Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(1.0, 1.0)))
+);
+written.createScaleLevel(
+    "s1",
+    Array.metadataBuilder().withShape(512, 512).withChunkShape(256, 256).withDataType(DataType.UINT16).build(),
+    Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(2.0, 2.0)))
+);
+```
+
+## Write entry points by version
+
+- `ome.v0_4.MultiscaleImage.create(...)`
+- `ome.v0_5.MultiscaleImage.create(...)`
+- `ome.v0_6.MultiscaleImage.create(...)`
+
+Use the corresponding metadata classes for each version package.

USERGUIDE.md

@@ -11,8 +11,9 @@
 7. [Storage Backends](#storage-backends)
 8. [Compression and Codecs](#compression-and-codecs)
 9. [Advanced Topics](#advanced-topics)
-10. [Examples](#examples)
-11. [Troubleshooting](#troubleshooting)
+10. [OME-Zarr](#ome-zarr-v04-v05-v06)
+11. [Examples](#examples)
+12. [Troubleshooting](#troubleshooting)
 ---
 ## Introduction
 zarr-java is a Java implementation of the [Zarr specification](https://zarr.dev/) for chunked, compressed, N-dimensional arrays. It supports both Zarr version 2 and version 3 formats, providing a unified API for working with large scientific datasets.
@@ -653,7 +654,6 @@ try {
 - `"No Zarr array found at the specified location"` - Check path and ensure `.zarray` (v2) or `zarr.json` (v3) exists
 - `"Requested data is outside of the array's domain"` - Verify that `offset + shape <= array.shape`
 - `"Failed to read from store"` - Check network connectivity, file permissions, or storage availability
----
 
 ### Best Practices
 1. **Chunk sizes for Best Performance**:
@@ -677,7 +677,14 @@ try {
    // For balanced 3D access
    .withChunkShape(100, 100, 100)  // Balanced for all dimensions
    ```
-  
+
+## OME-Zarr (v0.4, v0.5, v0.6)
+
+For a focused OME-Zarr API guide (metadata access, array access, version behavior, and concise examples),
+see:
+
+- [`USERGUIDE-OME-ZARR.md`](USERGUIDE-OME-ZARR.md)
+   
 ## Examples
 ### Complete Example: Creating a 3D Dataset
 ```java

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>dev.zarr</groupId>
     <artifactId>zarr-java</artifactId>
-    <version>0.1.0</version>
+    <version>0.1.1-SNAPSHOT</version>
 
     <name>zarr-java</name>
 

src/main/java/dev/zarr/zarrjava/core/codec/core/ZstdCodec.java

@@ -0,0 +1,35 @@
+package dev.zarr.zarrjava.core.codec.core;
+
+import com.github.luben.zstd.Zstd;
+import com.github.luben.zstd.ZstdCompressCtx;
+import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.codec.BytesBytesCodec;
+import dev.zarr.zarrjava.utils.Utils;
+
+import java.nio.ByteBuffer;
+
+public abstract class ZstdCodec extends BytesBytesCodec {
+
+    @Override
+    public ByteBuffer decode(ByteBuffer compressedBytes) throws ZarrException {
+        byte[] compressedArray = Utils.toArray(compressedBytes);
+        long originalSize = Zstd.getFrameContentSize(compressedArray);
+        if (originalSize < 0) {
+            throw new ZarrException("Failed to get decompressed zstd size.");
+        }
+        byte[] decompressed = Zstd.decompress(compressedArray, (int) originalSize);
+        return ByteBuffer.wrap(decompressed);
+    }
+
+    protected ByteBuffer encodeInternal(int level, boolean checksum, ByteBuffer chunkBytes)
+            throws ZarrException {
+        byte[] arr = Utils.toArray(chunkBytes);
+        byte[] compressed;
+        try (ZstdCompressCtx ctx = new ZstdCompressCtx()) {
+            ctx.setLevel(level);
+            ctx.setChecksum(checksum);
+            compressed = ctx.compress(arr);
+        }
+        return ByteBuffer.wrap(compressed);
+    }
+}

src/main/java/dev/zarr/zarrjava/experimental/ome/MultiscaleImage.java

@@ -0,0 +1,137 @@
+package dev.zarr.zarrjava.experimental.ome;
+
+import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.Node;
+import dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry;
+import dev.zarr.zarrjava.store.StoreHandle;
+import dev.zarr.zarrjava.utils.Utils;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Unified interface for reading OME-Zarr multiscale images across Zarr format versions.
+ */
+public interface MultiscaleImage {
+
+    /**
+     * Returns the store handle for this multiscale image node.
+     */
+    StoreHandle getStoreHandle();
+
+    /**
+     * Returns a {@link MultiscalesEntry} view of multiscale {@code i}, normalized to the shared
+     * metadata type. All axis and dataset information is accessible from the returned entry.
+     */
+    MultiscalesEntry getMultiscaleNode(int i) throws ZarrException;
+
+    /**
+     * Opens the scale level array at index {@code i} within the first multiscale entry.
+     */
+    dev.zarr.zarrjava.core.Array openScaleLevel(int i) throws IOException, ZarrException;
+
+    /**
+     * Returns the number of scale levels in the first multiscale entry.
+     */
+    int getScaleLevelCount() throws ZarrException;
+
+    /**
+     * Returns the axis names of the first multiscale entry.
+     */
+    default List<String> getAxisNames() throws ZarrException {
+        MultiscalesEntry entry = getMultiscaleNode(0);
+        List<String> names = new ArrayList<>();
+        for (dev.zarr.zarrjava.experimental.ome.metadata.Axis axis : entry.axes) {
+            names.add(axis.name);
+        }
+        return names;
+    }
+
+    /**
+     * Returns all label names from the {@code labels/} sub-group, or an empty list if none exist.
+     */
+    default List<String> getLabels() throws IOException, ZarrException {
+        StoreHandle labelsHandle = getStoreHandle().resolve("labels");
+
+        // Try v0.5: labels/zarr.json with {"attributes": {"labels": [...]}}
+        StoreHandle zarrJson = labelsHandle.resolve(Node.ZARR_JSON);
+        if (zarrJson.exists()) {
+            com.fasterxml.jackson.databind.ObjectMapper mapper = dev.zarr.zarrjava.v3.Node.makeObjectMapper();
+            byte[] bytes = Utils.toArray(zarrJson.readNonNull());
+            com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
+            com.fasterxml.jackson.databind.JsonNode attrs = root.get("attributes");
+            if (attrs != null && attrs.has("labels")) {
+                com.fasterxml.jackson.databind.JsonNode labelsNode = attrs.get("labels");
+                List<String> result = new ArrayList<>();
+                for (com.fasterxml.jackson.databind.JsonNode item : labelsNode) {
+                    result.add(item.asText());
+                }
+                return result;
+            }
+        }
+
+        // Try v0.4: labels/.zattrs with {"labels": [...]}
+        StoreHandle zattrs = labelsHandle.resolve(Node.ZATTRS);
+        if (zattrs.exists()) {
+            com.fasterxml.jackson.databind.ObjectMapper mapper = dev.zarr.zarrjava.v2.Node.makeObjectMapper();
+            byte[] bytes = Utils.toArray(zattrs.readNonNull());
+            com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
+            if (root.has("labels")) {
+                com.fasterxml.jackson.databind.JsonNode labelsNode = root.get("labels");
+                List<String> result = new ArrayList<>();
+                for (com.fasterxml.jackson.databind.JsonNode item : labelsNode) {
+                    result.add(item.asText());
+                }
+                return result;
+            }
+        }
+
+        return Collections.emptyList();
+    }
+
+    /**
+     * Opens the named label image from the {@code labels/} sub-group.
+     */
+    default MultiscaleImage openLabel(String name) throws IOException, ZarrException {
+        return MultiscaleImage.open(getStoreHandle().resolve("labels").resolve(name));
+    }
+
+    /**
+     * Opens an OME-Zarr multiscale image at the given store handle, auto-detecting the Zarr version.
+     *
+     * <p>Tries v0.6 (zarr.json with version "0.6"), then v0.5 (zarr.json with "ome" key), then v0.4 (.zattrs with "multiscales" key).
+     */
+    static MultiscaleImage open(StoreHandle storeHandle) throws IOException, ZarrException {
+        // Try version >= 0.5: zarr.json with "ome" key
+        StoreHandle zarrJson = storeHandle.resolve(Node.ZARR_JSON);
+        if (zarrJson.exists()) {
+            com.fasterxml.jackson.databind.ObjectMapper mapper = OmeObjectMappers.makeV3Mapper();
+            byte[] bytes = Utils.toArray(zarrJson.readNonNull());
+            com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
+            com.fasterxml.jackson.databind.JsonNode attrs = root.get("attributes");
+            if (attrs != null && attrs.has("ome")) {
+                com.fasterxml.jackson.databind.JsonNode omeNode = attrs.get("ome");
+                String version = omeNode.has("version") ? omeNode.get("version").asText() : "";
+                if (version.startsWith("0.6")) {
+                    return dev.zarr.zarrjava.experimental.ome.v0_6.MultiscaleImage.openMultiscaleImage(storeHandle);
+                }
+                return dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage.openMultiscaleImage(storeHandle);
+            }
+        }
+
+        // Try v0.4: .zattrs with "multiscales" key
+        StoreHandle zattrs = storeHandle.resolve(Node.ZATTRS);
+        if (zattrs.exists()) {
+            com.fasterxml.jackson.databind.ObjectMapper mapper = OmeObjectMappers.makeV2Mapper();
+            byte[] bytes = Utils.toArray(zattrs.readNonNull());
+            com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
+            if (root.has("multiscales")) {
+                return dev.zarr.zarrjava.experimental.ome.v0_4.MultiscaleImage.openMultiscaleImage(storeHandle);
+            }
+        }
+
+        throw new ZarrException("No OME-Zarr multiscale metadata found at " + storeHandle);
+    }
+}