Extract ome module

.gitignore

@@ -1,5 +1,9 @@
 target/
 !.mvn/wrapper/maven-wrapper.jar
+
+### Notebooks ###
+notebooks/*_executed.ipynb
+**/.ipynb_checkpoints/
 !**/src/main/**/target/
 !**/src/test/**/target/
 
@@ -40,10 +44,16 @@ build/
 ### Custom ###
 /testdata/l4_sample
 /testdata/l4_sample.zip
+zarr-java-core/testdata/l4_sample
+zarr-java-core/testdata/l4_sample.zip
 /testoutput
+zarr-java-core/testoutput
+zarr-java-ome/testoutput
 /.python-version
 /main.py
 /pyproject.toml
 /uv.lock
 **/__pycache__
 /dependency-reduced-pom.xml
+zarr-java-core/dependency-reduced-pom.xml
+zarr-java-ome/dependency-reduced-pom.xml

.gitmodules

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

README.md

@@ -56,6 +56,31 @@ data
 );
 ```
 
+## Interactive Notebooks
+
+The `notebooks/` directory contains IJava (Java kernel for Jupyter) notebooks that let you explore and verify the library interactively without publishing it.
+
+**Prerequisites:** Java 17+, Maven 3.6+, Python 3, `curl`, `unzip`
+
+```bash
+./notebooks/start.sh
+```
+
+This single command:
+1. Builds the project and installs JARs to your local Maven cache (`~/.m2`)
+2. Wires up the classpath so the notebooks can import the library directly — no internet access needed for the library itself
+3. Installs Jupyter and the IJava kernel into `~/.jupyter-venv` on first run (one-time, ~1 min)
+4. Opens JupyterLab in your browser
+
+Available notebooks (in `notebooks/notebooks/`):
+
+| Notebook | Covers |
+|---|---|
+| `zarr_core.ipynb` | v2/v3 arrays, stores, codecs, sharding, groups, attributes, ZIP |
+| `ome_zarr_integration.ipynb` | OME-Zarr v0.4/v0.5, multiscale images, HCS plates and wells |
+
+---
+
 ## Development Start-Guide
 
 ### Run Tests Locally

USERGUIDE-OME-ZARR.md

@@ -1,8 +1,35 @@
 # OME-Zarr Guide for zarr-java
 
+## Separate module
+
+OME-Zarr support lives in a dedicated module: **`zarr-java-ome`**.  
+Add it alongside the core library:
+
+### Maven
+```xml
+<dependency>
+    <groupId>dev.zarr</groupId>
+    <artifactId>zarr-java-core</artifactId>
+    <version>0.1.3</version>
+</dependency>
+<dependency>
+    <groupId>dev.zarr</groupId>
+    <artifactId>zarr-java-ome</artifactId>
+    <version>0.1.3</version>
+</dependency>
+```
+
+### Gradle
+```gradle
+dependencies {
+    implementation 'dev.zarr:zarr-java-core:0.1.3'
+    implementation 'dev.zarr:zarr-java-ome:0.1.3'
+}
+```
+
 ## Scope and supported versions
 
-`dev.zarr.zarrjava.experimental.ome` supports:
+`dev.zarr.omezarr` supports:
 
 - v0.4 (Zarr v2 layout)
 - v0.5 (Zarr v3 layout)
@@ -32,7 +59,7 @@ MultiscaleImage image = MultiscaleImage.open(s3);
 
 Metadata:
 
-- `getMultiscaleNode(int i)` → normalized `ome.metadata.MultiscalesEntry`
+- `getMultiscaleNode(int i)` → normalized `omezarr.metadata.MultiscalesEntry`
 - `getAxisNames()` → axis names from multiscale `0`
 - `getScaleLevelCount()` → number of datasets/levels in multiscale `0`
 - `getLabels()` / `openLabel(String)` → labels subgroup helpers
@@ -64,7 +91,7 @@ If you need the raw version-specific metadata model instead of normalized `Multi
 
 ## v0.6 Scene metadata
 
-Scene roots (groups with `ome.scene`) are supported via `dev.zarr.zarrjava.experimental.ome.v0_6.Scene`:
+Scene roots (groups with `ome.scene`) are supported via `dev.zarr.omezarr.v0_6.Scene`:
 
 - `Scene.openScene(StoreHandle)` / `Scene.open(StoreHandle)`
 - `Scene.createScene(StoreHandle, SceneMetadata)` / `Scene.create(...)`
@@ -79,9 +106,10 @@ Notes:
 ## 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.omezarr.MultiscaleImage;
+import dev.zarr.omezarr.Plate;
+import dev.zarr.omezarr.Well;
+import dev.zarr.omezarr.metadata.MultiscalesEntry;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
 
@@ -90,7 +118,7 @@ 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);
+MultiscalesEntry entry0 = image.getMultiscaleNode(0);
 
 dev.zarr.zarrjava.core.Array s0 = image.openScaleLevel(0);
 ucar.ma2.Array full = s0.read();
@@ -112,9 +140,10 @@ MultiscaleImage wellImage = well.openImage("0");
 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.omezarr.metadata.Axis;
+import dev.zarr.omezarr.metadata.Dataset;
+import dev.zarr.omezarr.metadata.MultiscalesEntry;
+import dev.zarr.omezarr.metadata.transform.CoordinateTransformation;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.v3.Array;
@@ -126,9 +155,9 @@ 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());
+    Collections.<Dataset>emptyList()
 );
-dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage.create(out, ms);
+dev.zarr.omezarr.v0_5.MultiscaleImage written = dev.zarr.omezarr.v0_5.MultiscaleImage.create(out, ms);
 
 written.createScaleLevel(
     "s0",
@@ -144,8 +173,8 @@ written.createScaleLevel(
 
 ## Write entry points by version
 
-- `ome.v0_4.MultiscaleImage.create(...)`
-- `ome.v0_5.MultiscaleImage.create(...)`
-- `ome.v0_6.MultiscaleImage.create(...)`
+- `dev.zarr.omezarr.v0_4.MultiscaleImage.create(...)`
+- `dev.zarr.omezarr.v0_5.MultiscaleImage.create(...)`
+- `dev.zarr.omezarr.v0_6.MultiscaleImage.create(...)`
 
 Use the corresponding metadata classes for each version package.

USERGUIDE.md

@@ -31,15 +31,25 @@ Add the following dependency to your `pom.xml`:
 ```xml
 <dependency>
     <groupId>dev.zarr</groupId>
-    <artifactId>zarr-java</artifactId>
-    <version>0.0.10</version>
+    <artifactId>zarr-java-core</artifactId>
+    <version>0.1.3</version>
+</dependency>
+```
+For OME-Zarr support, also add:
+```xml
+<dependency>
+    <groupId>dev.zarr</groupId>
+    <artifactId>zarr-java-ome</artifactId>
+    <version>0.1.3</version>
 </dependency>
 ```
 ### Gradle
 Add the following to your `build.gradle`:
 ```gradle
 dependencies {
-    implementation 'dev.zarr:zarr-java:0.0.10'
+    implementation 'dev.zarr:zarr-java-core:0.1.3'
+    // Optional: OME-Zarr support
+    implementation 'dev.zarr:zarr-java-ome:0.1.3'
 }
 ```
 ### Requirements
@@ -680,7 +690,9 @@ try {
 
 ## OME-Zarr (v0.4, v0.5, v0.6)
 
-For a focused OME-Zarr API guide (metadata access, array access, version behavior, and concise examples),
+OME-Zarr support is provided by the separate `zarr-java-ome` module (package `dev.zarr.omezarr`).
+
+For the full OME-Zarr API guide (installation, metadata access, array access, version behavior, and concise examples),
 see:
 
 - [`USERGUIDE-OME-ZARR.md`](USERGUIDE-OME-ZARR.md)