From 4afa6e56e5bc0c9683ad03fa946aef503895c51d Mon Sep 17 00:00:00 2001
From: Jacky Ko <ka.ko@kenn.ox.ac.uk>
Date: Wed, 24 Jan 2024 16:49:15 +0000
Subject: [PATCH 1/3] add doc

---
 aicsimageio/writers/ome_zarr_writer.py | 40 ++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/aicsimageio/writers/ome_zarr_writer.py b/aicsimageio/writers/ome_zarr_writer.py
index e28b0d95b..10c7d19db 100644
--- a/aicsimageio/writers/ome_zarr_writer.py
+++ b/aicsimageio/writers/ome_zarr_writer.py
@@ -178,6 +178,46 @@ def write_image(
         ... writer = OmeZarrWriter("/path/to/file.ome.zarr")
         ... writer.write_image(image0, "Image:0", ["C00","C01","C02"])
         ... writer.write_image(image1, "Image:1", ["C10","C11","C12"])
+
+        Write multi-scale image to OME-Zarr
+        >>> image = numpy.ndarray([3, 10, 1024, 2048])
+        ... writer = OmeZarrWriter("/path/to/file.ome.zarr")
+        ... writer.write_image(
+        ...     data, 
+        ...     image_name="Image:0", 
+        ...     channel_names=["C00","C01","C02"],
+        ...     scale_num_levels=3,
+        ...     scale_factor=2.0,
+        ...     dimension_order="CZYX"
+        ...     )
+
+        Write image channel color to OME-Zarr
+        >>> image = numpy.ndarray([3, 10, 1024, 2048])
+        ... channel_colors = ["FFFFFF","00FFFF","0000FF"]
+        ... int_color = [int(c, 16) for c in channel_colors]
+        ... writer = OmeZarrWriter("/path/to/file.ome.zarr")
+        ... writer.write_image(
+        ...     data, 
+        ...     image_name="Image:0", 
+        ...     channel_names=["C00","C01","C02"],
+        ...     channel_colors=int_color,
+        ...     dimension_order="CZYX"
+        ...     )
+
+        Write pixel size to OME-Zarr
+        >>> from aicsimageio import AICSImage, types
+        ... image = numpy.ndarray([3, 10, 1024, 2048])
+        ... channel_colors = ["FFFFFF","00FFFF","0000FF"]
+        ... int_color = [int(c, 16) for c in channel_colors]
+        ... writer = OmeZarrWriter("/path/to/file.ome.zarr")
+        ... writer.write_image(
+        ...     data, 
+        ...     image_name="Image:0", 
+        ...     physical_pixel_sizes=types.PhysicalPixelSizes(X=0.5, Y=0.5, Z=1.0)
+        ...     channel_names=["C00","C01","C02"],
+        ...     channel_colors=int_color,
+        ...     dimension_order="CZYX"
+        ...     )
         """
         ndims = len(image_data.shape)
         if ndims < 2 or ndims > 5:

From 82542a0131d76ae5367e83011e387814e1482bc4 Mon Sep 17 00:00:00 2001
From: Jacky Ko <ka.ko@kenn.ox.ac.uk>
Date: Wed, 24 Jan 2024 16:59:00 +0000
Subject: [PATCH 2/3] ome zarr

---
 README.md | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 19cc6511d..af77b4da8 100644
--- a/README.md
+++ b/README.md
@@ -304,7 +304,7 @@ as an OME-TIFF, the writer class can also be used to customize as needed.
 
 ```python
 import numpy as np
-from aicsimageio.writers import OmeTiffWriter
+from aicsimageio.writers.ome_tiff_writer import OmeTiffWriter
 
 image = np.random.rand(10, 3, 1024, 2048)
 OmeTiffWriter.save(image, "file.ome.tif", dim_order="ZCYX")
@@ -314,6 +314,35 @@ See
 [OmeTiffWriter documentation](./aicsimageio.writers.html#aicsimageio.writers.ome_tiff_writer.OmeTiffWriter.save)
 for more details.
 
+### Saving to OME-ZARR
+In-built writer for OME-ZARR output, effectively towards large image data
+
+```python
+from aicsimageio import AICSImage, types
+from aicsimageio.writers.ome_zarr_writer import OmeZarrWriter
+
+image = np.random.rand(3, 10, 1024, 2048)
+channel_colors = ["FFFFFF","00FFFF","0000FF"]
+int_color = [int(c, 16) for c in channel_colors]
+
+writer = OmeZarrWriter("./test.ome.zarr")
+
+writer.write_image(
+    image, 
+    image_name="Image:0", 
+    physical_pixel_sizes=types.PhysicalPixelSizes(X=0.5, Y=0.5, Z=1.0), # in um
+    channel_names=["C00","C01","C02"],
+    channel_colors=int_color,
+    scale_num_levels=3,
+    scale_factor=2.0,
+    dimension_order="CZYX"
+    )
+```
+
+See
+[OmeZarrWriter documentation](./aicsimageio.writers.html#aicsimageio.writers.ome_zarr_writer.OmeZarrWriter.save)
+for more details.
+
 #### Other Writers
 
 In most cases, `AICSImage.save` is usually a good default but there are other image

From f4a19773d5421dd6577f6f20b9f01cac1ed56575 Mon Sep 17 00:00:00 2001
From: Jacky Ko <ka.ko@kenn.ox.ac.uk>
Date: Wed, 24 Jan 2024 17:01:41 +0000
Subject: [PATCH 3/3] add zarr writer

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index af77b4da8..00cf2ca56 100644
--- a/README.md
+++ b/README.md
@@ -22,6 +22,7 @@ Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in P
     -   Files supported by [Bio-Formats](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html) -- (`pip install aicsimageio bioformats_jar`) (Note: requires `java` and `maven`, see below for details.)
 -   Supports writing metadata and imaging data for:
     -   `OME-TIFF`
+    -   `OME-ZARR`
     -   `PNG`, `GIF`, [etc.](https://github.com/imageio/imageio) -- (`pip install aicsimageio[base-imageio]`)
 -   Supports reading and writing to
     [fsspec](https://github.com/intake/filesystem_spec) supported file systems