From 3f02f9974fba7ea73fd7cc44e10ac1a77e8bd39f Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Wed, 28 Jan 2026 12:18:01 -0500
Subject: [PATCH] 3D example

---
 docs/notebooks/spatialdata_image_3d.ipynb | 211 ++++++++++++++++++++++
 1 file changed, 211 insertions(+)
 create mode 100644 docs/notebooks/spatialdata_image_3d.ipynb

diff --git a/docs/notebooks/spatialdata_image_3d.ipynb b/docs/notebooks/spatialdata_image_3d.ipynb
new file mode 100644
index 0000000..01a365b
--- /dev/null
+++ b/docs/notebooks/spatialdata_image_3d.ipynb
@@ -0,0 +1,211 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "1ca97045-ab06-4700-9870-5eef11f1e4e1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import easy_vitessce as ev"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "39f4b2fd-d3fd-4d27-83e2-9b804bd40863",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import zarr\n",
+    "\n",
+    "zarr_group = zarr.open(\n",
+    "    \"s3://idr/zarr/v0.4/idr0062A/6001240.zarr\",\n",
+    "    storage_options={\n",
+    "        \"anon\": True,\n",
+    "        \"client_kwargs\": {\n",
+    "            \"endpoint_url\": \"https://uk1s3.embassy.ebi.ac.uk\"\n",
+    "        }\n",
+    "    }\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "060f1e78-903f-4943-8d16-56b1e74169b1",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['0', '1', '2', 'labels']"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "list(zarr_group.keys())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "eb38c0d8-f0a1-4a03-8055-378a1895cefb",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'_creator': {'name': 'omero-zarr', 'version': '0.4.0'},\n",
+       " 'multiscales': [{'axes': [{'name': 'c', 'type': 'channel'},\n",
+       "    {'name': 'z', 'type': 'space', 'unit': 'micrometer'},\n",
+       "    {'name': 'y', 'type': 'space', 'unit': 'micrometer'},\n",
+       "    {'name': 'x', 'type': 'space', 'unit': 'micrometer'}],\n",
+       "   'datasets': [{'coordinateTransformations': [{'scale': [1.0,\n",
+       "        0.5002025531914894,\n",
+       "        0.3603981534640209,\n",
+       "        0.3603981534640209],\n",
+       "       'type': 'scale'}],\n",
+       "     'path': '0'},\n",
+       "    {'coordinateTransformations': [{'scale': [1.0,\n",
+       "        0.5002025531914894,\n",
+       "        0.7207963069280418,\n",
+       "        0.7207963069280418],\n",
+       "       'type': 'scale'}],\n",
+       "     'path': '1'},\n",
+       "    {'coordinateTransformations': [{'scale': [1.0,\n",
+       "        0.5002025531914894,\n",
+       "        1.4415926138560835,\n",
+       "        1.4415926138560835],\n",
+       "       'type': 'scale'}],\n",
+       "     'path': '2'}],\n",
+       "   'version': '0.4'}],\n",
+       " 'omero': {'channels': [{'active': True,\n",
+       "    'coefficient': 1.0,\n",
+       "    'color': '0000FF',\n",
+       "    'family': 'linear',\n",
+       "    'inverted': False,\n",
+       "    'label': 'LaminB1',\n",
+       "    'window': {'end': 1500.0, 'max': 65535.0, 'min': 0.0, 'start': 0.0}},\n",
+       "   {'active': True,\n",
+       "    'coefficient': 1.0,\n",
+       "    'color': 'FFFF00',\n",
+       "    'family': 'linear',\n",
+       "    'inverted': False,\n",
+       "    'label': 'Dapi',\n",
+       "    'window': {'end': 1500.0, 'max': 65535.0, 'min': 0.0, 'start': 0.0}}],\n",
+       "  'id': 1,\n",
+       "  'rdefs': {'defaultT': 0, 'defaultZ': 118, 'model': 'color'},\n",
+       "  'version': '0.4'}}"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dict(zarr_group.attrs)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "12f5ba16-4adc-423b-be4e-629d41c256cd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "img_arr = zarr_group['/1']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "a51fcb74-94b0-4a43-84af-89ee6fddae15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from spatialdata import SpatialData\n",
+    "from spatialdata.models import Image3DModel\n",
+    "\n",
+    "image = Image3DModel.parse(img_arr[()], dims=(\"c\",\"z\",\"y\",\"x\"), c_coords=[\"LaminB1\", \"Dapi\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "d2b2fc74-87ba-4c84-a577-b913726cb5a7",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "SpatialData object\n",
+       "└── Images\n",
+       "      └── 'image': DataArray[czyx] (2, 236, 137, 135)\n",
+       "with coordinate systems:\n",
+       "    ▸ 'global', with elements:\n",
+       "        image (Images)"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "sdata = SpatialData(images={\"image\": image})\n",
+    "sdata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "abca9477-feb7-4317-b77d-af021d5d30f0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw = (\n",
+    "    sdata\n",
+    "        .pl.render_images(\"image\")\n",
+    "        .pl.show()\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6e09f547-e1d3-4191-a5ae-6cce66e40faa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw.config.web_app()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}