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keller-mark merged 1 commit into from
Feb 3, 2026
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3D example #64

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211 changes: 211 additions & 0 deletions docs/notebooks/spatialdata_image_3d.ipynb
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{
"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
}