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Points improvements and multi-scale image fix #63

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d62b656
WIP: points improvements and multi-scale image fix
keller-mark Jan 20, 2026
74959bd
Add xenium notebook
keller-mark Jan 20, 2026
6cb0fd2
Merge
keller-mark Feb 3, 2026
bea5ac4
Update blobs notebook
keller-mark Feb 3, 2026
211551b
WIP: points support.
keller-mark Feb 3, 2026
9d1b092
Update blobs notebook
keller-mark Feb 5, 2026
0a93ae7
Update xenium nb
keller-mark Feb 5, 2026
ea82fb5
Update
keller-mark Feb 12, 2026
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102 changes: 96 additions & 6 deletions docs/notebooks/spatialdata_blobs.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,9 @@
"source": [
"import easy_vitessce as ev\n",
"import spatialdata\n",
"import spatialdata_plot"
"import spatialdata_plot\n",
"from anndata import AnnData\n",
"import pandas as pd"
]
},
{
Expand All @@ -54,7 +56,7 @@
"metadata": {},
"outputs": [],
"source": [
"# ev.config.set({ 'data.wrapper_param_suffix': '_store' })"
"# ev.config.set({ 'data.wrapper_param_suffix': '_store' }) # Caveat: https://github.com/vitessce/vitessce-python/issues/491"
]
},
{
Expand All @@ -74,6 +76,65 @@
"sdata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Create a Table with a `var` dataframe corresponding to the `genes` column of the Points table"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"ddf = sdata.points['blobs_points']\n",
"ddf"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# The current `table` element contains a `var` dataframe corresponding\n",
"# to the 3 image channels, rather than the 2 gene IDs.\n",
"print(sdata.tables['table'].var.index.tolist())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# We need to create another table which has a var.index column containing the gene IDs for the points.\n",
"unique_gene_ids = ddf[\"genes\"].unique().compute().tolist()\n",
"points_var_df = pd.DataFrame(index=unique_gene_ids, data=[], columns=[])\n",
"points_table = AnnData(var=points_var_df, obs=None, X=None)\n",
"sdata.tables['table_points'] = points_table"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"unique_gene_ids"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"sdata.write('data/blobs.sdata.zarr', overwrite=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -103,14 +164,14 @@
"metadata": {},
"outputs": [],
"source": [
"sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\").pl.render_points(\"blobs_points\").pl.show()"
"sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\", table_name=\"table\").pl.render_points(\"blobs_points\").pl.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Disable EasyVitessce"
"## Rendering a subset of points"
]
},
{
Expand All @@ -119,7 +180,13 @@
"metadata": {},
"outputs": [],
"source": [
"ev.disable_plots([\"spatialdata-plot\"])"
"vw = (sdata\n",
" .pl.render_images(\"blobs_image\")\n",
" #.pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\", table_name=\"table\")\n",
" .pl.render_points(\"blobs_points\", color=\"genes\", groups=[\"gene_a\", \"gene_b\"], palette=[\"orange\", \"yellow\"], table_name=\"table_points\", alpha=1.0)\n",
" .pl.show()\n",
")\n",
"vw"
]
},
{
Expand All @@ -135,6 +202,7 @@
"metadata": {},
"outputs": [],
"source": [
"ev.disable_plots([\"spatialdata-plot\"])\n",
"sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\").pl.show()"
]
},
Expand All @@ -144,9 +212,31 @@
"metadata": {},
"outputs": [],
"source": [
"sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\").pl.render_points(\"blobs_points\").pl.show()"
"sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\", table_name=\"table\").pl.render_points(\"blobs_points\").pl.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"vw = (sdata\n",
" .pl.render_images(\"blobs_image\")\n",
" #.pl.render_labels(\"blobs_labels\", color=\"channel_0_sum\", table_name=\"table\")\n",
" .pl.render_points(\"blobs_points\", color=\"genes\", groups=[\"gene_a\", \"gene_b\"], palette=[\"orange\", \"yellow\"], table_name=\"table_points\", alpha=1.0)\n",
" .pl.show()\n",
")\n",
"vw"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
Expand Down
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