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Clarify spatialdata_attrs in "spatialdata from scratch tutorial" #151

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Merged
LucaMarconato merged 4 commits into from
Dec 22, 2025
Merged

Clarify spatialdata_attrs in "spatialdata from scratch tutorial" #151

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dd1de93
Clarify spatialdata_attrs
grst Aug 27, 2025
ddc8a44
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 27, 2025
15e5038
Merge branch 'main' into update-spatialdata-from-scratch
LucaMarconato Dec 22, 2025
6a475d7
minor rephrasings
LucaMarconato Dec 22, 2025
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27 changes: 18 additions & 9 deletions notebooks/examples/sdata_from_scratch.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3653,12 +3653,22 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Connect the `AnnData` to the `Shapes` object"
"### Connect the `AnnData` to the `Shapes` object\n",
"\n",
"The connection between `AnnData` and `SpatialData` regions is recorded as a dict in `.uns[\"spatialdata_attrs\"]`. \n",
"The following entries are required: \n",
"\n",
" * `region`: This refers to the `SpatialData` element(s) that the `AnnData` object annotates. It is generally a string when the table annotates a single element, and it is a list of strings if multiple elements are annotated. In our case, it is the name of the Shapes element we will use later\n",
" (i.e. the object with centers and radii of the Visium spots).\n",
" * `region_key`: Name of the column in `adata.obs` that will link a given obs to the elements it annotates. This column may only contain\n",
" identifiers that are specified in the `region` key.\n",
" * `instance_key`: Name of the column that matches a given obs in the table to a given circle. It must contain values that are \n",
" in the dataframe index of the points/shapes element. "
]
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -3771,12 +3781,11 @@
],
"source": [
"adata_for_sdata.uns[\"spatialdata_attrs\"] = {\n",
" \"region\": \"spots\", # name of the Shapes element we will use later (i.e. the object with centers\n",
" # and radii of the Visium spots)\n",
" \"region_key\": \"region\", # column in adata.obs that will link a given obs to the elements it annotates\n",
" \"instance_key\": \"spot_id\", # column that matches a given obs in the table to a given circle\n",
" \"region\": \"spots\",\n",
" \"region_key\": \"region\",\n",
" \"instance_key\": \"spot_id\",\n",
"}\n",
"# all the rows of adata annotate the same element, called \"spots\" (as we declared above)\n",
"# In this example, all the rows of adata annotate the same element, called \"spots\" (as we declared above)\n",
"adata.obs[\"region\"] = pd.Categorical([\"spots\"] * len(adata))\n",
"adata.obs[\"spot_id\"] = shapes_for_sdata.index\n",
"adata.obs[[\"region\", \"spot_id\"]]"
Expand Down Expand Up @@ -4064,7 +4073,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -4078,7 +4087,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
"version": "3.13.0"
}
},
"nbformat": 4,
Expand Down