diff --git a/notebooks/examples/sdata_from_scratch.ipynb b/notebooks/examples/sdata_from_scratch.ipynb
index 8cada9a..baefc9b 100644
--- a/notebooks/examples/sdata_from_scratch.ipynb
+++ b/notebooks/examples/sdata_from_scratch.ipynb
@@ -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": [
     {
@@ -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\"]]"
@@ -4064,7 +4073,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -4078,7 +4087,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.13.0"
   }
  },
  "nbformat": 4,