From d62b6565e1456acd7b59447f82bd5bac994cafcf Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 20 Jan 2026 16:07:19 -0500
Subject: [PATCH 1/7] WIP: points improvements and multi-scale image fix

---
 pyproject.toml                        |   4 +-
 src/easy_vitessce/spatialdata_plot.py | 128 +++++++++++++++++++++++---
 2 files changed, 117 insertions(+), 15 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 45bc711..c8b0b9f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "easy_vitessce"
-version = "0.0.9"
+version = "0.0.10"
 authors = [
   {name="HIDIVE Lab"},
   {name="Selena Luo"}
@@ -24,7 +24,7 @@ dependencies = [
   'numpy>=1.21.2',
   'zarr>=2.5.0,<3',
   'numcodecs>=0.5.7,<0.16.0',
-  'vitessce[all]>=3.7.9',
+  'vitessce[all]>=3.8.0',
   'scanpy>=1.11.3',
   'anndata>=0.11.4',
   'spatialdata>=0.3.0',
diff --git a/src/easy_vitessce/spatialdata_plot.py b/src/easy_vitessce/spatialdata_plot.py
index 375a269..3199343 100644
--- a/src/easy_vitessce/spatialdata_plot.py
+++ b/src/easy_vitessce/spatialdata_plot.py
@@ -20,15 +20,15 @@
     vconcat,
 )
 
-from os.path import join
-
 from spatialdata_plot.pl.basic import PlotAccessor
 from spatialdata import get_element_annotators
 
-from easy_vitessce.widget import _to_widget, config
+from easy_vitessce.widget import _to_widget
 from easy_vitessce.colors import to_uint8_rgb
 from easy_vitessce.data import _get_sdata_wrapper_params
 
+from matplotlib.colors import is_color_like
+
 # Internal function for shared logic between render_shapes and render_labels.
 def _shared_render_shapes_and_labels(
         sdata, element, table_name, table_layer, color, cmap, norm, groups, palette, obs_type, feature_type, is_spots, fill_alpha, outline_alpha, outline_width, outline_color,
@@ -341,12 +341,16 @@ def render_images(
         # RGB vs. non-RGB logic in spatialdata-plot:
         # Reference: https://github.com/scverse/spatialdata-plot/blob/010560f7eebdd245693a8c55eede0f895a636f5c/src/spatialdata_plot/pl/render.py#L865
         img = self.sdata.images[element]
-        try:
-            all_channels = img.coords["c"].values.tolist()
-        except KeyError:
-            # TODO: use a better way than try/except of determining whether this is a multi-resolution image.
-            all_channels = img.scale0.coords["c"].values.tolist()
-        img_dtype = img.dtype
+        if hasattr(img, "dtype"):
+            img_arr = img
+        else:
+            # Assume multi-scale (DataTree).
+            # We use the highest resolution scale, 'scale0'.
+            # The image data is typically in the 'image' variable of the dataset.
+            img_arr = img["scale0"]["image"]
+
+        all_channels = img_arr.coords["c"].values.tolist()
+        img_dtype = img_arr.dtype
         img_dtype_is_uint8 = img_dtype.kind == 'u' and img_dtype.itemsize == 1
 
         # Not ideal logic. Should ideally only use the OME-NGFF color model metadata. But this is what spatialdata-plot does.
@@ -631,7 +635,17 @@ def render_labels(self,
     # References:
     # - https://spatialdata.scverse.org/projects/plot/en/latest/plotting.html#spatialdata_plot.pl.basic.PlotAccessor.render_points
     # - https://github.com/scverse/spatialdata-plot/blob/c9bae235c0521499fb4d1098b15c79619654e5dc/src/spatialdata_plot/pl/basic.py#L338
-    def render_points(self, element=None, **kwargs):
+    def render_points(self,
+            element=None,
+            color=None,
+            alpha=None,
+            groups=None,
+            palette=None,
+            # TODO: size
+            table_name=None,
+            table_layer=None,
+            **kwargs
+        ):
         """
         Renders points.
 
@@ -639,7 +653,17 @@ def render_points(self, element=None, **kwargs):
         :returns: Self, allows for chaining.
         """
         if not VitesscePlotAccessor._is_enabled:
-            return self._pl.render_points(element=element, **kwargs)
+            return self._pl.render_points(
+                element=element,
+                color=color,
+                alpha=alpha,
+                groups=groups,
+                palette=palette,
+                # TODO: size
+                table_name=table_name,
+                table_layer=table_layer,
+                **kwargs
+            )
         
         self._maybe_init()
 
@@ -664,10 +688,83 @@ def render_points(self, element=None, **kwargs):
             "obsType": obs_type,
             "obsHighlight": None,
             "fileUid": file_uid,
+            # TODO: featureSelection: None or list[str]
+            # TODO: featureFilterMode: None or 'featureSelection'
+            # TODO: obsColorEncoding: 'geneSelection' or 'spatialLayerColor' or 'randomByFeature' or 'random'
+            # TODO: featureColor: None or [ { name: str, color: [R, G, B] } ]
+            # TODO: spatialLayerColor: [R, G, B]
+            # TODO: spatialLayerOpacity: number
         }
+
+        # Coloring cases
+        # color param can be:
+        # - None (default color)
+        # - static color like "red" or "#FF0000"
+        # - name of the "feature_name" column of sdata.points table
         
+        # alpha param can be:
+        # - None (default opacity) 1.0
+        # - float between 0.0 and 1.0
+
+        # groups param:
+        # - None (all points)
+        # - str: a single gene name (when `color` param is the name of the column containing gene names)
+        # - list[str]: list of gene names (when `color` param is the name of the column containing gene names)
+
+        # palette param:
+        # - None (default color)
+        # - str: a single color (when `groups` param is a single gene name)
+        # - list[str]: list of colors (when `groups` param is a list of gene names) (the length must match the length of `groups`)
+
+        ddf = self.sdata.points[element]
+
+        obs_coordination = None
+        feature_coordination = None
+
+        if color is not None:
+            if is_color_like(color):
+                # static color
+                layer_coordination["spatialLayerColor"] = to_uint8_rgb(color)
+            elif color in ddf.columns:
+                # feature_name column
+                layer_coordination["obsColorEncoding"] = "randomByFeature"
+
+                if groups is not None:
+                    if type(groups) is str:
+                        groups = [groups]
+                    if palette is not None:
+                        if type(palette) is str:
+                            # Broadcast single color to all groups.
+                            palette = [palette for _ in groups]
+                        elif type(palette) is list and len(groups) != len(palette):
+                            raise ValueError("The length of 'groups' and 'palette' lists must be equal.")
+                        
+                        feature_color_val = [
+                            {
+                                "name": groups[i],
+                                "color": to_uint8_rgb(palette[i]),
+                            } for i in range(len(groups))
+                        ]
+
+                        layer_coordination["featureColor"] = feature_color_val
+                        layer_coordination["obsColorEncoding"] = "geneSelection"
+                    layer_coordination["featureSelection"] = groups
+                    layer_coordination["featureFilterMode"] = "featureSelection"
+            
+                feature_coordination = {
+                    "obsType": obs_type,
+                    "featureType": feature_type,
+                    "featureSelection": groups if groups is not None else None,
+                }
+
+        if alpha is not None:
+            layer_coordination["spatialLayerOpacity"] = alpha
+        
+        # TODO: perform the necessary operations on the points dataframe (sorting by morton code).
+        # Perhaps the user will need to opt-in via the global configuration.
+
         self.point_layers.append(
-            (wrapper_args, layer_coordination)
+            (wrapper_args, layer_coordination, obs_coordination, feature_coordination)
         )
 
         return self.sdata
@@ -714,7 +811,7 @@ def show(self, coordinate_systems=None, **kwargs):
             })
             dataset = dataset.add_object(spot_wrapper)
         
-        for (layer_wrapper_args, _) in self.point_layers:
+        for (layer_wrapper_args, _, _, _) in self.point_layers:
             points_wrapper = SpatialDataWrapper(**{
                 **self.shared_wrapper_args,
                 **({ "coordinate_system": coordinate_systems } if coordinate_systems is not None else {}),
@@ -746,6 +843,11 @@ def show(self, coordinate_systems=None, **kwargs):
                 obs_coordination.append(obs_coord)
             if feature_coord is not None:
                 feature_coordination.append(feature_coord)
+        for (_, _, obs_coord, feature_coord) in self.point_layers:
+            if obs_coord is not None:
+                obs_coordination.append(obs_coord)
+            if feature_coord is not None:
+                feature_coordination.append(feature_coord)
 
         # Add obsSet and featureList views.
         for obs_coord in obs_coordination:

From 74959bdb790cbe8e4bb6a6845cc46a56503c45c3 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 20 Jan 2026 17:35:35 -0500
Subject: [PATCH 2/7] Add xenium notebook

---
 docs/notebooks/spatialdata_xenium.ipynb | 300 ++++++++++++++++++++++++
 src/easy_vitessce/spatialdata_plot.py   |  28 ++-
 2 files changed, 320 insertions(+), 8 deletions(-)
 create mode 100644 docs/notebooks/spatialdata_xenium.ipynb

diff --git a/docs/notebooks/spatialdata_xenium.ipynb b/docs/notebooks/spatialdata_xenium.ipynb
new file mode 100644
index 0000000..8b022b0
--- /dev/null
+++ b/docs/notebooks/spatialdata_xenium.ipynb
@@ -0,0 +1,300 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "013a95d1",
+   "metadata": {},
+   "source": [
+    "# EasyVitessce Example: SpatialData-Plot with MERFISH dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "40c9b340",
+   "metadata": {},
+   "source": [
+    "## Downloading and importing necessary packages"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "846b644c",
+   "metadata": {},
+   "source": [
+    "By default, interactive plots are enabled upon importing easy_vitessce. This notebook aims to demonstrate the transition between static and interactive plots, so the interactive plots are initially turned off."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1b9e634a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip install easy_vitessce\n",
+    "!pip install spatialdata\n",
+    "!pip install spatialdata_plot"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "05991a70",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import easy_vitessce as ev \n",
+    "import spatialdata as sd\n",
+    "import spatialdata_plot\n",
+    "from os.path import join"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19bfbe14-2fa3-4d8a-b239-5e1385806bcb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from vitessce.data_utils import (\n",
+    "    sdata_morton_sort_points,\n",
+    "    sdata_points_process_columns,\n",
+    "    sdata_points_write_bounding_box_attrs,\n",
+    "    sdata_points_modify_row_group_size,\n",
+    "    sdata_morton_query_rect,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "594003c7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Disable interactive plots\n",
+    "ev.configure_plots(enable_plots=[\"spatialdata-plot\"])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b0fec04c-68a2-4df6-8ec5-093812c98a6d",
+   "metadata": {},
+   "source": [
+    "## Download the data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7a7f7f9a-2529-41bb-98c5-bbde65867356",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "from os.path import join, isfile, isdir\n",
+    "from urllib.request import urlretrieve\n",
+    "import zipfile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3016ea87-6388-4f43-8b92-6244d284b4e0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_dir = \"data\"\n",
+    "zip_path = join(data_dir, \"xenium_rep1_io.spatialdata.zarr.zip\")\n",
+    "sdata_path = join(data_dir, \"xenium_rep1_io.spatialdata.zarr\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b70f4ee6-f6da-49f0-8dba-9042259782b3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if not isdir(sdata_path):\n",
+    "    if not isfile(zip_path):\n",
+    "        os.makedirs(data_dir, exist_ok=True)\n",
+    "        urlretrieve('https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip', zip_path)\n",
+    "    with zipfile.ZipFile(zip_path,\"r\") as zip_ref:\n",
+    "        zip_ref.extractall(data_dir)\n",
+    "        os.rename(join(data_dir, \"data.zarr\"), sdata_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f7bebbc5",
+   "metadata": {},
+   "source": [
+    "## Read the data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e946174",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata = sd.read_zarr(sdata_path)\n",
+    "sdata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d5fc0fd3-3c35-4851-bc31-375fc89c350c",
+   "metadata": {},
+   "source": [
+    "## Make the points ready for tiled access\n",
+    "\n",
+    "References:\n",
+    "- https://vitessce.io/docs/data-troubleshooting/#points\n",
+    "- https://github.com/vitessce/vitessce-python/blob/main/docs/notebooks/spatial_data_xenium_morton.ipynb"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4a4cb7c5-1ce2-4573-9c1c-176538ab25f3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if \"transcripts_with_morton_codes\" not in sdata.points:\n",
+    "    sdata = sdata_morton_sort_points(sdata, \"transcripts\")\n",
+    "    \n",
+    "    # Add feature_index column to dataframe, and reorder columns so that feature_name (dict column) is the rightmost column.\n",
+    "    ddf = sdata_points_process_columns(sdata, \"transcripts\", var_name_col=\"feature_name\", table_name=\"table\")\n",
+    "    \n",
+    "    sdata[\"transcripts_with_morton_codes\"] = ddf\n",
+    "    sdata.write_element(\"transcripts_with_morton_codes\")\n",
+    "    \n",
+    "    sdata_points_write_bounding_box_attrs(sdata, \"transcripts_with_morton_codes\")\n",
+    "    \n",
+    "    sdata_points_modify_row_group_size(sdata, \"transcripts_with_morton_codes\", row_group_size=25_000)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "140217fb",
+   "metadata": {},
+   "source": [
+    "## Static plotting"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8383a98f-4090-44e2-b574-3531d3a96dfa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14f9d262-d853-456b-be5d-26a50975a047",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2035d286",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw = (\n",
+    "    sdata\n",
+    "        .pl.render_images(element=\"morphology_focus\")\n",
+    "        .pl.render_shapes(element=\"cell_boundaries\")\n",
+    "        .pl.render_points(element=\"transcripts_with_morton_codes\", color=\"feature_name\", groups=[\"ERBB2\"], palette=[\"red\"])\n",
+    "        .pl.show()\n",
+    ")\n",
+    "vw"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9d69cdee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# add another code block for the mouse liver dataset? "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "27b04c12",
+   "metadata": {},
+   "source": [
+    "## Activating interactive plots"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ddf74968",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Enable interactive plots\n",
+    "ev.configure_plots(enable_plots=[\"spatialdata-plot\"])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "23ffc21d-92ac-4066-b09a-b7a10307cbe6",
+   "metadata": {},
+   "source": [
+    "## Interactive plotting"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "63900fe4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata.pl.render_images(element=\"rasterized\").pl.render_shapes(element=\"cells\", color=\"Acta2\").pl.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed91d03f-098b-47b7-a397-4b2003c60a13",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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
+}
diff --git a/src/easy_vitessce/spatialdata_plot.py b/src/easy_vitessce/spatialdata_plot.py
index 3199343..59addac 100644
--- a/src/easy_vitessce/spatialdata_plot.py
+++ b/src/easy_vitessce/spatialdata_plot.py
@@ -29,15 +29,10 @@
 
 from matplotlib.colors import is_color_like
 
-# Internal function for shared logic between render_shapes and render_labels.
-def _shared_render_shapes_and_labels(
-        sdata, element, table_name, table_layer, color, cmap, norm, groups, palette, obs_type, feature_type, is_spots, fill_alpha, outline_alpha, outline_width, outline_color,
+def _shared_table_handling(sdata, element, table_name, table_layer, obs_type, feature_type,
         # Note: These dict params are modified by this function.
         wrapper_args, obs_type_to_num_rows, feature_type_to_num_rows,
     ):
-
-    extra_layer_coordination = {}
-
     if table_name is None:
         annotating_tables = list(get_element_annotators(sdata, element))
         if len(annotating_tables) > 0:
@@ -80,6 +75,19 @@ def _shared_render_shapes_and_labels(
         """
         pass
 
+# Internal function for shared logic between render_shapes and render_labels.
+def _shared_render_shapes_and_labels(
+        sdata, element, table_name, table_layer, color, cmap, norm, groups, palette, obs_type, feature_type, is_spots, fill_alpha, outline_alpha, outline_width, outline_color,
+        # Note: These dict params are modified by this function.
+        wrapper_args, obs_type_to_num_rows, feature_type_to_num_rows,
+    ):
+
+    extra_layer_coordination = {}
+
+    _shared_table_handling(sdata, element, table_name, table_layer, obs_type, feature_type,
+        wrapper_args, obs_type_to_num_rows, feature_type_to_num_rows,
+    )
+
     obs_coordination = None
     feature_coordination = None
     is_maybe_static_color = False
@@ -240,7 +248,7 @@ def _init_params(self):
             # Tuples of (wrapper_args, spot_layer_coordination, obs_coordination, feature_coordination)
         ]
         self.point_layers = [
-            # Tuples of (wrapper_args, point_layer_coordination)
+            # Tuples of (wrapper_args, point_layer_coordination, obs_coordination, feature_coordination)
         ]
 
         # For ensuring that counts of obs/var match if used for multiple layers.
@@ -684,6 +692,10 @@ def render_points(self,
             }
         }
 
+        _shared_table_handling(self.sdata, element, table_name, table_layer, obs_type, feature_type,
+            wrapper_args, self.obs_type_to_num_rows, self.feature_type_to_num_rows,
+        )
+
         layer_coordination = {
             "obsType": obs_type,
             "obsHighlight": None,
@@ -953,7 +965,7 @@ def show(self, coordinate_systems=None, **kwargs):
                         **obs_coordination_by_key.get(layer_dict.get("obsType"), {}),
                         **layer_dict,
                     }
-                    for (_, layer_dict) in self.point_layers
+                    for (_, layer_dict, _, _) in self.point_layers
                 ]),
             }, meta=True, scope_prefix=get_initial_coordination_scope_prefix(dataset_uid, "obsPoints"))
 

From bea5ac434492d331455dc1f955ce6c1aa2d3fd24 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 3 Feb 2026 12:05:10 -0500
Subject: [PATCH 3/7] Update blobs notebook

---
 docs/notebooks/spatialdata_blobs.ipynb | 54 +++++++++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/docs/notebooks/spatialdata_blobs.ipynb b/docs/notebooks/spatialdata_blobs.ipynb
index e25eedb..c257aed 100644
--- a/docs/notebooks/spatialdata_blobs.ipynb
+++ b/docs/notebooks/spatialdata_blobs.ipynb
@@ -29,7 +29,10 @@
    "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\n",
+    "from vitessce.data_utils import sdata_points_process_columns"
    ]
   },
   {
@@ -74,6 +77,55 @@
     "sdata"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Create a feature_index column for 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": [
+    "print(sdata.tables['table'].var.index.tolist())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# The sdata.tables['table'].var table does not contain genes as indices; it contains channels.\n",
+    "# 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": [
+    "sdata.points['blobs_points'] = sdata_points_process_columns(sdata, \"blobs_points\", var_name_col=\"genes\", table_name=\"table_points\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

From 211551b070128ade08d52b5e1211e80fbce0f793 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 3 Feb 2026 12:45:16 -0500
Subject: [PATCH 4/7] WIP: points support.

---
 docs/notebooks/spatialdata_blobs.ipynb  | 239 ++++++++++++++++--
 docs/notebooks/spatialdata_xenium.ipynb | 308 ++++++++++++++++++++++--
 src/easy_vitessce/spatialdata_plot.py   |  18 ++
 uv.lock                                 |   8 +-
 4 files changed, 531 insertions(+), 42 deletions(-)

diff --git a/docs/notebooks/spatialdata_blobs.ipynb b/docs/notebooks/spatialdata_blobs.ipynb
index c257aed..623d18b 100644
--- a/docs/notebooks/spatialdata_blobs.ipynb
+++ b/docs/notebooks/spatialdata_blobs.ipynb
@@ -21,11 +21,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "scrolled": true
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
+      "  from pkg_resources import DistributionNotFound, get_distribution\n"
+     ]
+    }
+   ],
    "source": [
     "import easy_vitessce as ev\n",
     "import spatialdata\n",
@@ -37,9 +48,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<donfig.config_obj.ConfigSet at 0x3351bbbc0>"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "ev.config.set({ 'data.overwrite': True })"
    ]
@@ -53,7 +75,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -69,9 +91,45 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/spatialdata/models/models.py:1144: UserWarning: Converting `region_key: region` to categorical dtype.\n",
+      "  return convert_region_column_to_categorical(adata)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "SpatialData object\n",
+       "├── Images\n",
+       "│     ├── 'blobs_image': DataArray[cyx] (3, 512, 512)\n",
+       "│     └── 'blobs_multiscale_image': DataTree[cyx] (3, 512, 512), (3, 256, 256), (3, 128, 128)\n",
+       "├── Labels\n",
+       "│     ├── 'blobs_labels': DataArray[yx] (512, 512)\n",
+       "│     └── 'blobs_multiscale_labels': DataTree[yx] (512, 512), (256, 256), (128, 128)\n",
+       "├── Points\n",
+       "│     └── 'blobs_points': DataFrame with shape: (<Delayed>, 4) (2D points)\n",
+       "├── Shapes\n",
+       "│     ├── 'blobs_circles': GeoDataFrame shape: (5, 2) (2D shapes)\n",
+       "│     ├── 'blobs_multipolygons': GeoDataFrame shape: (2, 1) (2D shapes)\n",
+       "│     └── 'blobs_polygons': GeoDataFrame shape: (5, 1) (2D shapes)\n",
+       "└── Tables\n",
+       "      └── 'table': AnnData (26, 3)\n",
+       "with coordinate systems:\n",
+       "    ▸ 'global', with elements:\n",
+       "        blobs_image (Images), blobs_multiscale_image (Images), blobs_labels (Labels), blobs_multiscale_labels (Labels), blobs_points (Points), blobs_circles (Shapes), blobs_multipolygons (Shapes), blobs_polygons (Shapes)"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "sdata = spatialdata.datasets.blobs()\n",
     "sdata"
@@ -86,9 +144,78 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div><strong>Dask DataFrame Structure:</strong></div>\n",
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>x</th>\n",
+       "      <th>y</th>\n",
+       "      <th>genes</th>\n",
+       "      <th>instance_id</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>npartitions=1</th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>int64</td>\n",
+       "      <td>int64</td>\n",
+       "      <td>category[known]</td>\n",
+       "      <td>int64</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>199</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>\n",
+       "<div>Dask Name: from_pandas, 1 graph layer</div>"
+      ],
+      "text/plain": [
+       "Dask DataFrame Structure:\n",
+       "                   x      y            genes instance_id\n",
+       "npartitions=1                                           \n",
+       "0              int64  int64  category[known]       int64\n",
+       "199              ...    ...              ...         ...\n",
+       "Dask Name: from_pandas, 1 graph layer"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "ddf = sdata.points['blobs_points']\n",
     "ddf"
@@ -96,16 +223,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['channel_0_sum', 'channel_1_sum', 'channel_2_sum']\n"
+     ]
+    }
+   ],
    "source": [
     "print(sdata.tables['table'].var.index.tolist())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,13 +254,47 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/core.py:4448: UserWarning: \n",
+      "You did not provide metadata, so Dask is running your function on a small dataset to guess output types. It is possible that Dask will guess incorrectly.\n",
+      "To provide an explicit output types or to silence this message, please provide the `meta=` keyword, as described in the map or apply function that you are using.\n",
+      "  Before: .apply(func)\n",
+      "  After:  .apply(func, meta=('genes', 'category'))\n",
+      "\n",
+      "  warnings.warn(meta_warning(meta))\n",
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/spatialdata/_core/_elements.py:115: UserWarning: Key `blobs_points` already exists. Overwriting it in-memory.\n",
+      "  self._check_key(key, self.keys(), self._shared_keys)\n"
+     ]
+    }
+   ],
    "source": [
     "sdata.points['blobs_points'] = sdata_points_process_columns(sdata, \"blobs_points\", var_name_col=\"genes\", table_name=\"table_points\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[34mINFO    \u001b[0m The Zarr backing store has been changed from data/\u001b[93m1953eb5a-d483-4694-ad80-4c247689706a\u001b[0m.sdata.zarr the new \n",
+      "         file path: data/blobs_with_feature_index.sdata.zarr                                                       \n"
+     ]
+    }
+   ],
+   "source": [
+    "sdata.write('data/blobs_with_feature_index.sdata.zarr')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -135,9 +304,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "5ff620a24d5d47d5b87af121e7f1a7a1",
+       "version_major": 2,
+       "version_minor": 1
+      },
+      "text/plain": [
+       "VitessceWidget(js_dev_mode=True, uid='5508')"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\").pl.show()"
    ]
@@ -151,11 +336,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "f088ce8aa15c40ba9628e1cadc59fc02",
+       "version_major": 2,
+       "version_minor": 1
+      },
+      "text/plain": [
+       "VitessceWidget(js_dev_mode=True, uid='b28f')"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "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()"
    ]
   },
   {
diff --git a/docs/notebooks/spatialdata_xenium.ipynb b/docs/notebooks/spatialdata_xenium.ipynb
index 8b022b0..e9fb85a 100644
--- a/docs/notebooks/spatialdata_xenium.ipynb
+++ b/docs/notebooks/spatialdata_xenium.ipynb
@@ -38,10 +38,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "05991a70",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
+      "  from pkg_resources import DistributionNotFound, get_distribution\n"
+     ]
+    }
+   ],
    "source": [
     "import easy_vitessce as ev \n",
     "import spatialdata as sd\n",
@@ -51,7 +62,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "19bfbe14-2fa3-4d8a-b239-5e1385806bcb",
    "metadata": {},
    "outputs": [],
@@ -67,10 +78,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "594003c7",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Warning: SpatialData.pl has already been monkeypatched.\n"
+     ]
+    }
+   ],
    "source": [
     "# Disable interactive plots\n",
     "ev.configure_plots(enable_plots=[\"spatialdata-plot\"])"
@@ -86,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "7a7f7f9a-2529-41bb-98c5-bbde65867356",
    "metadata": {},
    "outputs": [],
@@ -99,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "3016ea87-6388-4f43-8b92-6244d284b4e0",
    "metadata": {},
    "outputs": [],
@@ -111,7 +130,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "b70f4ee6-f6da-49f0-8dba-9042259782b3",
    "metadata": {},
    "outputs": [],
@@ -135,10 +154,45 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "4e946174",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "version mismatch: detected: RasterFormatV02, requested: FormatV04\n",
+      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/zarr/creation.py:610: UserWarning: ignoring keyword argument 'read_only'\n",
+      "  compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs)\n",
+      "version mismatch: detected: RasterFormatV02, requested: FormatV04\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "SpatialData object, with associated Zarr store: /Users/mkeller/research/dbmi/vitessce/easy_vitessce/docs/notebooks/data/xenium_rep1_io.spatialdata.zarr\n",
+       "├── Images\n",
+       "│     ├── 'morphology_focus': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
+       "│     └── 'morphology_mip': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
+       "├── Points\n",
+       "│     ├── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)\n",
+       "│     └── 'transcripts_with_morton_codes': DataFrame with shape: (<Delayed>, 12) (3D points)\n",
+       "├── Shapes\n",
+       "│     ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
+       "│     └── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
+       "└── Tables\n",
+       "      └── 'table': AnnData (167780, 313)\n",
+       "with coordinate systems:\n",
+       "    ▸ 'global', with elements:\n",
+       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), transcripts_with_morton_codes (Points), cell_boundaries (Shapes), cell_circles (Shapes)"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "sdata = sd.read_zarr(sdata_path)\n",
     "sdata"
@@ -158,7 +212,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "4a4cb7c5-1ce2-4573-9c1c-176538ab25f3",
    "metadata": {},
    "outputs": [],
@@ -187,28 +241,244 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "id": "8383a98f-4090-44e2-b574-3531d3a96dfa",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "SpatialData object, with associated Zarr store: /Users/mkeller/research/dbmi/vitessce/easy_vitessce/docs/notebooks/data/xenium_rep1_io.spatialdata.zarr\n",
+       "├── Images\n",
+       "│     ├── 'morphology_focus': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
+       "│     └── 'morphology_mip': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
+       "├── Points\n",
+       "│     ├── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)\n",
+       "│     └── 'transcripts_with_morton_codes': DataFrame with shape: (<Delayed>, 12) (3D points)\n",
+       "├── Shapes\n",
+       "│     ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
+       "│     └── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
+       "└── Tables\n",
+       "      └── 'table': AnnData (167780, 313)\n",
+       "with coordinate systems:\n",
+       "    ▸ 'global', with elements:\n",
+       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), transcripts_with_morton_codes (Points), cell_boundaries (Shapes), cell_circles (Shapes)"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "sdata"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "14f9d262-d853-456b-be5d-26a50975a047",
+   "execution_count": 11,
+   "id": "e5a21a04-8b45-4f69-9115-98341bd7a76a",
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div><strong>Dask DataFrame Structure:</strong></div>\n",
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>x</th>\n",
+       "      <th>y</th>\n",
+       "      <th>z</th>\n",
+       "      <th>cell_id</th>\n",
+       "      <th>overlaps_nucleus</th>\n",
+       "      <th>transcript_id</th>\n",
+       "      <th>qv</th>\n",
+       "      <th>x_uint</th>\n",
+       "      <th>y_uint</th>\n",
+       "      <th>morton_code_2d</th>\n",
+       "      <th>feature_name_codes</th>\n",
+       "      <th>feature_name</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>npartitions=8</th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th></th>\n",
+       "      <td>float32</td>\n",
+       "      <td>float32</td>\n",
+       "      <td>float32</td>\n",
+       "      <td>int32</td>\n",
+       "      <td>uint8</td>\n",
+       "      <td>uint64</td>\n",
+       "      <td>float32</td>\n",
+       "      <td>uint32</td>\n",
+       "      <td>uint32</td>\n",
+       "      <td>uint32</td>\n",
+       "      <td>int32</td>\n",
+       "      <td>category[unknown]</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th></th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th></th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th></th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>\n",
+       "<div>Dask Name: read-parquet, 1 graph layer</div>"
+      ],
+      "text/plain": [
+       "Dask DataFrame Structure:\n",
+       "                     x        y        z cell_id overlaps_nucleus transcript_id       qv  x_uint  y_uint morton_code_2d feature_name_codes       feature_name\n",
+       "npartitions=8                                                                                                                                                \n",
+       "               float32  float32  float32   int32            uint8        uint64  float32  uint32  uint32         uint32              int32  category[unknown]\n",
+       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
+       "...                ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
+       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
+       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
+       "Dask Name: read-parquet, 1 graph layer"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "sdata.points[\"transcripts_with_morton_codes\"]"
+   ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
+   "id": "1b41a4bb-e552-41c7-a0c4-f9b70847d5cb",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'transform': {'global': Scale (x, y, z)\n",
+       "      [4.70588235 4.70588235 1.        ]},\n",
+       " 'spatialdata_attrs': {'feature_key': 'feature_name',\n",
+       "  'instance_key': 'cell_id'}}"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "sdata.points[\"transcripts_with_morton_codes\"].attrs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
    "id": "2035d286",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "aca392bdcba64975bf8f8c088c5e6e49",
+       "version_major": 2,
+       "version_minor": 1
+      },
+      "text/plain": [
+       "VitessceWidget(js_dev_mode=True, uid='eed7')"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "vw = (\n",
     "    sdata\n",
diff --git a/src/easy_vitessce/spatialdata_plot.py b/src/easy_vitessce/spatialdata_plot.py
index 59addac..eb8e0d3 100644
--- a/src/easy_vitessce/spatialdata_plot.py
+++ b/src/easy_vitessce/spatialdata_plot.py
@@ -729,6 +729,18 @@ def render_points(self,
         # - list[str]: list of colors (when `groups` param is a list of gene names) (the length must match the length of `groups`)
 
         ddf = self.sdata.points[element]
+        
+        try:
+            # Check if the dataframe contains a _codes column.
+            # Reference: https://github.com/vitessce/vitessce-python/blob/adb066c088307b658a45ca9cf2ab2d63effaa5ef/src/vitessce/data_utils/spatialdata_points_zorder.py#L458
+            feature_key_col = ddf.attrs["spatialdata_attrs"]["feature_key"]
+            # Note: this should be the default behavior on the JS side, so this may be unnecessary to do here.
+            # Reference: https://github.com/vitessce/vitessce/blob/0ff9f3b43ca28ef9858d3db0ce06417f6dd174a9/packages/file-types/spatial-zarr/src/spatialdata-loaders/SpatialDataObsPointsLoader.js#L126
+            codes_col = f"{feature_key_col}_codes"
+            if codes_col in ddf.columns:
+                wrapper_args["obs_points_feature_index_column"] = codes_col
+        except KeyError:
+            pass
 
         obs_coordination = None
         feature_coordination = None
@@ -741,6 +753,12 @@ def render_points(self,
                 # feature_name column
                 layer_coordination["obsColorEncoding"] = "randomByFeature"
 
+                # In case the value of `color` does not match spatialdata_attrs.feature_key
+                codes_col = f"{color}_codes"
+                if codes_col in ddf.columns:
+                    # Note: this overwrites any existing feature index column value in the dict.
+                    wrapper_args["obs_points_feature_index_column"] = codes_col
+
                 if groups is not None:
                     if type(groups) is str:
                         groups = [groups]
diff --git a/uv.lock b/uv.lock
index 6fdb3c4..2f1c6b3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1023,7 +1023,7 @@ wheels = [
 
 [[package]]
 name = "easy-vitessce"
-version = "0.0.8"
+version = "0.0.10"
 source = { editable = "." }
 dependencies = [
     { name = "anndata", version = "0.11.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
@@ -1085,7 +1085,7 @@ requires-dist = [
     { name = "sphinx", marker = "extra == 'docs'" },
     { name = "sphinx-book-theme", marker = "extra == 'docs'" },
     { name = "sphinx-copybutton", marker = "extra == 'docs'" },
-    { name = "vitessce", extras = ["all"], specifier = ">=3.7.9" },
+    { name = "vitessce", extras = ["all"], specifier = ">=3.8.0" },
     { name = "xarray", specifier = ">=2024.10.0,<=2025.3.0" },
     { name = "zarr", specifier = ">=2.5.0,<3" },
 ]
@@ -4904,7 +4904,7 @@ wheels = [
 
 [[package]]
 name = "vitessce"
-version = "3.7.9"
+version = "3.8.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "black" },
@@ -4918,7 +4918,7 @@ dependencies = [
     { name = "zarr", version = "2.18.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
 ]
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/b6/79/ef9dcc1dc0ead62e143194606b65a00761f43dbc22df3bca248c1c78115d/vitessce-3.7.9-py3-none-any.whl", hash = "sha256:b54cc4a73991d07b1ccf2617062705ae708508a18fde338790b7fea381ee30ba", size = 79840 },
+    { url = "https://files.pythonhosted.org/packages/d3/60/b5c82868f136eff8c2d3a8cae675c63b4e9e65b10f6c36861d49aade32ce/vitessce-3.8.0-py3-none-any.whl", hash = "sha256:763f9b8f411d103cd577789acba2baa16b938969826d6ead10dde46f916dda4a", size = 79843 },
 ]
 
 [package.optional-dependencies]

From 9d1b09215efe357459d8ada5dad0de8104f92410 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 5 Feb 2026 13:09:44 -0500
Subject: [PATCH 5/7] Update blobs notebook

---
 docs/notebooks/spatialdata_blobs.ipynb | 281 ++++++-------------------
 pyproject.toml                         |   2 +-
 2 files changed, 60 insertions(+), 223 deletions(-)

diff --git a/docs/notebooks/spatialdata_blobs.ipynb b/docs/notebooks/spatialdata_blobs.ipynb
index 623d18b..88d3f4c 100644
--- a/docs/notebooks/spatialdata_blobs.ipynb
+++ b/docs/notebooks/spatialdata_blobs.ipynb
@@ -21,47 +21,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {
     "scrolled": true
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
-      "  warnings.warn(\n",
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
-      "  from pkg_resources import DistributionNotFound, get_distribution\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import easy_vitessce as ev\n",
     "import spatialdata\n",
     "import spatialdata_plot\n",
     "from anndata import AnnData\n",
-    "import pandas as pd\n",
-    "from vitessce.data_utils import sdata_points_process_columns"
+    "import pandas as pd"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<donfig.config_obj.ConfigSet at 0x3351bbbc0>"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ev.config.set({ 'data.overwrite': True })"
    ]
@@ -75,11 +52,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "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"
    ]
   },
   {
@@ -91,45 +68,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/spatialdata/models/models.py:1144: UserWarning: Converting `region_key: region` to categorical dtype.\n",
-      "  return convert_region_column_to_categorical(adata)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "SpatialData object\n",
-       "├── Images\n",
-       "│     ├── 'blobs_image': DataArray[cyx] (3, 512, 512)\n",
-       "│     └── 'blobs_multiscale_image': DataTree[cyx] (3, 512, 512), (3, 256, 256), (3, 128, 128)\n",
-       "├── Labels\n",
-       "│     ├── 'blobs_labels': DataArray[yx] (512, 512)\n",
-       "│     └── 'blobs_multiscale_labels': DataTree[yx] (512, 512), (256, 256), (128, 128)\n",
-       "├── Points\n",
-       "│     └── 'blobs_points': DataFrame with shape: (<Delayed>, 4) (2D points)\n",
-       "├── Shapes\n",
-       "│     ├── 'blobs_circles': GeoDataFrame shape: (5, 2) (2D shapes)\n",
-       "│     ├── 'blobs_multipolygons': GeoDataFrame shape: (2, 1) (2D shapes)\n",
-       "│     └── 'blobs_polygons': GeoDataFrame shape: (5, 1) (2D shapes)\n",
-       "└── Tables\n",
-       "      └── 'table': AnnData (26, 3)\n",
-       "with coordinate systems:\n",
-       "    ▸ 'global', with elements:\n",
-       "        blobs_image (Images), blobs_multiscale_image (Images), blobs_labels (Labels), blobs_multiscale_labels (Labels), blobs_points (Points), blobs_circles (Shapes), blobs_multipolygons (Shapes), blobs_polygons (Shapes)"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata = spatialdata.datasets.blobs()\n",
     "sdata"
@@ -139,83 +80,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create a feature_index column for the Points table"
+    "### Create a Table with a `var` dataframe corresponding to the `genes` column of the Points table"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div><strong>Dask DataFrame Structure:</strong></div>\n",
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>x</th>\n",
-       "      <th>y</th>\n",
-       "      <th>genes</th>\n",
-       "      <th>instance_id</th>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>npartitions=1</th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>int64</td>\n",
-       "      <td>int64</td>\n",
-       "      <td>category[known]</td>\n",
-       "      <td>int64</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>199</th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>\n",
-       "<div>Dask Name: from_pandas, 1 graph layer</div>"
-      ],
-      "text/plain": [
-       "Dask DataFrame Structure:\n",
-       "                   x      y            genes instance_id\n",
-       "npartitions=1                                           \n",
-       "0              int64  int64  category[known]       int64\n",
-       "199              ...    ...              ...         ...\n",
-       "Dask Name: from_pandas, 1 graph layer"
-      ]
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ddf = sdata.points['blobs_points']\n",
     "ddf"
@@ -223,28 +95,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['channel_0_sum', 'channel_1_sum', 'channel_2_sum']\n"
-     ]
-    }
-   ],
+   "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": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# The sdata.tables['table'].var table does not contain genes as indices; it contains channels.\n",
     "# 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",
@@ -254,45 +119,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/core.py:4448: UserWarning: \n",
-      "You did not provide metadata, so Dask is running your function on a small dataset to guess output types. It is possible that Dask will guess incorrectly.\n",
-      "To provide an explicit output types or to silence this message, please provide the `meta=` keyword, as described in the map or apply function that you are using.\n",
-      "  Before: .apply(func)\n",
-      "  After:  .apply(func, meta=('genes', 'category'))\n",
-      "\n",
-      "  warnings.warn(meta_warning(meta))\n",
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/spatialdata/_core/_elements.py:115: UserWarning: Key `blobs_points` already exists. Overwriting it in-memory.\n",
-      "  self._check_key(key, self.keys(), self._shared_keys)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "sdata.points['blobs_points'] = sdata_points_process_columns(sdata, \"blobs_points\", var_name_col=\"genes\", table_name=\"table_points\")"
+    "unique_gene_ids"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[34mINFO    \u001b[0m The Zarr backing store has been changed from data/\u001b[93m1953eb5a-d483-4694-ad80-4c247689706a\u001b[0m.sdata.zarr the new \n",
-      "         file path: data/blobs_with_feature_index.sdata.zarr                                                       \n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "sdata.write('data/blobs_with_feature_index.sdata.zarr')"
+    "sdata.write('data/blobs.sdata.zarr', overwrite=True)"
    ]
   },
   {
@@ -304,25 +144,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "5ff620a24d5d47d5b87af121e7f1a7a1",
-       "version_major": 2,
-       "version_minor": 1
-      },
-      "text/plain": [
-       "VitessceWidget(js_dev_mode=True, uid='5508')"
-      ]
-     },
-     "execution_count": 15,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\").pl.show()"
    ]
@@ -336,25 +160,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f088ce8aa15c40ba9628e1cadc59fc02",
-       "version_major": 2,
-       "version_minor": 1
-      },
-      "text/plain": [
-       "VitessceWidget(js_dev_mode=True, uid='b28f')"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "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()"
    ]
@@ -363,7 +171,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Disable EasyVitessce"
+    "## Rendering a subset of points"
    ]
   },
   {
@@ -372,7 +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"
    ]
   },
   {
@@ -388,6 +202,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "ev.disable_plots([\"spatialdata-plot\"])\n",
     "sdata.pl.render_images(\"blobs_image\").pl.render_labels(\"blobs_labels\").pl.show()"
    ]
   },
@@ -397,9 +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,
diff --git a/pyproject.toml b/pyproject.toml
index c8b0b9f..c08f328 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   'numpy>=1.21.2',
   'zarr>=2.5.0,<3',
   'numcodecs>=0.5.7,<0.16.0',
-  'vitessce[all]>=3.8.0',
+  'vitessce[all]>=3.8.1',
   'scanpy>=1.11.3',
   'anndata>=0.11.4',
   'spatialdata>=0.3.0',

From 0a93ae706bfbeeca3e5ad1dc075902b8ca883113 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 5 Feb 2026 15:07:43 -0500
Subject: [PATCH 6/7] Update xenium nb

---
 docs/notebooks/spatialdata_xenium.ipynb | 308 +++---------------------
 uv.lock                                 |   7 +-
 2 files changed, 34 insertions(+), 281 deletions(-)

diff --git a/docs/notebooks/spatialdata_xenium.ipynb b/docs/notebooks/spatialdata_xenium.ipynb
index e9fb85a..68e8d01 100644
--- a/docs/notebooks/spatialdata_xenium.ipynb
+++ b/docs/notebooks/spatialdata_xenium.ipynb
@@ -38,21 +38,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "05991a70",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
-      "  warnings.warn(\n",
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
-      "  from pkg_resources import DistributionNotFound, get_distribution\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import easy_vitessce as ev \n",
     "import spatialdata as sd\n",
@@ -62,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "19bfbe14-2fa3-4d8a-b239-5e1385806bcb",
    "metadata": {},
    "outputs": [],
@@ -78,18 +67,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "594003c7",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Warning: SpatialData.pl has already been monkeypatched.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Disable interactive plots\n",
     "ev.configure_plots(enable_plots=[\"spatialdata-plot\"])"
@@ -105,7 +86,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "7a7f7f9a-2529-41bb-98c5-bbde65867356",
    "metadata": {},
    "outputs": [],
@@ -118,7 +99,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "3016ea87-6388-4f43-8b92-6244d284b4e0",
    "metadata": {},
    "outputs": [],
@@ -130,7 +111,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "b70f4ee6-f6da-49f0-8dba-9042259782b3",
    "metadata": {},
    "outputs": [],
@@ -154,45 +135,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "4e946174",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "version mismatch: detected: RasterFormatV02, requested: FormatV04\n",
-      "/Users/mkeller/research/dbmi/vitessce/easy_vitessce/.venv/lib/python3.12/site-packages/zarr/creation.py:610: UserWarning: ignoring keyword argument 'read_only'\n",
-      "  compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs)\n",
-      "version mismatch: detected: RasterFormatV02, requested: FormatV04\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "SpatialData object, with associated Zarr store: /Users/mkeller/research/dbmi/vitessce/easy_vitessce/docs/notebooks/data/xenium_rep1_io.spatialdata.zarr\n",
-       "├── Images\n",
-       "│     ├── 'morphology_focus': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
-       "│     └── 'morphology_mip': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
-       "├── Points\n",
-       "│     ├── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)\n",
-       "│     └── 'transcripts_with_morton_codes': DataFrame with shape: (<Delayed>, 12) (3D points)\n",
-       "├── Shapes\n",
-       "│     ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
-       "│     └── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
-       "└── Tables\n",
-       "      └── 'table': AnnData (167780, 313)\n",
-       "with coordinate systems:\n",
-       "    ▸ 'global', with elements:\n",
-       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), transcripts_with_morton_codes (Points), cell_boundaries (Shapes), cell_circles (Shapes)"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata = sd.read_zarr(sdata_path)\n",
     "sdata"
@@ -212,7 +158,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "4a4cb7c5-1ce2-4573-9c1c-176538ab25f3",
    "metadata": {},
    "outputs": [],
@@ -241,255 +187,61 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "8383a98f-4090-44e2-b574-3531d3a96dfa",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "SpatialData object, with associated Zarr store: /Users/mkeller/research/dbmi/vitessce/easy_vitessce/docs/notebooks/data/xenium_rep1_io.spatialdata.zarr\n",
-       "├── Images\n",
-       "│     ├── 'morphology_focus': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
-       "│     └── 'morphology_mip': DataTree[cyx] (1, 25778, 35416), (1, 12889, 17708), (1, 6444, 8854), (1, 3222, 4427), (1, 1611, 2213)\n",
-       "├── Points\n",
-       "│     ├── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)\n",
-       "│     └── 'transcripts_with_morton_codes': DataFrame with shape: (<Delayed>, 12) (3D points)\n",
-       "├── Shapes\n",
-       "│     ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
-       "│     └── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
-       "└── Tables\n",
-       "      └── 'table': AnnData (167780, 313)\n",
-       "with coordinate systems:\n",
-       "    ▸ 'global', with elements:\n",
-       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), transcripts_with_morton_codes (Points), cell_boundaries (Shapes), cell_circles (Shapes)"
-      ]
-     },
-     "execution_count": 9,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "e5a21a04-8b45-4f69-9115-98341bd7a76a",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div><strong>Dask DataFrame Structure:</strong></div>\n",
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>x</th>\n",
-       "      <th>y</th>\n",
-       "      <th>z</th>\n",
-       "      <th>cell_id</th>\n",
-       "      <th>overlaps_nucleus</th>\n",
-       "      <th>transcript_id</th>\n",
-       "      <th>qv</th>\n",
-       "      <th>x_uint</th>\n",
-       "      <th>y_uint</th>\n",
-       "      <th>morton_code_2d</th>\n",
-       "      <th>feature_name_codes</th>\n",
-       "      <th>feature_name</th>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>npartitions=8</th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th></th>\n",
-       "      <td>float32</td>\n",
-       "      <td>float32</td>\n",
-       "      <td>float32</td>\n",
-       "      <td>int32</td>\n",
-       "      <td>uint8</td>\n",
-       "      <td>uint64</td>\n",
-       "      <td>float32</td>\n",
-       "      <td>uint32</td>\n",
-       "      <td>uint32</td>\n",
-       "      <td>uint32</td>\n",
-       "      <td>int32</td>\n",
-       "      <td>category[unknown]</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th></th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>...</th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th></th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th></th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>\n",
-       "<div>Dask Name: read-parquet, 1 graph layer</div>"
-      ],
-      "text/plain": [
-       "Dask DataFrame Structure:\n",
-       "                     x        y        z cell_id overlaps_nucleus transcript_id       qv  x_uint  y_uint morton_code_2d feature_name_codes       feature_name\n",
-       "npartitions=8                                                                                                                                                \n",
-       "               float32  float32  float32   int32            uint8        uint64  float32  uint32  uint32         uint32              int32  category[unknown]\n",
-       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
-       "...                ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
-       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
-       "                   ...      ...      ...     ...              ...           ...      ...     ...     ...            ...                ...                ...\n",
-       "Dask Name: read-parquet, 1 graph layer"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata.points[\"transcripts_with_morton_codes\"]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "id": "1b41a4bb-e552-41c7-a0c4-f9b70847d5cb",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'transform': {'global': Scale (x, y, z)\n",
-       "      [4.70588235 4.70588235 1.        ]},\n",
-       " 'spatialdata_attrs': {'feature_key': 'feature_name',\n",
-       "  'instance_key': 'cell_id'}}"
-      ]
-     },
-     "execution_count": 12,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "sdata.points[\"transcripts_with_morton_codes\"].attrs"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "2035d286",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "aca392bdcba64975bf8f8c088c5e6e49",
-       "version_major": 2,
-       "version_minor": 1
-      },
-      "text/plain": [
-       "VitessceWidget(js_dev_mode=True, uid='eed7')"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "vw = (\n",
     "    sdata\n",
     "        .pl.render_images(element=\"morphology_focus\")\n",
     "        .pl.render_shapes(element=\"cell_boundaries\")\n",
-    "        .pl.render_points(element=\"transcripts_with_morton_codes\", color=\"feature_name\", groups=[\"ERBB2\"], palette=[\"red\"])\n",
+    "        .pl.render_points(element=\"transcripts_with_morton_codes\", color=\"feature_name\", groups=[\"ERBB2\"], palette=[\"red\"], table_name=\"table\")\n",
     "        .pl.show()\n",
     ")\n",
     "vw"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5433ec21-e385-4667-a45d-e184611fdde0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw.config.to_dict(base_url=\"\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/uv.lock b/uv.lock
index 2f1c6b3..dcc92c4 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1085,7 +1085,7 @@ requires-dist = [
     { name = "sphinx", marker = "extra == 'docs'" },
     { name = "sphinx-book-theme", marker = "extra == 'docs'" },
     { name = "sphinx-copybutton", marker = "extra == 'docs'" },
-    { name = "vitessce", extras = ["all"], specifier = ">=3.8.0" },
+    { name = "vitessce", extras = ["all"], specifier = ">=3.8.1" },
     { name = "xarray", specifier = ">=2024.10.0,<=2025.3.0" },
     { name = "zarr", specifier = ">=2.5.0,<3" },
 ]
@@ -4904,7 +4904,7 @@ wheels = [
 
 [[package]]
 name = "vitessce"
-version = "3.8.0"
+version = "3.8.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "black" },
@@ -4917,8 +4917,9 @@ dependencies = [
     { name = "zarr", version = "2.18.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
     { name = "zarr", version = "2.18.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
 ]
+sdist = { url = "https://files.pythonhosted.org/packages/4a/c8/f5a7928e5521611e1d128d37d336078c9324198929e261524eda15a6559a/vitessce-3.8.1.tar.gz", hash = "sha256:293b99a0b66721368b0500c328f9d7879f6ab08bdce949b749c4a23271d8f397", size = 332200 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/d3/60/b5c82868f136eff8c2d3a8cae675c63b4e9e65b10f6c36861d49aade32ce/vitessce-3.8.0-py3-none-any.whl", hash = "sha256:763f9b8f411d103cd577789acba2baa16b938969826d6ead10dde46f916dda4a", size = 79843 },
+    { url = "https://files.pythonhosted.org/packages/d0/8d/cfd9eb3fdc3d37ae12ad3aa4e3b01ea7d886e2941adf212d1be1a7085552/vitessce-3.8.1-py3-none-any.whl", hash = "sha256:7a98683da82d5ffa5b1d7aea3f4a687e7a45090fabded8250895c7912230fbfc", size = 80024 },
 ]
 
 [package.optional-dependencies]

From ea82fb59283c4464827d0ad3e0ad6780ef8191cb Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 12 Feb 2026 08:50:50 -0500
Subject: [PATCH 7/7] Update

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c08f328..ca6795c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   'numpy>=1.21.2',
   'zarr>=2.5.0,<3',
   'numcodecs>=0.5.7,<0.16.0',
-  'vitessce[all]>=3.8.1',
+  'vitessce[all]>=3.8.2',
   'scanpy>=1.11.3',
   'anndata>=0.11.4',
   'spatialdata>=0.3.0',