Updates

Author: keller-mark

docs/notebooks/spatial_data_xenium_morton.ipynb

@@ -70,7 +70,7 @@
    "source": [
     "data_dir = \"data\"\n",
     "zip_filepath = join(data_dir, \"xenium_rep1_io.spatialdata.zarr.zip\")\n",
-    "spatialdata_filepath = join(data_dir, \"xenium_rep1_io2.spatialdata.zarr\")"
+    "spatialdata_filepath = join(data_dir, \"xenium_rep1_io.spatialdata.zarr\")"
    ]
   },
   {
@@ -313,7 +313,8 @@
     "    image_path=\"images/morphology_focus\",\n",
     "    table_path=\"tables/table\",\n",
     "    obs_feature_matrix_path=\"tables/table/X\",\n",
-    "    obs_spots_path=\"shapes/cell_circles\",\n",
+    "    #obs_spots_path=\"shapes/cell_circles\",\n",
+    "    obs_segmentations_path=\"shapes/cell_boundaries\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        # The following tells Vitessce to consider each observation as a \"spot\"\n",
@@ -339,11 +340,21 @@
     "layer_controller = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
     "obs_sets = vc.add_view(\"obsSets\", dataset=dataset)\n",
     "\n",
+    "\"\"\"\n",
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    'spotLayer': CL([{\n",
     "        'obsType': 'cell',\n",
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSpots\"))\n",
+    "\"\"\"\n",
+    "\n",
+    "vc.link_views_by_dict([spatial, layer_controller], {\n",
+    "    'segmentationLayer': CL([{\n",
+    "        'segmentationChannel': CL([{\n",
+    "            'obsType': 'cell',\n",
+    "        }]),\n",
+    "    }]),\n",
+    "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
     "\n",
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    'pointLayer': CL([{\n",

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.8.4"
+version = "3.9.0"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

src/vitessce/widget.py

@@ -796,7 +796,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.9.9').tag(sync=True)
+    js_package_version = Unicode('3.9.10').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -809,7 +809,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.9.9', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.9.10', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
         """
         Construct a new Vitessce widget. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
@@ -1024,7 +1024,7 @@ async def _dispatch_command(self, msg: dict, buffers: list[bytes]) -> None:
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.9.9', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.9.10', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)