Add 3D ROI loading example

Author: jluethi

demo-october-2022/ROIs_and_FeatureVis.ipynb

@@ -37,6 +37,9 @@
     "import anndata as ad\n",
     "import dask.array as da\n",
     "import numpy as np\n",
+    "import pandas as pd\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
     "from utils_roi_loading import convert_ROI_table_to_indices, load_label_roi, load_intensity_roi, prepare_feature_vis"
    ]
   },
@@ -246,13 +249,7 @@
    "id": "b6a8391f-de20-4856-8244-47997a486391",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "import pandas as pd\n",
-    "import napari\n",
-    "from pathlib import Path\n",
-    "import matplotlib.pyplot as plt\n",
-    "import numpy as np"
-   ]
+   "source": []
   },
   {
    "cell_type": "code",
@@ -409,7 +406,15 @@
    "execution_count": 11,
    "id": "3d843d31-3f25-4553-b8b2-a447bc95e88e",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "no parent found for <ome_zarr.reader.Label object at 0x2a9c7da60>: None\n"
+     ]
+    }
+   ],
    "source": [
     "colors, label_properties = prepare_feature_vis(feature_df, feature='area')\n",
     "label_layer.properties = label_properties\n",
@@ -423,6 +428,24 @@
    "metadata": {},
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ecd035fb-92e6-47b1-aeca-622670fa9f98",
+   "metadata": {},
+   "source": [
+    "# 3D example"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8e76c1b4-21dc-46b2-95b1-4f5c9cdf0272",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "zarr_url = Path('/Users/joel/Desktop/20220928_2x2_Zenodo/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr')"
+   ]
   }
  ],
  "metadata": {