DOC: Add scikit-image example to LabelImages example

Author: dani-lbnl

examples/LabelImages.ipynb

@@ -9,12 +9,12 @@
     "# Install dependencies for this example\n",
     "# Note: This does not include itkwidgets, itself\n",
     "import sys\n",
-    "!{sys.executable} -m pip install -U itk itk-totalvariation"
+    "!{sys.executable} -m pip install -U itk itk-totalvariation scikit-image"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -23,14 +23,15 @@
     "\n",
     "import itk\n",
     "import numpy as np\n",
+    "import skimage.io, skimage.filters, skimage.measure\n",
     "\n",
     "from itkwidgets import view\n",
     "import itkwidgets"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,13 +45,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "530d6f97e04e4dab86bbb00ddcc799bb",
+       "model_id": "436f06a0454f4e0abee8cbf15573015e",
        "version_major": 2,
        "version_minor": 0
       },
@@ -70,7 +71,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -197,15 +198,73 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can also combine the intensity images, weighted and blended with the label maps, with iso-surface geometry."
+    "The images and labels can, of course, also come from *scikit-image*."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "8327687db5c64422a16af110bb597b76",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Viewer(annotations=False, cmap=['BrBG'], geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "image = skimage.io.imread(file_name)\n",
+    "\n",
+    "view(image, cmap=itkwidgets.cm.BrBG, annotations=False, vmax=800, ui_collapsed=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# Segment the cells\n",
+    "smoothed = skimage.filters.gaussian(image)\n",
+    "\n",
+    "threshold = skimage.filters.threshold_isodata(smoothed)\n",
+    "thresholded = smoothed > threshold\n",
+    "\n",
+    "connected_components = skimage.measure.label(thresholded)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "cdc8480801bc4792b2053812febdf00f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Viewer(geometries=[], gradient_opacity=0.22, interpolation=False, point_sets=[], rendered_label_image=<itk.itk…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "view(label_image=connected_components)"
+   ]
   }
  ],
  "metadata": {