Update elastix notebook

Author: adamltyson

Diff for: .gitignore

@@ -83,4 +83,4 @@ target/
 stage1_train
 serial2p_subset
 DAPI.tif
-
+coronal_section.tif

Diff for: coronal_section.tif

@@ -181,7 +181,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "4485eddf-ea28-4d88-b48b-98c791665d92",
    "metadata": {},
    "outputs": [],
@@ -192,18 +192,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "3e35422d-9592-45b7-b7cc-2cd987453831",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Image layer 'registered_image' at 0x7fcd036661d0>"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "# Visualise the result\n",
     "viewer.add_image(registered_image)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "90a58717-2138-464d-ae59-5a03ac8322bf",
    "metadata": {},
    "outputs": [],
@@ -234,10 +245,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "id": "62055f12-bd92-4ab2-9466-da9e5d533b90",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Labels layer 'warped_annotations' at 0x7fce025e67d0>"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "# Apply transformation to the annotations image\n",
     "warped_annotations = transform_additional_image(atlas.annotation[atlas_plane], result_transform_parameters, mask=True)\n",
@@ -246,10 +268,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "id": "343c7871-5663-4d3c-927c-a41aceb9d7e5",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'acronym': 'CP',\n",
+      " 'id': 672,\n",
+      " 'mesh': None,\n",
+      " 'mesh_filename': PosixPath('/home/adam/.brainglobe/allen_mouse_25um_v1.2/meshes/672.obj'),\n",
+      " 'name': 'Caudoputamen',\n",
+      " 'rgb_triplet': [152, 214, 249],\n",
+      " 'structure_id_path': [997, 8, 567, 623, 477, 485, 672]}\n"
+     ]
+    }
+   ],
    "source": [
     "# Pick a value from atlas to inspect\n",
     "from pprint import pprint\n",