Behnam: registration, done

imsb-uke · Aug 27, 2024 · d180805 · d180805
1 parent 0bcb6e8
commit d180805
Showing 1 changed file with 40 additions and 0 deletions.
diff --git a/notebooks/03_image_registration/plot_example.ipynb b/notebooks/03_image_registration/plot_example.ipynb
@@ -102,6 +102,46 @@
    "metadata": {},
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "de054d59-620c-4b6b-8826-0e11f25380d4",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "6724f98c-26fa-4c94-84f3-cb3d4d7822c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata_dir = \"data_level_1/adata/\"\n",
+    "he_image_dir = \"data_level_1/he_registered_old/\"\n",
+    "save_dir = \"data_level_1/adata_with_he/\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2535521a-dfaf-44f8-ba78-bb79ea60d2f5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for sample in tqdm(range(1:57)):\n",
+    "\n",
+    "    sample = f\"X{sample}\"\n",
+    "    adata = sc.read_h5ad(adata_dir + f'{sample}.h5ad')\n",
+    "    he_image = plt.imread(he_image_dir + f'{sample}.tiff')\n",
+    "\n",
+    "    slide_id = adata.obs['Slide_ID'][0]\n",
+    "    adata.uns['spatial'][slide_id]['images']['he_downscaled_aligned'] = he_image  \n",
+    "    adata.uns['spatial'][slide_id]['scalefactors']['tissue_he_downscaled_aligned_scalef'] = 1\n",
+    "\n",
+    "    adata.write_h5ad(save_dir + f'{sample}.h5ad')"
+   ]
   }
  ],
  "metadata": {