crop display roi

Author: ziw-liu

examples/virtual_staining/vcp_tutorials/quick_start.ipynb

@@ -377,16 +377,19 @@
    "outputs": [],
    "source": [
     "# Read images from Zarr stores\n",
+    "# Choose the ROI for better visualization\n",
+    "y_slice = slice(0, 512)\n",
+    "x_slice = slice(0, 512)\n",
     "\n",
     "# Open the prediction store and get the 2D images from 5D arrays (t,c,z,y,x)\n",
     "with open_ome_zarr(output_path / fov) as vs_store:\n",
-    "    vs_nucleus = vs_store[0][0, 0, 0]\n",
-    "    vs_membrane = vs_store[0][0, 1, 0]\n",
+    "    vs_nucleus = vs_store[0][0, 0, 0, y_slice, x_slice]\n",
+    "    vs_membrane = vs_store[0][0, 1, 0, y_slice, x_slice]\n",
     "\n",
     "# Open the experimental fluorescence dataset\n",
     "with open_ome_zarr(input_data_path / fov) as fluor_store:\n",
-    "    fluor_nucleus = fluor_store[0][0, 1, 0]\n",
-    "    fluor_membrane = fluor_store[0][0, 2, 0]"
+    "    fluor_nucleus = fluor_store[0][0, 1, 0, y_slice, x_slice]\n",
+    "    fluor_membrane = fluor_store[0][0, 2, 0, y_slice, x_slice]"
    ]
   },
   {

examples/virtual_staining/vcp_tutorials/quick_start.py

@@ -250,16 +250,19 @@
 
 # %%
 # Read images from Zarr stores
+# Choose the ROI for better visualization
+y_slice = slice(0, 512)
+x_slice = slice(0, 512)
 
 # Open the prediction store and get the 2D images from 5D arrays (t,c,z,y,x)
 with open_ome_zarr(output_path / fov) as vs_store:
-    vs_nucleus = vs_store[0][0, 0, 0]
-    vs_membrane = vs_store[0][0, 1, 0]
+    vs_nucleus = vs_store[0][0, 0, 0, y_slice, x_slice]
+    vs_membrane = vs_store[0][0, 1, 0, y_slice, x_slice]
 
 # Open the experimental fluorescence dataset
 with open_ome_zarr(input_data_path / fov) as fluor_store:
-    fluor_nucleus = fluor_store[0][0, 1, 0]
-    fluor_membrane = fluor_store[0][0, 2, 0]
+    fluor_nucleus = fluor_store[0][0, 1, 0, y_slice, x_slice]
+    fluor_membrane = fluor_store[0][0, 2, 0, y_slice, x_slice]
 
 # %%
 # Plot