fix error in rendering processing notebook

docs/notebooks/processing.ipynb

@@ -56,7 +56,7 @@
     "\n",
     "mip_ngff = ngff_image.derive_new_image(\"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0_mip\",\n",
     "                                       name=\"MIP\",\n",
-    "                                       shape=(3, 1, 4320, 5120))"
+    "                                       shape=(1, 1, 2160, 5120))"
    ]
   },
   {
@@ -131,7 +131,7 @@
     "\n",
     "image_after_consolidation = mip_image_2.get_data(c=0, z=0)\n",
     "\n",
-    "fig, axs = plt.subplots(1, 2, figsize=(10, 5))\n",
+    "fig, axs = plt.subplots(2, 1, figsize=(10, 5))\n",
     "axs[0].set_title(\"Before consolidation\")\n",
     "axs[0].imshow(image_before_consolidation, cmap=\"gray\")\n",
     "axs[1].set_title(\"After consolidation\")\n",
@@ -255,17 +255,17 @@
     "    print(\" - Processing ROI\", roi.field_index)\n",
     "    patch = source_image.get_data_from_roi(roi, c=dapi_idx)\n",
     "    segmentation = otsu_threshold_segmentation(patch, max_label)\n",
-    "    \n",
+    "\n",
     "    # Add the max label of the previous segmentation to avoid overlapping labels\n",
     "    max_label = segmentation.max()\n",
-    "    \n",
+    "\n",
     "    nuclei_image.set_data_from_roi(patch=segmentation, roi=roi)\n",
-    "    \n",
+    "\n",
     "# Consolidate the segmentation image\n",
     "nuclei_image.consolidate()\n",
     "\n",
     "print(\"Segmentation image saved\")\n",
-    "fig, axs = plt.subplots(1, 2, figsize=(10, 5))\n",
+    "fig, axs = plt.subplots(2, 1, figsize=(10, 5))\n",
     "axs[0].set_title(\"MIP\")\n",
     "axs[0].imshow(source_image.array[0, 0], cmap=\"gray\")\n",
     "axs[1].set_title(\"Nuclei segmentation\")\n",