update notebooks

Author: FynnBe

example/dataset_creation.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# ⚠️ this notebook needs to be updated "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/dataset_statistics_demo.ipynb

@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "29ff046c",
+   "metadata": {},
+   "source": [
+    "# ⚠️ this notebook needs to be updated "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

example/model_usage.ipynb

@@ -8,23 +8,32 @@
     "# bioimageio.core usage examples"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "275284b2",
+   "metadata": {},
+   "source": [
+    "# ⚠️ this notebook needs to be updated "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "c72ba149",
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import hashlib\n",
+    "import os\n",
     "\n",
-    "import bioimageio.core\n",
     "import imageio\n",
     "\n",
     "# we use napari for visualising images, you can install it via `pip install napari` or`conda install napari`\n",
     "import napari\n",
     "import numpy as np\n",
-    "import xarray as xr"
+    "import xarray as xr\n",
+    "\n",
+    "import bioimageio.core"
    ]
   },
   {
@@ -359,15 +368,14 @@
    "source": [
     "# The convenience function `predict_images` can be use to run prediction for many images stored on disc\n",
     "# Note: this only works for models which have a single input and output!\n",
-    "from bioimageio.core.prediction import predict_images\n",
-    "\n",
     "# Here we use a small subset of the dsb challenge data for prediction.\n",
     "# The original data is available at https://github.com/stardist/stardist/releases/download/0.1.0/dsb2018.zip.\n",
     "# We have added a few images to the repository so that the notebook runs out of the box.\n",
-    "\n",
     "# Get all paths to the images in the \"example-images\" folder.\n",
     "from glob import glob\n",
     "\n",
+    "from bioimageio.core.prediction import predict_images\n",
+    "\n",
     "inputs = glob(\"./example-images/*.png\")\n",
     "\n",
     "# Create an output folder and specify the output path for each image.\n",
@@ -443,7 +451,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,