Merged predict notebooks into one

templates/1_Nimbus_Predict.ipynb

@@ -34,7 +34,8 @@
    "metadata": {},
    "source": [
     "## 0: Set root directory and download example dataset\n",
-    "Here we are using the example data located in `/data/example_dataset/input_data`. To modify this notebook to run using your own data, simply change `base_dir` to point to your own sub-directory within the data folder. Set `base_dir`, the path to all of your imaging data (i.e. multiplexed images and segmentation masks). Subdirectory `nimbus_output` will contain all of the data generated by this notebook. In the following, we expect this folder structure:\n",
+    "Here we are using the example data located in `/data/example_dataset/input_data`. To modify this notebook to run using your own data, simply change `base_dir` to point to your own sub-directory within the data folder. Set `base_dir`, the path to all of your imaging data (i.e. multiplexed images and segmentation masks). Subdirectory `nimbus_output` will contain all of the data generated by this notebook. In the following, we expect this folder structure, with `fov_1` and `fov_2` either being folders of individual channel images or `.ome.tiff` files that contain all channels in a single file.\n",
+    "```bash\n",
     "```\n",
     "|-- base_dir\n",
     "|   |-- image_data\n",
@@ -177,7 +178,7 @@
    "id": "e7717960",
    "metadata": {},
    "source": [
-    "Next we will use the `MultiplexDataset` class to abstract away differences in data representation. The class takes `fov_paths`, `segmentation_naming_convention` and a `suffix` and provides methods `.get_channel(fov, channel)` and `.get_segmentation(fov)` to access the data. The `suffix` is used to filter out files that do not end with the specified suffix."
+    "Next we will use the `MultiplexDataset` class to abstract away differences in data representation. The class takes `fov_paths`, `segmentation_naming_convention` and a `suffix` and provides methods `.get_channel(fov, channel)` and `.get_segmentation(fov)` to access the data. The `suffix` is used to filter out files that do not end with the specified suffix. When you use `.ome.tiff` files make sure to set the suffix to `.ome.tiff`, otherwise the ViewerWidget won't be able to display the images."
    ]
   },
   {
@@ -189,7 +190,7 @@
    "source": [
     "dataset = MultiplexDataset(\n",
     "    fov_paths=fov_paths,\n",
-    "    suffix=\".tiff\",\n",
+    "    suffix=\".tiff\", # or .png, .jpg, .jpeg, .tif or .ome.tiff\n",
     "    include_channels=include_channels,\n",
     "    segmentation_naming_convention=segmentation_naming_convention,\n",
     ")"