Merge 0c3f0f6 into f25f809

angelolab · Nov 15, 2022 · 00f850e · 00f850e
2 parents f25f809 + 0c3f0f6
commit 00f850e
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Showing 5 changed files with 33 additions and 20 deletions.
diff --git a/templates/1_Segment_Image_Data.ipynb b/templates/1_Segment_Image_Data.ipynb
@@ -97,7 +97,9 @@
     "\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 the `base_dir` to point to your own sub-directory within the data folder, rather than `'example_dataset'`. \n",
     "\n",
-    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset)."
+    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset).\n",
+    "\n",
+    "* `overwrite_existing`: If set to `False`, it will not overwrite existing data in the `data/example_dataset`. Recommended setting it to `True` for Notebook 1, so it will always download the example_dataset data."
    ]
   },
   {
@@ -381,7 +383,7 @@
  ],
  "metadata": {
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+   "display_name": "Python 3.8.15 64-bit ('ark38')",
    "language": "python",
    "name": "python3"
   },
@@ -395,11 +397,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.15"
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diff --git a/templates/2_Cluster_Pixels.ipynb b/templates/2_Cluster_Pixels.ipynb
@@ -94,7 +94,9 @@
     "\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 the `base_dir` to point to your own sub-directory within the data folder, rather than `'example_dataset'`. \n",
     "\n",
-    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset)."
+    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset).\n",
+    "\n",
+    "* `overwrite_existing`: If set to `False`, it will not overwrite existing data in the `data/example_dataset`. Recommended setting to `False` if you are running Notebooks 1,2,3 and 4 in succession. Set to `True` if you are just running Notebook 2."
    ]
   },
   {
@@ -892,7 +894,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.8.15 64-bit ('ark38')",
    "language": "python",
    "name": "python3"
   },
@@ -906,14 +908,14 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.15"
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diff --git a/templates/3_Cluster_Cells.ipynb b/templates/3_Cluster_Cells.ipynb
@@ -104,7 +104,9 @@
     "\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 the `base_dir` to point to your own sub-directory within the data folder, rather than `'example_dataset'`. \n",
     "\n",
-    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset)."
+    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset).\n",
+    "\n",
+    "* `overwrite_existing`: If set to `False`, it will not overwrite existing data in the `data/example_dataset`. Recommended setting to `False` if you are running Notebooks 1,2,3 and 4 in succession. Set to `True` if you are just running Notebook 3."
    ]
   },
   {
@@ -736,7 +738,7 @@
  ],
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   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.8.15 64-bit ('ark38')",
    "language": "python",
    "name": "python3"
   },
@@ -750,11 +752,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.15"
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diff --git a/templates/4_Post_Clustering.ipynb b/templates/4_Post_Clustering.ipynb
@@ -90,7 +90,9 @@
     "\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 the `base_dir` to point to your own sub-directory within the data folder, rather than `'example_dataset'`. \n",
     "\n",
-    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset)."
+    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset).\n",
+    "\n",
+    "* `overwrite_existing`: If set to `False`, it will not overwrite existing data in the `data/example_dataset`. Recommended setting to `False` if you are running Notebooks 1,2,3 and 4 in succession. Set to `True` if you are just running Notebook 4."
    ]
   },
   {
@@ -463,7 +465,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.8.15 64-bit ('ark38')",
    "language": "python",
    "name": "python3"
   },
@@ -477,11 +479,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.15"
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diff --git a/templates/example_fiber_segmentation.ipynb b/templates/example_fiber_segmentation.ipynb
@@ -66,7 +66,12 @@
    "metadata": {},
    "source": [
     "### Download the Example Dataset\n",
-    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels."
+    "\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 the `base_dir` to point to your own sub-directory within the data folder, rather than `'example_dataset'`. \n",
+    "\n",
+    "If you would like to test the features in Ark with an example dataset, run the cell below. It will download a dataset consisting of 11 FOVs with 22 channels. You may find more information about the example dataset in the [README](../README.md#example-dataset).\n",
+    "\n",
+    "* `overwrite_existing`: If set to `False`, it will not overwrite existing data in the `data/example_dataset`. Recommended setting to `False` if you have the results of the other notebooks. Set to `True` if you are just running the Example Fiber Segmentation Notebook."
    ]
   },
   {
@@ -203,7 +208,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.8.13 64-bit ('ark38')",
+   "display_name": "Python 3.8.15 64-bit ('ark38')",
    "language": "python",
    "name": "python3"
   },
@@ -217,11 +222,11 @@
    "name": "python",
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    "pygments_lexer": "ipython3",
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