- Update Jupyter Notebook links

TissueImageAnalytics · Dec 5, 2024 · a6755fd · a6755fd
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diff --git a/benchmarks/annotation_store.ipynb b/benchmarks/annotation_store.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "# Benchmarking Annotation Storage\n",
     "\n",
-    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/tree/develop/benchmarks/annotation_store.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/benchmarks/annotation_store.ipynb)\\]\\[[Kaggle](https://kaggle.com/kernels/welcome?src=https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/benchmarks/annotation_store.ipynb)\\]\n",
+    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/tree/master/benchmarks/annotation_store.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/benchmarks/annotation_store.ipynb)\\]\n",
     "\n"
    ]
   },

diff --git a/examples/01-wsi-reading.ipynb b/examples/01-wsi-reading.ipynb
diff --git a/examples/02-stain-normalization.ipynb b/examples/02-stain-normalization.ipynb
diff --git a/examples/03-tissue-masking.ipynb b/examples/03-tissue-masking.ipynb
diff --git a/examples/04-patch-extraction.ipynb b/examples/04-patch-extraction.ipynb
diff --git a/examples/05-patch-prediction.ipynb b/examples/05-patch-prediction.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "# Patch Prediction Models\n",
     "\n",
-    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/05-patch-prediction.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/05-patch-prediction.ipynb)\\]\n",
+    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/05-patch-prediction.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/05-patch-prediction.ipynb)\\]\n",
     "\n"
    ]
   },
@@ -92,7 +92,7 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install tiatoolbox | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },

diff --git a/examples/06-semantic-segmentation.ipynb b/examples/06-semantic-segmentation.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "# Semantic Segmentation Models\n",
     "\n",
-    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/06-semantic-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/06-semantic-segmentation.ipynb)\\]\n",
+    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/06-semantic-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/06-semantic-segmentation.ipynb)\\]\n",
     "\n"
    ]
   },
@@ -83,7 +83,7 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install tiatoolbox | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },

diff --git a/examples/07-advanced-modeling.ipynb b/examples/07-advanced-modeling.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "# Advanced Model Handling in TIAToolbox\n",
     "\n",
-    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/07-advanced-modeling.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/07-advanced-modeling.ipynb)\\]\n",
+    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/07-advanced-modeling.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/07-advanced-modeling.ipynb)\\]\n",
     "\n"
    ]
   },
@@ -93,7 +93,7 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install tiatoolbox | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },

diff --git a/examples/08-nucleus-instance-segmentation.ipynb b/examples/08-nucleus-instance-segmentation.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "# Nucleus Instance Segmentation\n",
     "\n",
-    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/08-nucleus-instance-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/08-nucleus-instance-segmentation.ipynb)\\]\n",
+    "Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/08-nucleus-instance-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/08-nucleus-instance-segmentation.ipynb)\\]\n",
     "\n"
    ]
   },
@@ -79,7 +79,7 @@
    "source": [
     "%%bash\n",
     "apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
-    "pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
+    "pip install tiatoolbox | tail -n 1\n",
     "echo \"Installation is done.\""
    ]
   },