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- Update Jupyter Notebook links
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‎benchmarks/annotation_store.ipynb‎

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"source": [
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"# Benchmarking Annotation Storage\n",
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"\n",
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"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",
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"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",
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"\n"
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]
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},

‎examples/01-wsi-reading.ipynb‎

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‎examples/02-stain-normalization.ipynb‎

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‎examples/03-tissue-masking.ipynb‎

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‎examples/04-patch-extraction.ipynb‎

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‎examples/05-patch-prediction.ipynb‎

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"source": [
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"# Patch Prediction Models\n",
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"\n",
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"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",
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"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",
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},
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"source": [
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"%%bash\n",
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"apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
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"pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
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"pip install tiatoolbox | tail -n 1\n",
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"echo \"Installation is done.\""
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]
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},

‎examples/06-semantic-segmentation.ipynb‎

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"source": [
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"# Semantic Segmentation Models\n",
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"\n",
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"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",
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"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",
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"\n"
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"source": [
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"%%bash\n",
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"apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
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"pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
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"pip install tiatoolbox | tail -n 1\n",
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"echo \"Installation is done.\""
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]
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},

‎examples/07-advanced-modeling.ipynb‎

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"source": [
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"# Advanced Model Handling in TIAToolbox\n",
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"\n",
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"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",
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"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",
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"\n"
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"source": [
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"%%bash\n",
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"apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
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"pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
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"pip install tiatoolbox | tail -n 1\n",
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"echo \"Installation is done.\""
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]
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},

‎examples/08-nucleus-instance-segmentation.ipynb‎

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"source": [
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"# Nucleus Instance Segmentation\n",
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"\n",
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"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",
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"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",
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"\n"
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"source": [
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"%%bash\n",
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"apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools libpixman-1-dev | tail -n 1\n",
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"pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
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"pip install tiatoolbox | tail -n 1\n",
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"echo \"Installation is done.\""
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]
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},

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