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Merged
shaneahmed merged 22 commits into from
May 5, 2023
Merged

🔖 Release 1.4.0 #600

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1c11b1e
REL: Release 1.3.0 (#496)
shaneahmed Oct 21, 2022
075c472
:bookmark: REL: Release 1.3.0 (#523)
shaneahmed Dec 20, 2022
79d26e9
:bookmark: REL: Release 1.3.1 (#523)
shaneahmed Dec 20, 2022
ce788a3
Merge remote-tracking branch 'origin/master'
shaneahmed Dec 20, 2022
24390e5
🔖 REL: Release 1.3.2 (#541)
shaneahmed Feb 17, 2023
d548b33
🔖 REL: Release 1.3.3 (#552)
shaneahmed Mar 2, 2023
9eb04b2
:memo: Update HISTORY.md with release notes
shaneahmed Apr 24, 2023
66ef49c
:memo: Update HISTORY.md with release notes
shaneahmed Apr 24, 2023
ab4c64f
Bump version: 1.3.3 → 1.4.0
shaneahmed Apr 24, 2023
8e3dcba
:memo: Update Jupyter notebook links
shaneahmed Apr 24, 2023
1358c79
:pushpin: Pin dependencies for long term stable release
shaneahmed Apr 24, 2023
8fdabbf
Merge branch 'develop' into pre-release
shaneahmed Apr 27, 2023
be40b1a
Merge branch 'develop' into pre-release
shaneahmed May 3, 2023
c6273dd
:pushpin: Update `numpy` pin
shaneahmed May 3, 2023
0438f4b
Merge branch 'develop' into pre-release
shaneahmed May 5, 2023
74d04b9
:memo: Update HISTORY.md
shaneahmed May 5, 2023
3e56f5f
:pushpin: Pin dependecies
shaneahmed May 5, 2023
1524323
Merge branch 'master' into pre-release
shaneahmed May 5, 2023
eefcc9f
:rewind: Revert updates to notebooks
shaneahmed May 5, 2023
b71c87d
:rewind: Revert changes to requirements.txt
shaneahmed May 5, 2023
7922120
:rewind: Revert changes to requirements.txt
shaneahmed May 5, 2023
f0b8a06
[skip ci] :rewind: Revert changes to notebooks
shaneahmed May 5, 2023
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⏪ Revert updates to notebooks 
- Revert updates to notebooks
  • Loading branch information
@shaneahmed
shaneahmed committed May 5, 2023
commit eefcc9f9657591001f336b80a6bbe8892799d4a3
4 changes: 2 additions & 2 deletions examples/01-wsi-reading.ipynb
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"source": [
"# Read and Visualize a WSI\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/01-wsi-reading.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/01-wsi-reading.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/01-wsi-reading.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/01-wsi-reading.ipynb)\\]\n",
"\n"
]
},
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"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/02-stain-normalization.ipynb
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"source": [
"# Stain Normalization\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/02-stain-normalization.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/02-stain-normalization.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/02-stain-normalization.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/02-stain-normalization.ipynb)\\]\n",
"\n"
]
},
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"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/03-tissue-masking.ipynb
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"source": [
"# Masking tissue region in whole slide images\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/03-tissue-masking.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/03-tissue-masking.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/03-tissue-masking.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/03-tissue-masking.ipynb)\\]\n",
"\n"
]
},
Expand Down Expand Up @@ -72,7 +72,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/04-patch-extraction.ipynb
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"source": [
"# Patch extraction from Histology Images\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/04-patch-extraction.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/04-patch-extraction.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/04-patch-extraction.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/04-patch-extraction.ipynb)\\]\n",
"\n"
]
},
Expand Down Expand Up @@ -72,7 +72,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/05-patch-prediction.ipynb
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"source": [
"# Patch Prediction Models\n",
"\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",
"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",
"\n"
]
},
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"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/06-semantic-segmentation.ipynb
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"source": [
"# Semantic Segmentation Models\n",
"\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",
"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",
"\n"
]
},
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"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail --line 1\n",
"!pip install tiatoolbox | tail --line 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail --line 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/07-advanced-modeling.ipynb
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"source": [
"# Advanced Model Handling in TIAToolbox\n",
"\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",
"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",
"\n"
]
},
Expand Down Expand Up @@ -92,7 +92,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/08-nucleus-instance-segmentation.ipynb
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"source": [
"# Nucleus Instance Segmentation\n",
"\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",
"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",
"\n"
]
},
Expand Down Expand Up @@ -78,7 +78,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail --line 1\n",
"!pip install tiatoolbox | tail --line 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail --line 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/09-multi-task-segmentation.ipynb
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"source": [
"# Multi-Task Segmentation Models\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/09-multi-task-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/09-multi-task-segmentation.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/09-multi-task-segmentation.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/09-multi-task-segmentation.ipynb)\\]\n",
"\n"
]
},
Expand Down Expand Up @@ -73,7 +73,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"\n",
"print(\"Installation is done.\")"
]
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4 changes: 2 additions & 2 deletions examples/10-wsi-registration.ipynb
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"source": [
"# Whole Slide Image Registration\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/10-wsi-registration.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/10-wsi-registration.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/10-wsi-registration.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/10-wsi-registration.ipynb)\\]\n",
"\n"
],
"metadata": {
Expand Down Expand Up @@ -74,7 +74,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail --line 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail --line 1\n",
"\n",
"print(\"Installation is done.\")"
],
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4 changes: 2 additions & 2 deletions examples/inference-pipelines/idars.ipynb
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"source": [
"# Prediction of Molecular Pathways and Key Mutations\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/inference-pipelines/idars.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/inference-pipelines/idars.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/inference-pipelines/idars.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/inference-pipelines/idars.ipynb)\\]\n",
"\n"
]
},
Expand Down Expand Up @@ -105,7 +105,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail -n 1\n",
"!pip install tiatoolbox | tail -n 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail -n 1\n",
"print(\"Installation is done.\")"
]
},
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4 changes: 2 additions & 2 deletions examples/inference-pipelines/slide-graph.ipynb
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"source": [
"# Slide Graph Pipeline\n",
"\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/examples/inference-pipelines/slide-graph.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/master/examples/inference-pipelines/slide-graph.ipynb)\\]\n",
"Click to open in: \\[[GitHub](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/inference-pipelines/slide-graph.ipynb)\\]\\[[Colab](https://colab.research.google.com/github/TissueImageAnalytics/tiatoolbox/blob/develop/examples/inference-pipelines/slide-graph.ipynb)\\]\n",
"\n"
]
},
Expand Down Expand Up @@ -125,7 +125,7 @@
"outputs": [],
"source": [
"!apt-get -y install libopenjp2-7-dev libopenjp2-tools openslide-tools | tail --line 1\n",
"!pip install tiatoolbox | tail --line 1\n",
"!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail --line 1\n",
"\n",
"print(\"Installation is done.\")"
]
Expand Down