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Fix/broken images in notebooks #10

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Merged
MarcelRosier merged 7 commits into from
Jan 12, 2024
Merged

Fix/broken images in notebooks #10

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7bc5f2e
- reruns
MarcelRosier Jan 9, 2024
e01ad81
- test different image loading
MarcelRosier Jan 9, 2024
009d406
- updated image integration to pure md syntax
MarcelRosier Jan 9, 2024
14ebac2
- test reference to local figure
MarcelRosier Jan 9, 2024
7e0e108
- change remaining notebooks to reference local figure
MarcelRosier Jan 9, 2024
234cc28
Merge branch 'main' into fix/broken-images-in-notebooks
MarcelRosier Jan 12, 2024
0a7c109
Autoformat with black
brainless-bot[bot] Jan 12, 2024
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6 changes: 3 additions & 3 deletions panoptica/example_spine_matched_instance.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: panoptica in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (0.5.19.post2.dev0+dd3ef62)\n",
"Requirement already satisfied: panoptica in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (0.5.20)\n",
"Requirement already satisfied: auxiliary in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.38)\n",
"Requirement already satisfied: rich in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (13.6.0)\n",
"Requirement already satisfied: numpy in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.25.2)\n",
Expand Down Expand Up @@ -79,7 +79,7 @@
"To demonstrate we use a reference and predicition of spine a segmentation with matched instances.\n",
"\n",
"\n",
"<img src=\"https://github.com/BrainLesion/panoptica/blob/main/examples/figures/matched_instance.png?raw=true\" alt=\"matched_instance_figure\" height=\"300\"/>\n"
"![matched_figure](figures/matched_instance.png)"
]
},
{
Expand Down Expand Up @@ -192,7 +192,7 @@
"text": [
"Panoptic: Start Evaluation\n",
"-- Got MatchedInstancePair, will evaluate instances\n",
"-- evaluate took 1.9782342910766602 seconds to execute.\n"
"-- evaluate took 1.7750227451324463 seconds to execute.\n"
]
}
],
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