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Merge pull request #8 from BrainLesion/feature/update-for-citation-reminder
- add citation to readme and notebooks
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‎panoptica/README.md‎

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In this case module 3 can be used to directly report panoptic metrics without requiring any internal preprocessing.
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[Jupyter Notebook Example](https://github.com/BrainLesion/tutorials/tree/main/panoptica/example_spine_matched_instance.ipynb)
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## Citation
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If you use panoptica in your research, please cite it to support the development!
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Kofler, F., Möller, H., Buchner, J. A., de la Rosa, E., Ezhov, I., Rosier, M., Mekki, I., Shit, S., Negwer, M., Al-Maskari, R., Ertürk, A., Vinayahalingam, S., Isensee, F., Pati, S., Rueckert, D., Kirschke, J. S., Ehrlich, S. K., Reinke, A., Menze, B., Wiestler, B., & Piraud, M. (2023). _Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps._ [arXiv preprint arXiv:2312.02608](https://arxiv.org/abs/2312.02608).
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```
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@misc{kofler2023panoptica,
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title={Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps},
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author={Florian Kofler and Hendrik Möller and Josef A. Buchner and Ezequiel de la Rosa and Ivan Ezhov and Marcel Rosier and Isra Mekki and Suprosanna Shit and Moritz Negwer and Rami Al-Maskari and Ali Ertürk and Shankeeth Vinayahalingam and Fabian Isensee and Sarthak Pati and Daniel Rueckert and Jan S. Kirschke and Stefan K. Ehrlich and Annika Reinke and Bjoern Menze and Benedikt Wiestler and Marie Piraud},
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year={2023},
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eprint={2312.02608},
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archivePrefix={arXiv},
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primaryClass={cs.CV}
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}
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```

‎panoptica/example_spine_matched_instance.ipynb‎

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"Requirement already satisfied: panoptica in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (0.5.11)\n",
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #00ff00; text-decoration-color: #00ff00\">────────────────────────────────────────── </span>Thank you for using <span style=\"font-weight: bold\">panoptica</span><span style=\"color: #00ff00; text-decoration-color: #00ff00\"> ──────────────────────────────────────────</span>\n",
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"\u001b[92m────────────────────────────────────────── \u001b[0mThank you for using \u001b[1mpanoptica\u001b[0m\u001b[92m ──────────────────────────────────────────\u001b[0m\n"
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"> Please support our development by citing \n",
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" \u001b[4;94mhttps://github.com/BrainLesion/panoptica#citation\u001b[0m -- Thank you! \n"
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"evaluate took 2.727099895477295 seconds to execute.\n"
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"Panoptic: Start Evaluation\n",
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"-- Got MatchedInstancePair, will evaluate instances\n",
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"Recognition Quality / F1 Score (RQ): 0.8636363636363636\n",
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"DSC-based Segmentation Quality (DQ_DSC): 0.900292616009954 ± 0.10253566174957332\n",
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"Average symmetric surface distance (ASSD): 0.250331887879225 ± 0.07696680402317076\n",
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