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README.md

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## Installation
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💻 See the [Installation page] in the documentation for detailed instructions.
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💻 See the [Installation page](https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html) in the documentation for detailed instructions.
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## Documentation
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📚 A lot of documentation is available at https://AdaptiveMotorControlLab.github.io/CellSeg3D
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📚 A lot of documentation is available at [https://AdaptiveMotorControlLab.github.io/CellSeg3D
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](https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html)
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You can also generate docs by running ``make html`` in the docs/ folder.
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## Quick Start
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## News
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**New version : v0.2.0**
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**New version: v0.2.0**
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- Changed project name to "napari_cellseg3d" to avoid setuptools deprecation
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- Small API changes for training/inference from a script
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- Some fixes to WandB integration ad csv saving after training
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Previous additions :
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Previous additions:
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- v0.1.2 :Fixed manifest issue for PyPi
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- v0.1.2: Fixed manifest issue for PyPi
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- Improved training interface
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- Unsupervised model : WNet3D
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- Generate labels directly from raw data!
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[MONAI's optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies
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[MONAI]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies
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## Citation
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```
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@article {Achard2024,
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author = {Achard, Cyril and Kousi, Timokleia and Frey, Markus and Vidal, Maxime and Paychere, Yves and Hofmann, Colin and Iqbal, Asim and Hausmann, Sebastien B. and Pages, Stephane and Mathis, Mackenzie W.},
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title = {CellSeg3D: self-supervised 3D cell segmentation for microscopy},
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elocation-id = {2024.05.17.594691},
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year = {2024},
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doi = {10.1101/2024.05.17.594691},
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publisher = {Cold Spring Harbor Laboratory},
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URL = {https://www.biorxiv.org/content/early/2024/05/17/2024.05.17.594691},
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eprint = {https://www.biorxiv.org/content/early/2024/05/17/2024.05.17.594691.full.pdf},
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journal = {bioRxiv}
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}
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```
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## Acknowledgements
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This plugin was developed by originally Cyril Achard, Maxime Vidal, Mackenzie Mathis.

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