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Expand Up @@ -16,12 +16,12 @@

## Installation

💻 See the [Installation page] in the documentation for detailed instructions.
💻 See the [Installation page](https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html) in the documentation for detailed instructions.

## Documentation

📚 A lot of documentation is available at https://AdaptiveMotorControlLab.github.io/CellSeg3D

📚 A lot of documentation is available at [https://AdaptiveMotorControlLab.github.io/CellSeg3D
](https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html)
You can also generate docs by running ``make html`` in the docs/ folder.

## Quick Start
Expand All @@ -39,15 +39,15 @@ Then go into Plugins > napari-cellseg3d, and choose which tool to use.

## News

**New version : v0.2.0**
**New version: v0.2.0**

- Changed project name to "napari_cellseg3d" to avoid setuptools deprecation
- Small API changes for training/inference from a script
- Some fixes to WandB integration ad csv saving after training

Previous additions :
Previous additions:

- v0.1.2 :Fixed manifest issue for PyPi
- v0.1.2: Fixed manifest issue for PyPi
- Improved training interface
- Unsupervised model : WNet3D
- Generate labels directly from raw data!
Expand Down Expand Up @@ -158,6 +158,21 @@ Distributed under the terms of the [MIT] license.
[MONAI's optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies
[MONAI]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies

## Citation

```
@article {Achard2024,
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.},
title = {CellSeg3D: self-supervised 3D cell segmentation for microscopy},
elocation-id = {2024.05.17.594691},
year = {2024},
doi = {10.1101/2024.05.17.594691},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2024/05/17/2024.05.17.594691},
eprint = {https://www.biorxiv.org/content/early/2024/05/17/2024.05.17.594691.full.pdf},
journal = {bioRxiv}
}
```
## Acknowledgements

This plugin was developed by originally Cyril Achard, Maxime Vidal, Mackenzie Mathis.
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