Home - CellSeg3D figures

Welcome to the CellSeg3D figures book

This book contains the code to generate the figures used in the publication of CellSeg3D.

Should you encounter any issues with the code, data, etc, please open an issue on this repository or the main repository.

@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}
}

Data

Annotated dataset

Please find the dataset online at Zenodo

Figures data

The data for the figures is hosted on the following Drive : LINK TO DATA

The data (RESULTS folder) should then be placed on your desktop, in a folder called CELLSEG_BENCHMARK.

This repository also contains various scripts for training and finding model hyperparameters. Please contact us if you need more details regarding the data or the scripts.

Available figures’ code

Figures

• Figure 1.b - Supervised model performance
• Figure 1.f/g : Training efficiency
• Figure 1.h - Retraining of a supervised 3D model with unsupervised labels
• Figure 2.b-c : Showing qualitative WNet3D performance on additional datasets
• Supp. Figure 2 - Examples of WNet3D losses, and output during training

Other figures

Other figures were made using napari, PowerPoint, and other software. They are not included in this book. The data used for the screenshots may be shared upon request.

• Figure 1 :

  • Fig 1a : napari screenshots

  • Fig 1c : napari screenshots

  • Fig 1d : Custom model schema made in PowerPoint and edited in Figma

  • Fig 1e : napari screenshots

• Figure 2:

  • Fig 2a : napari screenshots & PowerPoint schema

  • Fig 2c : napari screenshots

  • Fig 2d : napari screenshots

• Supplemental Figure 2:

  • Fig S2a : napari screenshots taken during training with the cellseg3d plugin