Welcome to Sketchpose’s documentation!

Sketchpose is a Napari plugin developed in Python, dedicated to cells and bacteria segmentation.

The CNN is based on Cellpose architecture, but works for very sparse annotations. Its main advantage is that it allows frugal annotation, in the sense that you can annotate only pieces of cells and backgrounds, as well as their borders.

Our method can be primarily used in two ways: either through the Napari plugin, or directly via command line if you already have your dataset partially or completely annotated. The advantage of the plugin is that it allows for interactive work, which means you can observe the progress of training and add annotations on the fly.

You can learn more about our method reading the related paper.

First check out the Installation section to know how to install it.

If you use this plugin, please cite the paper:

Clément Cazorla, Nathanaël Munier, Renaud Morin, Pierre Weiss. Sketchpose: Learning to Segment Cells with Partial Annotations. 2023. ffhal-04330824f

@unpublished{cazorla:hal-04330824,
  TITLE = {{Sketchpose: Learning to Segment Cells with Partial Annotations}},
  AUTHOR = {Cazorla, Cl{\'e}ment and Munier, Nathana{\"e}l and Morin, Renaud and Weiss, Pierre},
  URL = {https://hal.science/hal-04330824},
  NOTE = {working paper or preprint},
  YEAR = {2023},
  MONTH = Dec,
  KEYWORDS = {Cellpose -Segmentation -Frugal learning -Napari -Deep learning -Distance map},
  PDF = {https://hal.science/hal-04330824/file/sketchpose_hal.pdf},
  HAL_ID = {hal-04330824},
  HAL_VERSION = {v1},
}

Note

This project is still under active development. We welcome any suggestions for improvement from users.: Thank you

Welcome to Sketchpose’s documentation!

Contents