rpegment

rpegment is a package designed to segment RPE (Retinal Pigment Epithelium) confocal images using Cellpose 3 and to interactively clean the segmentation information.

Features

• Segmentation: Utilizes Cellpose 3.0 [1] for accurate segmentation of RPE confocal images.
• Interactive Cleaning: Provides tools for interactive cleaning and refinement of segmentation results.
• Morphology Metrics: Visually shows a handful of metrics taken from [2], ready to download as csv.

Installation

To install rpegment, you can use the following command:

pip install rpegment

Usage

Here's a basic example of how to use rpegment:

from rpegment import app

app.run(debug=True, port=8001)

References

@article{stringer2024cellpose3,
title={Cellpose3: one-click image restoration for improved cellular segmentation},
author={Stringer, Carsen and Pachitariu, Marius},
journal={bioRxiv},
pages={2024--02},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@article{ortolan2022single,
title={Single-cell--resolution map of human retinal pigment epithelium helps discover subpopulations with differential disease sensitivity},
author={Ortolan, Davide and Sharma, Ruchi and Volkov, Andrei and Maminishkis, Arvydas and Hotaling, Nathan A and Huryn, Laryssa A and Cukras, Catherine and Di Marco, Stefano and Bisti, Silvia and Bharti, Kapil},
journal={Proceedings of the National Academy of Sciences},
volume={119},
number={19},
pages={e2117553119},
year={2022},
publisher={National Acad Sciences}
}