No project description provided
Project description
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}
}
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
rpegment-1.0.2.tar.gz
(10.2 kB
view details)
Built Distribution
rpegment-1.0.2-py3-none-any.whl
(12.9 kB
view details)
File details
Details for the file rpegment-1.0.2.tar.gz
.
File metadata
- Download URL: rpegment-1.0.2.tar.gz
- Upload date:
- Size: 10.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.8.4 CPython/3.13.0 Windows/10
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 70677aa30e1d68785ab709e2550f0335202a97656585fcab91820d35391633ba |
|
MD5 | a2a4d0f662ad6239d32bfd245dfbc78a |
|
BLAKE2b-256 | d21c8f667850e9fdeba0a31b29112638f6917b1dad6e73295e2e9add9fe4252d |
File details
Details for the file rpegment-1.0.2-py3-none-any.whl
.
File metadata
- Download URL: rpegment-1.0.2-py3-none-any.whl
- Upload date:
- Size: 12.9 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.8.4 CPython/3.13.0 Windows/10
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 774b03a60f1c129bb42ca5736447b5188498b59df9c95f6a71c3ba78f79c77c7 |
|
MD5 | e1544fe41dce2f5cdbf360dbd9b284e5 |
|
BLAKE2b-256 | 1735df1b366de70b4816c91979b269d3cdc6a54cc371d9d9faa7821d9b36ece1 |