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cellseg_sribd_napari
A napari plugin for Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images - an anatomical segmentation tool for multi-modal cell images
This napari plugin was generated with Cookiecutter using [@napari]'s cookiecutter-napari-plugin template. Most of the UI design is following the codes of cellpose-napari.
<!-- Don't miss the full getting started guide to set up your new package: https://github.com/napari/cookiecutter-napari-plugin#getting-started and review the napari docs for plugin developers: https://napari.org/stable/plugins/index.html -->Installation
You can install cellseg-sribd via following commands:
conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env
pip install "napari[all]"
cd cellseg_sribd_napari
pip install -r requirements.txt
pip install -e .
Running the software
napari -w cellseg-sribd
There is sample data in the [imgs], or get started with your own images!
Source codes and training
The source codes of cellseg-sribd model and the training process are in cellseg-sribd.
License
Distributed under the terms of the BSD-3 license,"cellseg-sribd" is free and open source software
Dependencies
cellseg-sribd relies on the following excellent packages (which are automatically installed with conda/pip if missing):
Issues
If you encounter any problems, please [file an issue] along with a detailed description.
Citation
If any part of this code is used, please acknowledge it appropriately and cite the paper:
@misc{
lou2022multistream,
title={Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images},
author={WEI LOU and Xinyi Yu and Chenyu Liu and Xiang Wan and Guanbin Li and Siqi Liu and Haofeng Li},
year={2022},
url={https://openreview.net/forum?id=G24BybwKe9}
}