napari-vemseg

napari-vemseg

A simple plugin for semi-automated segmentation of volume electron microscopy images.

License BSD-3 PyPI Python Version tests codecov napari hub

A simple plugin to do semi-automated segmentation within napari using vemseg built on XGBoost.

Installation

conda Installation and Environment Creation

To start with a conda environment must be created.

conda create -n vemseg-env python=3.8
conda activate vemseg-env

napari Instillation

We must then install napari:

pip install "napari[all]"

napari-vemseg Instillation

You can finally install napari-vemseg via pip:

conda install pyopencl
pip install napari-vemseg

Usage

Train VEMClassifier

Predict Using Pretrained VEMClassifier

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-vemseg" is free and open source software

Issues

If you encounter any problems, please [file an issue] along with a detailed description.

Version:

  • 0.0.9

Last updated:

  • 15 March 2023

First released:

  • 14 March 2023

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 0
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • Information not submitted

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