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

Project description


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.


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


Train VEMClassifier

Predict Using Pretrained VEMClassifier


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.


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


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

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napari-vemseg-0.0.9.tar.gz (33.2 kB view hashes)

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