napari-yapic-prediction

napari widget that performs image segmentation with yapic model in the napari window. Install TENSORFLOW to use this plugin.


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A napari widget plugin to perform YAPiC model segmentation prediction in the napari window.


This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Description

This napari plugin provides a widget to upload a YAPiC trained model and perform segmentation over all the present images in the napari window. The segmentation results are uploaded as napari layers into the viewer automatically with the name structure of imgename_prediction.

Installation

  1. Please install either GPU or CPU version of tensorflow that is compatible with your cuda and cudnn libraries before installing the plugin depending on your system. One of the plugin dependency is yapic that currently has sensitivity to tensorflow versions.

  2. You can install napari-yapic-prediction via pip:

    pip install napari-yapic-prediction

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 GNU GPL v3.0 license, "napari-yapic-prediction" is free and open source software

Issues

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

Version:

  • 0.2.0

Release date:

  • 04 February 2022

First released:

  • 19 April 2021

License:

  • GPL-3.0

Supported data:

  • Information not submitted

GitHub activity:

  • Stars: 0
  • Forks: 3
  • Issues + PRs: 1

Python versions supported:

Operating system:

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • numpy
  • napari[all]
  • yapic
  • scikit-image

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