napari-deepfinder

A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.

    Workflow step:
    Visualization
    Image annotation
    Image Segmentation
    Image SegmentationModel-based segmentation
    Clustering
    Image modality:
    Electron microscopyCryo electron microscopyElectron cryotomography
    Electron microscopyTransmission electron microscopyElectron tomographyElectron cryotomography

View project data

License GNU GPL v3.0 PyPI Python Version tests codecov napari hub

A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.

The documentation for users is available here.


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

Installation

You can install napari-deepfinder via pip:

pip install napari-deepfinder

To install latest development version :

pip install git+https://github.com/deep-finder/napari-deepfinder.git

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-deepfinder" is free and open source software

Issues

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

Version:

  • 0.0.1

Release date:

  • 25 July 2022

First released:

  • 25 July 2022

License:

  • GPL-3.0

Supported data:

GitHub activity:

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

Python versions supported:

Operating system:

Requirements:

  • em-deepfinder
  • numpy
  • magicgui
  • qtpy
  • napari
  • scikit-image
  • typing
  • pandas
  • lxml
  • pillow
  • h5py
  • mrcfile
  • scipy

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