napari-filaments

A napari plugin for filament analysis


    License BSD-3 PyPI Python Version tests codecov napari hub

    A napari plugin for filament analysis.

    This plugin helps you to manually track filaments using path shapes of Shapes layer.

    Currently implemented functions

    • Fit paths to filaments in an image as a 2-D spline curve.
    • Clip/extend paths.
    • Measurement of filament length at sub-pixel precision.
    • Basic quantification (mean, std, etc.) along paths.
    • Import paths from ImageJ ROI file.

    Basic Usage

    Click Layers > open image to open a tif file. You'll find the image you chose and a shapes layer are added to the layer list.

    • The "target filaments" box shows the working shapes layer.
    • The "target image" box shows the image layer on which fitting and quantification will be conducted.
    • The "filament" box shows currently selected shape (initially this box is empty).

    Add path shapes and push key F1 to fit the shape to the filament in the target image layer.


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

    Installation

    You can install napari-filaments via pip:

    pip install napari-filaments

    To install latest development version :

    pip install git+https://github.com/hanjinliu/napari-filaments.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 BSD-3 license, "napari-filaments" is free and open source software

    Issues

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

    Version:

    • 0.2.1

    Release date:

    • 16 July 2022

    First released:

    • 01 July 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

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

    Python versions supported:

    Operating system:

    Requirements:

    • magic-class (>=0.6.7)
    • magicgui
    • matplotlib
    • numpy
    • qtpy
    • scipy

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