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napari filaments

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.

  • In the "Spline" tab, you can cut/extend or re-fit splines.
  • In the "Measure" tab, click "measure property" to measure mean instensity etc along each spline.

How it works

Spline fitting is done as following.


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:

  • 0.3.0

Last updated:

  • 04 June 2023

First released:

  • 01 July 2022

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 9
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • magic-class (>=0.7.3)
  • magicgui
  • matplotlib
  • numpy
  • qtpy
  • scipy

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