A napari plugin for filament analysis
A napari plugin for filament analysis.
This plugin helps you to manually track filaments using path shapes of
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.
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.
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
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-filaments" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
- 04 June 2023
- 01 July 2022
- Information not submitted
- Stars: 9
- Forks: 1
- Issues + PRs: 0