Object annotation in Napari using magic wands (shortest path algorithms). This plugin supports annotation in 2D (grayscale and RGB), 2D+t (grayscale, frame by frame) and 3D images (slice by slice). It can be used to annotate paths or the contour of solid objects.
The plugin provides two annotation functions:
- The Magic wand tool is based on the PyIFT library. Use it to trace annotations that follow the intensity gradients in the image.
- The Brightest path tool is based on the Brightest Path Lib library. Use it to trace annotations that follow the brightest (or darkest) path between two points.
Related plugins
Take a look at these related plugins that offer similar functionality and slightly different user interactions.
- grabber-ift which is based on pyift.
- napari-tracing which is based on brightest-path-lib.
You can install napari-magic-wand
via pip:
pip install napari-magic-wand
- Select the tool of your choice from the
Plugins
menu of Napari. - Open an image to annotate (2D, 2D+t, or 3D).
- Click on the button "Start live wire". A new
Labels
layer Live wire (current edit) should appear. - Click on the image to annotate paths interactively.
- Double-click to confirm an annotation and move to the next.
Options and parameters
- Close and fill objects: You can fill (or not) the inside of the annotated object. Do not tick this option if you are annotating paths (e.g. filament-like strucutres).
- Auto-increment label index: Tick this option to increment the label index every time a new object is completed (e.g. if you are annotating multiple objects).
- Sigma: Higher values of sigma increase the "stickiness" of the object boundaries to the magic wand.
- Black ridges: Tick this checkbox if you are annotating dark paths on a bright background.
Contributions are very welcome. Please get in touch if you'd like to be involved in improving or extending the package.
Distributed under the terms of the BSD-3 license, "napari-magic-wand" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
This tool is being developed by the EPFL Center for Imaging as part of a collaborative project with the Laboratory of Hydraulic Constructions.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.