🪄 napari-magic-wand

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.

Installation

You can install napari-magic-wand via pip:

pip install napari-magic-wand

Usage

• 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.

Contributing

Contributions are very welcome. Please get in touch if you'd like to be involved in improving or extending the package.

License

Distributed under the terms of the BSD-3 license, "napari-magic-wand" is free and open source software

Issues

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

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