napari-magic-wand 0.0.2

Livewire-based annotation of objects.

🪄 napari-magic-wand

Object annotation in Napari using a magic wand (shortest path algorithm). This plugin is based on the PyIFT library. This tool 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 solid objects via their contour.

Please also take a look at the grabber-ift plugin, which offers similar functionality but slightly different user interactions.

Installation

You can install napari-magic-wand via pip:

pip install napari-magic-wand

Usage

• Select the plugin from the Plugins menu of Napari.
• Open an image to annotate (2D, 2D+t, or 3D).
• Click on the button "Start live wire" or press S. A new Labels layer Live wire (current edit) should appear.
• With the Live wire layer selected, click on the image to annotate the contour of an object.
• Double-click to confirm the annotation path.

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.

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.

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