napari-3d-label-eraser

A simple tool to erase a selected label across an entire 3D volume in napari.

Overview

napari-3d-label-eraser provides a fast and convenient way to remove all voxels belonging to a given label in a 3D Labels layer.
This is useful for cleaning segmentation results, removing misdetected objects, or performing manual corrections in volumetric datasets.

The plugin adds a dock widget featuring:

• a dropdown menu to select the target Labels layer,
• a button to erase the currently selected label across the entire 3D volume,
• optional usage instructions.

A keyboard shortcut (A) can also be used to trigger the erase operation directly from the viewer.

Features

• Erase all voxels of the selected label throughout a 3D volume.
• Dropdown to choose the active Labels layer.
• Compatible with napari’s label picker (L key).
• Optional keyboard shortcut (A) for quick editing.
• Minimal, lightweight, and easy to integrate into existing workflows.

Installation

Install with pip:

pip install napari-3d-label-eraser

Or install from the napari plugin manager:

Plugins → Install/Uninstall Plugins

For development installation:

git clone https://github.com/koopa31/napari-3d-label-eraser.git
cd napari-3d-label-eraser
pip install -e .

Usage

1. Load a Labels layer in napari.
2. Open the plugin:
   Plugins → 3D Label Eraser → 3D Label Eraser
3. In the widget:
   • Select your target Labels layer.
   • Choose the label to erase using the label picker (L key).
   • Click the button to erase that label across the full 3D volume.
4. Alternatively, press A to erase the current label directly from the viewer (focus must be on the viewer).

Notes

• The plugin operates only on Labels layers.
• The erase action sets all voxels with the selected label to 0.
• The A shortcut is registered automatically when the widget is opened.

Contributing

Issues, feature requests, and pull requests are welcome.

License

This project is released under the MIT License.