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A lightweight plugin extending label layer control

Project description

napari-annotator

License PyPI Python Version tests codecov napari hub

A lightweight plugin extending label layer control.


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

Description

This lightweight plugin helps you navigate your labels layer. It is intended to ease your manual annotation work. Overview image

  • Select a label from the list.
  • Toggle the visibility of individual label entries.
  • Move to the centroid of a label at the current zoom.
  • Change the color of individual labels.
  • Erase all drawn pixels of a given label.

Usage

Start the plugin Plugins > napari-annotator: Annotator.

The plugin will list available labels once a labels layer is selected and labels drawn.

Color shuffling for labels will not work, since the plugin sets the color mode of the layer to direct. But you can always change the color of individual labels, using the color picker.

Known limitations

  1. Lag when drawing (probably related to this issue).
  2. Erasing a label is not un-doable.
  3. Locating / moving to the center of a label only works on 2D/3D label layers, i.e.:
    1. single- / multi-channel 2D label layers.
    2. single-channel 3D label layers (the third dimension being either Z or T).
  4. Maximum 255 labels supported. Increasing number of supported label is possible, but when increasing it, colors in the canvas will mismatch the layer control and plugin entries (probably related to this issue)

Note to self:

I am using a private object/methods for accessing napari icons (i.e. _icons.get_icon_path('picker')). This is not amethod directly directly from the viewer or layer, but is it still OK?

Installation

Not yet available via pip. Only from source.

To install latest development version :

pip install git+https://github.com/loicsauteur/napari-annotator.git

Contributing

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.

License

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

Issues

If you encounter any problems, please file an issue along with a detailed description. Or open a thread on forum.image.sc with a detailed description and a @loicsauteur tag.

Project details


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