napari-swc-editor

Use point and shape layer to edit swc format in napari.

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This napari plugin was generated with copier using the napari-plugin-template.

Features

Peek.2024-12-03.16-43.mp4

IO

READER

• Your .swc should follow the following specs: http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
• the reader will create 2 napari layer: point_layer and shape_layer. Only point_layer is interactive, shape_layer is used to render path between swc points.
• The raw swc can be accessed in the point layer metadata. Such as point_layer.metadata["raw_swc"]
• A pd.DataFrame object is also saved in the metadata: point_layer.metadata["swc_data"]

WRITER

• With the point_layer selected, you can use napari interface to save with .swc extension name.
• You can also do it in command line: napari.save_layers('test.swc', [point_layer])

Napari Interface

Structure ID and point symbol

In swc, structure id allow to label the type of neuron structure the point belongs to. In this plugin by default, the points will follow this symbol mapping:

SWC_SYMBOL = {
    0: "clobber",  # undefined
    1: "star",  # soma
    2: "disc",  # axon
    3: "triangle_down",  # basal dendrite
    4: "triangle_up",  # apical dendrite
}

You can also visualize the swc data in a table using the widget under Plugin > SWC Editor Widget

When using the "Show swc table" you will have an interactive table widget:

• left-click on table: highlight + center on the corresponding point
• double-left-click on table: highlight + center on the correspongind point + zoom
• selection on the point layer: highlight the corresponding row on the table

SWC Edition

ALL INTERACTIONS ARE ONLY BOUND TO THE point_layer THERE IS NO CTRL-Z (please save your progress)

• Add point: You can edit the "r" and the "structure_id" using the point_size and symbol
• Remove point: (Select the point and press 1 or suppr or delete) All the link pointing to this point will be removed
• Add edge: Select 2 or more point(s) and press on your keyboard l (aka: link).
• Remove edge: Select 1 or more point(s) and press on your keyboard u (aka: unlink).

If you want to link point as you are adding them you have two solutions:

• press "CTRL" while you add points, this will create a link with the previously selected point
• use the Plugin > SWC Editor Widget Checkbox ("link previous node with new node (same as using CTRL+Click)"): when selected, all new points will be selected with the previously selected point

Peek.2025-01-05.01-53.mp4

Installation

You can install napari-swc-editor via pip:

pip install napari-swc-editor

To install latest development version :

pip install git+https://github.com/LaboratoryOpticsBiosciences/napari-swc-editor.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-swc-editor" is free and open source software

Issues

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