napari-tree-rings 0.1.3

A tool to delineate bark, pith and xylem annual rings and to measure their area and thickness on circular sections of tree trunks.

napari-tree-rings

A tool to delineate bark, pith and xylem annual rings and to measure their property parameters on circular sections of tree trunks.

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

How to use it?

Users can export the segmentation findings and estimate bark, ring borders, and pith with ease using the Napari Tree Rings plugin:

• Run button on the Segment Trunk tag: find the outermost bark just on image
• Run button on the Segment Rings tag: find the pith and annual rings just one image.
• Run Batch button on the Batch Segment Trunk tag: runs all the images in the folder.

Users can also modify certain parameters, including the batch size or the expected ring thickness (in pixels). The interface's goal is to assist biologists without having programming expertise by being user-friendly.

If accessible, the unit of micrometres will be used to determine the parameters; if not, pixels will be used. The calculated parameters are made up of:

• bbox: The bounding box's minimum and maximum coordinates on the horizontal and vertical axes make up the calculated parameters.
• area: region's area.
• area_convex: area, which is the smallest convex polygon enclosing the region, of the convex hull image.
• axis_major_length: length of the ring borders' main axis
• axis_minor_length: length of the ring borders' minor axis
• eccentricity: The eccentricity, which ranges from 0 to 1, is the focal distance divided by the major axis length. When the maximum Feret's diameter, which is the largest distance between points across the convex hull, is zero, the region becomes a circle.
• orientation: angle, measured in radians and ranging from $-pi/2$ to $pi/2$ anticlockwise, between the main axis and the vertical axis.
• area_growth: the area between the two ring boundaries that experiences growth over the course of a year.

Installation

You can install napari-tree-rings via pip:

pip install napari-tree-rings

Adding other measurements

If you would like to add other measurements while running batch, you can modify BatchSegmentTrunk.run in the src/napari_tree_rings/image/process.py. There is an example of area_growth for you to see and refer to.

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 MIT license, "napari-tree-rings" is free and open source software

Issues

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