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.

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 Rings tag: find the rings in 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. 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.

• perimeter: perimeter of the region, measured as the length of the contour.

• area: Region’s area.

• area_convex: Area of the convex hull image, which is the smallest convex polygon enclosing the region.

• axis_major_length: Length of the ring boundaries’ major axis.

• axis_minor_length: Length of the ring boundaries’ minor axis.

• eccentricity: The eccentricity, which ranges from 0 to 1, is the focal distance divided by the major axis length. When the eccentricity is zero, the region becomes a circle.

• feret_diameter_max: The maximum Feret's diameter, which is the largest distance between points across the convex hull.

• orientation: Angle between the major axis and the vertical axis, measured in radians and ranging from -pi/2 to pi/2 anticlockwise.

• area_growth: The area between the two ring boundaries that experiences growth over a year (except the cases of pith and bark).

• For more details, check the detailed documentation.

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.