Phenotastic

3D plant phenotyping package for segmentation of early flower organs (primordia) from shoot apical meristems in 3D images.

PyPI version Build Status

Features

  • 3D Image Contouring: Morphological active contour methods for extracting surfaces from 3D image stacks

  • Mesh Processing: Smoothing, remeshing, and repair operations for 3D meshes

  • Domain Segmentation: Curvature-based segmentation of meshes into regions (domains)

  • Pipeline System: Configurable recipe-style pipelines for reproducible workflows

Quick Example

from phenotastic import PhenoMesh, load_preset
import pyvista as pv

# Load a mesh
mesh = PhenoMesh(pv.read("my_mesh.vtk"))

# Process with the default pipeline
pipeline = load_preset()
result = pipeline.run(mesh)

# Access results
print(f"Found {len(result.domains.unique())} domains")

Documentation

Getting Started

User Guide

API Reference

Citation

If you use Phenotastic in your research, please cite:

Åhl, H., Zhang, Y., & Jönsson, H. (2022). High-throughput 3D phenotyping of plant shoot apical meristems from tissue-resolution data. Frontiers in Plant Science, 13, 827147.

BibTeX:

@article{aahl2022high,
  title={High-throughput 3d phenotyping of plant shoot apical meristems from tissue-resolution data},
  author={{\AA}hl, Henrik and Zhang, Yi and J{\"o}nsson, Henrik},
  journal={Frontiers in Plant Science},
  volume={13},
  pages={827147},
  year={2022},
  publisher={Frontiers Media SA}
}

Indices and tables