pykarambola: Minkowski tensor morphometry of 3D structures

Three-dimensional biological morphologies encode functional and physiological state, yet their directional, orientational, and topological properties are rarely captured by morphometric tools in bioimage analysis. Minkowski tensors encode surface curvature and directionality for arbitrary topologies; their eigensystems directly quantify elongation axes and anisotropy. A C++ implementation, karambola, computes Minkowski tensors for triangulated surfaces but is inaccessible within Python-based bioimage workflows.

We present pykarambola, a Python package that accepts NumPy arrays and standard mesh formats and returns Minkowski tensors, including derived anisotropy and orientation quantities. A high-level label-image interface converts 3D integer arrays into per-object Minkowski tensors in a single call, making pykarambola directly compatible with the output of segmentation tools. An optional Cython extension accelerates graph-traversal steps of mesh initialization for large-scale analyses. Validated on synthetic meshes spanning three topologies and benchmarked on 1584 adrenal gland meshes, pykarambola reproduces all 121 karambola features to near-floating-point agreement and is 2.8-fold faster, with speedups primarily attributable to per-object file input/output.

pykarambola is distributed under the BSD 3-Clause License and is available on GitHub at https://github.com/Ishihara-SynthMorph/pykarambola. It can be installed via pip.