Bone Microarchitecture

Lightweight microarchitecture measurements from binary masks and optional calibrated grayscale arrays.

This package intentionally has no Slicer dependency and no image I/O dependency. Callers are responsible for loading images, calibration, and putting masks on a common grid.

GPU Backends

Exact Hildebrand sphere fitting supports three diameter-accumulation backends:

  • cpu: NumPy/SciPy fallback.
  • mps: native Apple Metal backend for macOS.
  • opencl: OpenCL backend for Windows/Linux systems with pyopencl and a working GPU OpenCL runtime.

Use thickness_backend="auto" to select Metal on macOS when available, OpenCL on Windows/Linux when available, and CPU otherwise.

Optional installs:

pip install "bone-microarchitecture[mps]"
pip install "bone-microarchitecture[opencl]"
pip install "bone-microarchitecture[gpu]"

Parameter Definitions

  • Tb.BMD: mean calibrated grayscale value inside the trabecular compartment.
  • Tb.BV/TV: trabecular bone volume divided by trabecular total volume.
  • Tb.Th: maximal-sphere local thickness of trabecular bone.
  • Tb.Sp: maximal-sphere local thickness of non-bone space in the trabecular compartment.
  • Tb.N: inverse ridge-to-ridge spacing estimate in the trabecular compartment.
  • Tb.1/N.SD: standard deviation of ridge-to-ridge spacing.
  • Tb.BV: trabecular bone volume.
  • Tb.TV: trabecular compartment volume.
  • Ct.BMD: mean calibrated grayscale value inside the cortical compartment.
  • Ct.Th: maximal-sphere local thickness of cortical bone.
  • Ct.Po: cortical pore volume divided by cortical total volume.
  • Ct.Po.V: cortical pore volume.
  • Ct.Po.Dm: maximal-sphere local diameter of cortical pore space.
  • Ct.BV: cortical bone volume.
  • Ct.TV: cortical compartment volume.

Project links

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Newer release available (0.2.1)

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Credits

Author: Matthias Walle

GitHub Statistics

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MIT
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Requires

Python >=3.10

Provides Extra

test dev mps opencl gpu

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