ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing

TL;DR

The paper introduces ORMIR_XCT, an open-source Python package designed to enhance HR-pQCT image processing by enabling advanced, flexible workflows outside the proprietary scanner software environment.

Contribution

It reimplements existing IPL workflows in Python, providing a reproducible, extendable tool for high-resolution bone imaging analysis.

Findings

Improved flexibility in HR-pQCT image processing workflows.

Open-source Python package facilitates advanced analysis.

Enhances reproducibility of bone imaging studies.

Abstract

High resolution peripheral quantitative computed tomography (HR-pQCT) is an imaging technique capable of imaging trabecular bone in-vivo. HR-pQCT has a wide range of applications, primarily focused on bone to improve our understanding of musculoskeletal diseases, assess epidemiological associations, and evaluate the effects of pharmaceutical interventions. Processing HR-pQCT images has largely been supported using the scanner manufacturer scripting language (Image Processing Language, IPL, Scanco Medical). However, by expanding image processing workflows outside of the scanner manufacturer software environment, users have the flexibility to apply more advanced mathematical techniques and leverage modern software packages to improve image processing. The ORMIR_XCT Python package was developed to reimplement some existing IPL workflows and provide an open and reproducible package allowing for the development of advanced HR-pQCT data processing workflows.