Fitting-free algorithm for efficient quantification of collagen fiber alignment in SHG imaging applications

Gunnsteinn Hall, Wenxuan Liang, Xingde Li

Research output: Contribution to journalArticlepeer-review


Collagen fiber alignment derived from second harmonic generation (SHG) microscopy images can be important for disease diagnostics. Image processing algorithms are needed to robustly quantify the alignment in images with high sensitivity and reliability. Fourier transform (FT) magnitude, 2D power spectrum, and image autocorrelation have previously been used to extract fiber information from images by assuming a certain mathematical model (e.g. Gaussian distribution of the fiber-related parameters) and fitting. The fitting process is slow and fails to converge when the data is not Gaussian. Herein we present an efficient constant-time deterministic algorithm which characterizes the symmetricity of the FT magnitude image in terms of a single parameter, named the fiber alignment anisotropy R ranging from 0 (randomized fibers) to 1 (perfect alignment). This represents an important improvement of the technology and may bring us one step closer to utilizing the technology for various applications in real time. In addition, we present a digital image phantom-based framework for characterizing and validating the algorithm, as well as assessing the robustness of the algorithm against different perturbations.

Original languageEnglish (US)
Article number#305215
Pages (from-to)4609-4620
Number of pages12
JournalBiomedical Optics Express
Issue number10
StatePublished - Oct 1 2017


  • (100.2960) imaging analysis
  • (180.4315) nonlinear microscopy
  • (180.6900) three-dimensional microscopy

ASJC Scopus subject areas

  • Biotechnology
  • Atomic and Molecular Physics, and Optics


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