A New Automated Histomorphometric MATLAB Algorithm for Immunohistochemistry Analysis Using Whole Slide Imaging

Tissue Eng Part C Methods. 2020 Sep;26(9):462-474. doi: 10.1089/ten.TEC.2020.0153.


The use of animal models along with the employment of advanced and sophisticated stereological methods for assessing bone quality combined with the use of statistical methods to evaluate the effectiveness of bone therapies has made it possible to investigate the pathways that regulate bone responses to medical devices. Image analysis of histomorphometric measurements remains a time-consuming task, as the image analysis software currently available does not allow for automated image segmentation. Such a feature is usually obtained by machine learning and with software platforms that provide image-processing tools such as MATLAB. In this study, we introduce a new MATLAB algorithm to quantify immunohistochemically stained critical-sized bone defect samples and compare the results with the commonly available Aperio Image Scope Positive Pixel Count (PPC) algorithm. Bland and Altman analysis and Pearson correlation showed that the measurements acquired with the new MATLAB algorithm were in excellent agreement with the measurements obtained with the Aperio PPC algorithm, and no significant differences were found within the histomorphometric measurements. The ability to segment whole slide images, as well as defining the size and the number of regions of interest to be quantified, makes this MATLAB algorithm a potential histomorphometric tool for obtaining more objective, precise, and reproducible quantitative assessments of entire critical-sized bone defect image data sets in an efficient and manageable workflow.

Keywords: MATLAB algorithm; critical-sized bone defect; histomorphometry; whole slide imaging.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Automation
  • Bone and Bones / physiology
  • Collagen Type I / metabolism
  • Humans
  • Image Processing, Computer-Assisted*
  • Immunohistochemistry
  • Sheep
  • Tissue Engineering


  • Collagen Type I