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FEXHIP-Histology

Repository used for the histology part of the FEXHIP project abbreviated FEXHIS Linked to the article "Automatic Segmentation of Cortical Bone Microstructure: Application and Analysis of Three Proximal Femur Sites"

Starting

  • Install Anaconda

  • Create virtual environment with conda env create -f filename.yml. "filename.yml" is "Linux_Requirements.yml" if working on a linux station or "WSL_Requirements.yml" if working with Windows subsystem for linux.

  • Activate the virtual environment with conda activate FEXHIS

  • Test installation by running "Test.ipynb" JupyterLab Notebook

Overview

  • Step 0: Draw lines to define quadrants (inferior, superior, anterior, and posterior) based on uCT scans and slice geometry
  • Step 1: Design a model to perform automatic segmentation based on manual segmentations performed by multiple operators
  • Step 2: Select regions of interest (ROIs) to perform automatic segmentation
  • Step 3: Segment selected ROIs
  • Step 4: Analysis of segmentation results (Extract data)
  • Step 5: Perform statistics