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"
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Install Anaconda
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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
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Test installation by running "Test.ipynb" JupyterLab Notebook
- 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