Quick Start

Input Format

• HE-stained skeletal muscle biopsy whole slide images
• Supported formats: SVS, NDPI, TIFF, or other common WSI formats

Usage

# Analyze a single slide
python myopath_analyze.py \
    --input slide.svs \
    --output results/

Output

The analysis generates:

• Fat infiltration ratio — percentage of adipose tissue area
• Fibrosis ratio — percentage of fibrotic tissue area
• Fiber statistics — mean diameter, cross-sectional area, coefficient of variation
• Segmentation mask — color-coded overlay of detected tissue types
• Summary report — CSV with all quantitative metrics