Origami

Origami analyzes three-dimensional epithelial morphogenesis by quantifying direction-variant cell shape features along the apico-basal axis from fluorescence microscopy images.

Key Features:

• MATLAB implementation: Implemented as a MATLAB-based image analysis pipeline for processing microscopy datasets.
• Direction-variant cell shape analysis: Computes cell shape features that vary along the apico-basal axis to quantify cellular deformation and alignment.
• Automated axis detection: Automatically identifies apico-basal direction vectors, including in regions with opposing epithelial curvatures.
• Fluorescence microscopy compatibility: Processes fluorescence microscopy images of curved epithelia to extract quantitative cell-shape metrics.
• Integration with biomechanical modeling: Combines image-derived measurements with biomechanical modeling to analyze morphogenetic processes.

Scientific Applications:

• Morphogenesis analysis: Quantifies epithelial sheet folding and deformation during developmental morphogenesis.
• Zebrafish embryo studies: Detects distinct cell shape signatures in the developing zebrafish inner ear where epithelial deformation occurs in opposite orientations.
• Developmental biology and tissue engineering: Provides quantitative measures of epithelial shape dynamics to support studies in developmental biology and tissue engineering.

Methodology:

MATLAB-based image analysis pipeline that processes fluorescence microscopy data, extracts direction-variant cell shape features along the apico-basal axis, automatically identifies apico-basal direction vectors (including opposing curvatures), and integrates image-derived measurements with biomechanical modeling.