Anatomy Volume Analysis

MATLAB class to fill models with points, build watertight hulls, and derive volume models of a complex surface model for anatomical analysis

The MATLAB class Anatomy Volume Analysis provides a volume-oriented workflow for anatomical surface meshes. It detects boundary loops, patches holes, generates shrink-wrapped surfaces, reconstructs surfaces from point clouds, and fills regions with structured point sets for intersection/volume computations. The volume class is for geometry-processing tasks where robust, watertight models and volumetric point sets are required.

Key Features:

1. Edge Detection: Boundary vertex/edge extraction and automatic loop grouping

2. Hole Patching: Fill holes with triangulated patches

3. Point Filling: Fill reference and anatomical model with points (grid points)

4. Shrink-Wrap Surfaces: Alpha shape hulls with UI or auto iteration to closed meshes

5. Reference Intersection Support: Identification of reference model parts within alpha shape hulls and assignment of grid points for subsequent volume/intersection steps

6. Point Filtering: Remove grid points outside anatomical model

7. Volume Reconstruction: Refined alpha shape hull with grid points

How to Use:

1. Code structure: The volume class can be integrated into a corresponding main script. The key parts of the code are extracted into individual functions for reuse. Provide the mesh as an STL file (triangulated).

2. Import: Import the anatomical model data and any reference model in STL format.

3. Run Volume Calculations

4. Results: Use the grid points and closed hulls for voxel/point-based volume or intersection analysis subsequently.

Use Cases:

• Generating watertight hulls from surface meshes
• Preparing regions for voxel/point intersection and volume computation
• Reconstructing surfaces from point clouds
• Computing distance maps for quantitative mesh comparison

Benefits:

• Robust to real data: handles holes, open boundaries, and noisy points
• Interactive where needed: quick UI checks
• Automatable: workflow with auto-closure of alpha shapes
• Volume-ready outputs: inside/outside masks, alpha shapes, and dense grid points
• Modular: single functions can be dropped into custom workflows

Keywords:

anatomy, volume analysis, shrink wrap, alpha shape, mesh repair, hole filling, boundary detection, clustering, KDE, DBSCAN, point cloud, defect filling, watertight mesh, biomedical geometry

References:

• N. Douillet, ‘‘Discrete contour mesh patch,’’ MATLAB Central File Exchange, 2025. [Online]. Available: https://de.mathworks.com/matlabcentral/fileexchange/78901-discrete-contour-mesh-patch-2d-3d
• Sven, ‘‘inpolyhedron - Are points inside a triangulated volume?’’ MATLAB Central File Exchange, 2024. [Online]. Available: https://de.mathworks.com/matlabcentral/fileexchange/37856-inpolyhedron-are-points-inside-a-triangulated-volume
• S. de Wolski, ‘‘File Exchange Pick of the Week - INPOLYHEDRON,’’ 2013. [Online]. Available: https://blogs.mathworks.com/pick/2013/09/06/inpolyhedron/