3D printed tumor moulds for guided tissue sampling

This software should be cited with the DOI 10.5281/zenodo.3066305.

Requirements

• MATLAB
• CERR (https://github.com/cerr/CERR)
• Python (with modules as listed in requirements.txt)
• Meshlab (with meshlabserver)
• OpenSCAD

Examples

Rotation and habitat map generation

Images are processed in MATLAB to generate habitat maps and correctly oriented volumes for printing. To test the code, run the following commands in a MATLAB prompt:

>> rotateTumour /path/to/CERR

This script creates two .mat files:

1. transf_patient.mat (containing the transformation matrices required to rotate the image to the desired orientation)
2. aligned_tumour.mat (containing a 3D matrix with the volume to print, already rotated) In addition, the script creates multiple 2D and 3D visualizations of the tumour.

>> makeHabitats /path/to/CERR

This script creates one .png image per mould slice, containing the habitat maps. In addition, it creates a series of histograms comparing multiple imaging parameters for each habitat.

Mould generation

python generate_mould.py example_data/aligned_tumour.mat will result in three .stl files:

1. Patient.stl (containing the mould with holes for projected centroids of tumour and kidney)
2. Patient_tumour.stl (containing the fill-in for the tumour centroid hole)
3. Patient_kidney.stl (containing the fill-in for the kidney centroid hole) cutter