Shape Manifold Embedding

Run 2-ShapeManifoldEmbedding > RunShapeManifoldEmbedding.m, which asks for the Analysis folder as input and gives the user the option of using sparse decomposition.

Once correctly completed, a file called CellShapeData.mat is created in the Analysis folder

This process is relatively slow: for a set of 4000 shapes, it takes about 8 minutes, while for 37818 shapes, the calculations require about 31 hours, approximately 1.5 to 2 days. The sparse implementation is much faster, requiring only 5 hours for 37818 shapes. It uses MATLAB’s eigs function rather than eig. It is correct up to a +/- sign. This effects how the data is viewed in shape space but does not effect any subsequent measurements.