Shape component analysis: structure-preserving dimension reduction on biological shape spaces.

ABSTRACT

MOTIVATION Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques. RESULTS: We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins. AVAILABILITY AND IMPLEMENTATION Source code and data for reproducing results of this article are freely available at https//github.com/ccdlcmu/shape_component_analysis_Matlab The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS. CONTACT geyang@andrew.cmu.edu.