Philip Saponaro

P. Saponaro, W. Treible, A. Kolagunda et al.

Automating the extraction and quantification of features from three-dimensional (3-D) image stacks is a critical task for advancing computer vision research. The union of 3-D image acquisition and analysis enables the quantification of biological resistance of a plant tissue to fungal infection through the analysis of attributes such as fungal penetration depth, fungal mass, and branching of the fungal network of connected cells. From an image processing perspective, these tasks reduce to segmentation of vessel-like structures and the extraction of features from their skeletonization. In order to sample multiple infection events for analysis, we have developed an approach we refer to as macroscopic microscopy. However, macroscopic microscopy produces high-resolution image stacks that pose challenges to routine approaches and are difficult for a human to annotate to obtain ground truth data. We present a synthetic hyphal network generator, a comparison of several vessel segmentation methods, and a minimum spanning tree method for connecting small gaps resulting from imperfections in imaging or incomplete skeletonization of hyphal networks. Qualitative results are shown for real microscopic data. We believe the comparison of vessel detectors on macroscopic microscopy data, the synthetic vessel generator, and the gap closing technique are beneficial to the image processing community.

Abhishek Kolagunda, Scott Sorensen, Philip Saponaro et al.

Shape registration is the process of aligning one 3D model to another. Most previous methods to align shapes with no known correspondences attempt to solve for both the transformation and correspondences iteratively. We present a shape registration approach that solves for the transformation using fuzzy correspondences to maximize the overlap between the given shape and the target shape. A coarse to fine approach with Levenberg-Marquardt method is used for optimization. Real and synthetic experiments show our approach is robust and outperforms other state of the art methods when point clouds are noisy, sparse, and have non-uniform density. Experiments show our method is more robust to initialization and can handle larger scale changes and rotation than other methods. We also show that the approach can be used for 2D-3D alignment via ray-point alignment.