Anna Grim

Anna Grim, Jayaram Chandrashekar, Uygar Sumbul

Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors, as multiple entangled neuronal arbors is a challenging instance segmentation problem. More broadly, segmentation of curvilinear, filamentous structures continues to pose significant challenges. To address this problem, we extend the notion of simple points from digital topology to connected sets of voxels (i.e. supervoxels) and propose a topology-aware neural network segmentation method with minimal computational overhead. We demonstrate its effectiveness on a new public dataset of 3-d light microscopy images of mouse brains, along with the benchmark datasets DRIVE, ISBI12, and CrackTree.

Anna Grim, Pedro Felzenszwalb

We present new message passing algorithms for performing inference with graphical models. Our methods are designed for the most difficult inference problems where loopy belief propagation and other heuristics fail to converge. Belief propagation is guaranteed to converge when the underlying graphical model is acyclic, but can fail to converge and is sensitive to initialization when the underlying graph has complex topology. This paper describes modifications to the standard belief propagation algorithms that lead to methods that converge to unique solutions on graphical models with arbitrary topology and potential functions.