Biologically-Constrained Graphs for Global Connectomics Reconstruction

by   Haidong Zhu, et al.

Most current state-of-the-art connectome reconstruction pipelines have two major steps: initial pixel-based segmentation with affinity prediction and watershed transform, and refined segmentation by merging over-segmented regions. These methods rely only on local context and are typically agnostic to the underlying biology. Since a few merge errors can lead to several incorrectly merged neuronal processes, these algorithms are currently tuned towards over-segmentation producing an overburden of costly proofread- ing. We propose a third step for connectomics reconstruction pipelines to refine an over-segmentation using both local and global contexts with an emphasis on adhering to the underlying biology. We first extract a graph from an input segmentation where nodes correspond to segment labels and edges indicate potential split errors in the over-segmentation. To increase throughput and allow for large- scale reconstruction, we employ biologically inspired geometric constraints based on neuron morphology to reduce the number of nodes and edges. Next, two neural networks learn these neuronal shapes to aid the graph construction process further. Lastly, we reformulate the region merging problem as a graph partitioning one to leverage global context. We demonstrate the performance of our approach on four real-world connectomics datasets with an average variation of information improvement of 21.3%.


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