SANTIAGO: Spine Association for Neuron Topology Improvement and Graph Optimization

TL;DR

This paper introduces a biologically inspired, network-centric approach to improve neuron connectivity graph reconstruction from electron micrographs, significantly reducing errors like spine-shaft fragmentation in connectomics.

Contribution

It presents a novel pipeline for reconnecting fragmented spines to dendrites, curates the first reference dataset for spine-shaft analysis, and demonstrates substantial improvements in graph reconstruction accuracy.

Findings

Automated approach improves local subgraph score by over four times

Full graph score increases by 60% with the new method

Curated the first reference dataset for spine-shaft algorithm analysis

Abstract

Developing automated and semi-automated solutions for reconstructing wiring diagrams of the brain from electron micrographs is important for advancing the field of connectomics. While the ultimate goal is to generate a graph of neuron connectivity, most prior automated methods have focused on volume segmentation rather than explicit graph estimation. In these approaches, one of the key, commonly occurring error modes is dendritic shaft-spine fragmentation. We posit that directly addressing this problem of connection identification may provide critical insight into estimating more accurate brain graphs. To this end, we develop a network-centric approach motivated by biological priors image grammars. We build a computer vision pipeline to reconnect fragmented spines to their parent dendrites using both fully-automated and semi-automated approaches. Our experiments show we can learn valid connections despite uncertain segmentation paths. We curate the first known reference dataset for analyzing the performance of various spine-shaft algorithms and demonstrate promising results that recover many previously lost connections. Our automated approach improves the local subgraph score by more than four times and the full graph score by 60 percent. These data, results, and evaluation tools are all available to the broader scientific community. This reframing of the connectomics problem illustrates a semantic, biologically inspired solution to remedy a major problem with neuron tracking.