Connecting the Connectome Automating segmentation of neurons from tissue imaging

Abstract

Recent studies in neuroscience have shown the great promise of an approach known as connectomics, which seeks to map the brain by the connections between neurons. Attempts to study the brain in this way extract brain tissue and capture sequential cross-sectional images with an electron microscope. These projects are currently limited by the image processing stage of the pipeline, which turns these images into digitally reconstructed neurons, as state-of-the-art computer vision systems are unable to segment neurons with sufficient reliability. The SNEMI3D challenge is an open con- test that offers a benchmark on the effectiveness of automated neuron segmentation systems and invites researchers to compete in their ability to segment the challenge dataset. GALA is an open source software project to perform automated segmentation created by researchers at the Janelia Farm research campus. In this paper, I detail my efforts to improve the performance of GALA, which was narrowly in second place in the SNEMI3D contest when I began the project. I succeeded in improving GALA's performance and have now decisively taken the top spot in the contest.