Immersive environment for creating, proofreading, and exploring skeletons of nanometric scale neural structures

Abstract

We present a novel immersive environment for the exploratory analysis of nanoscale cellular reconstructions of rodent brain samples acquired through electron microscopy. The system is focused on medial axis representations (skeletons) of branched and tubular structures of brain cells, and it is specifically designed for: i) effective semi-automatic creation of skeletons from surface-based representations of cells and structures, ii) fast proofreading, i.e., correcting and editing of semi-automatically constructed skeleton representations, and iii) useful exploration, i.e., measuring, comparing, and analyzing geometric features related to cellular structures based on medial axis representations. The application runs in a standard PC-tethered virtual reality (VR) setup with a head mounted display (HMD), controllers, and tracking sensors. The system is currently used by neuroscientists for performing morphology studies on sparse reconstructions of glial cells and neurons extracted from a sample of the somatosensory cortex of a juvenile rat.