Virtual environment for processing medial axis representations of 3D nanoscale reconstructions of brain cellular structures

Daniya Boges, Corrado Calì, Pierre J. Magistretti, Markus Hadwiger, Ronell Sicat, Marco Agus

Abstract: We present a novel immersive environment for the interactive 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.