DOI: 10.5061/dryad.808k4r0
title: GLAM: Glycogen-derived Lactate Absorption Map for visual analysis of dense and sparse surface reconstructions of rodent brain structures on desktop systems and virtual environments

description: Human brain accounts for about one hundred billion neurons, but they
 cannot work properly without ultrastructural and metabolic support. For
 this reason, mammalian brains host another type of cells called “glial
 cells”, whose role is to maintain proper conditions for efficient neuronal
 function. One type of glial cell, astrocytes, are involved in particular
 in the metabolic support of neurons, by feeding them with lactate, one
 byproduct of glucose metabolism that they can take up from blood vessels,
 and store it under another form, glycogen granules. These energy-storage
 molecules, whose morphology resembles to spheres with a diameter ranging
 10–80 nanometers roughly, can be easily recognized using electron
 microscopy, the only technique whose resolution is high enough to resolve
 them. Understanding and quantifying their distribution is of particular
 relevance for neuroscientists, in order to understand where and when
 neurons use energy under this form. To answer this question, we developed
 a visualization technique, dubbed GLAM (Glycogen-derived Lactate
 Absorption Map), and customized for the analysis of the interaction of
 astrocytic glycogen on surrounding neurites in order to formulate
 hypotheses on the energy absorption mechanisms. The method integrates
 high-resolution surface reconstruction of neurites, astrocytes, and the
 energy sources in form of glycogen granules from different automated
 serial electron microscopy methods, like focused ion beam scanning
 electron microscopy (FIB-SEM) or serial block face electron microscopy
 (SBEM), together with an absorption map computed as a radiance transfer
 mechanism. The resulting visual representation provides an immediate and
 comprehensible illustration of the areas in which the probability of
 lactate shuttling is higher. The computed dataset can be then explored and
 quantified in a 3D space, either using 3D modeling software or virtual
 reality environments. Domain scientists have evaluated the technique by
 either using the computed maps for formulating functional hypotheses or
 for planning sparse reconstructions to avoid excessive occlusion.
 Furthermore, we conducted a pioneering user study showing that immersive
 VR setups can ease the investigation of the areas of interest and the
 analysis of the absorption patterns in the cellular structures.
description: VR Data Interact
 executable file + application data files folderVR Data Interact is a
 virtual reality software application that was developed using the Unity
 game engine (V5.6.3f1) with the support of SteamVR and VRTK assets
 libraries (Unity plugins). It allows the end user to import 3D models in
 an OBJ format. Two of its main features are the Stack Interact menu and
 the Object Interact menu. The former is customized for electron microscopy
 z stacks that corresponds with the reconstructed 3D models. This feature
 allows neuroscientists to proofread their models, as well as conduct
 explorative analysis by correlating the imported 3D model with its
 surrounding structures in the corresponding 2D EM slice. The application
 is equipped with a demo model that includes 4 cellular/intracellular
 structures from rat hippocampus: Glia, axons, dendrites, and glycogen
 granules. The demo files are included in a separate zipped folder
 "KB008_bundle". This current zipped folder
 "dryad-ready.zip" contains one file
 "VR-DataInteract.exe" and one folder
 "VR-DataInteract_Data".dryad-ready.zipDemo FilesThis folder contains the demo files, must be placed in the same path as the executable file.KB008_bundle.zip