Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three‐dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug‐ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. J. Comp. Neurol. 524:23–38, 2016. © 2015 Wiley Periodicals, Inc.

Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three‐dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug‐ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. J. Comp. Neurol. 524:23–38, 2016. © 2015 Wiley Periodicals, Inc.

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Virtual reality systems are an excellent environment for stereo panorama displays. The acquisition and display methods described here combine high-resolution photography with surround vision and full stereo view in an immersive environment. This combination provides photographic stereo-panoramas for a variety of VR displays, including the StarCAVE[1], NexCAVE [2] , and CORNEA [3] . The zero parallax point used in conventional panorama photography is also the center of horizontal and vertical rotation when creating photographs for stereo panoramas. The two photographically created images are displayed on a cylinder or a sphere. The radius from the viewer to the image is set at approximately 20 feet, or at the object of major interest.A full stereo view is presented in all directions. The interocular distance, as seen from the viewer's perspective, displaces the two spherical images horizontally. This presents correct stereo separation in whatever direction the viewer is looking, even up and down. Objects at infinity will move with the viewer, contributing to an immersive experience. Stereo panoramas created with this acquisition and display technique can be applied without modification to a large array of VR devices having different screen arrangements and different VR libraries.

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