ExMicroVR Application

ExMicroVR is a tool for viewing and manipulating multichannel confocal microscope image-stacks in immersive Virtual Reality. It was developed in a collaboration between Immersive Science, Benaroya Research Institute, and Carnegie Mellon University. The tool allows researchers to explore details of cell structure in images. Use ImageJ (free from NIH) to convert confocal microscope image stacks into 3D volumetric object files (NIfTI ) that you can then view in VR.

This software is licensed for free to non-profit applications.


  • This application is not compatible with mobile phone based VR systems because of the compute power needed to render high fidelity volumetric images within a fully immersive 6DOF experience
  • Only compatible with Windows OS, because currently this is the only compute platform supporting the VR hardware systems

Sample Expansion Microscopy

Multichannel Image Stacks


Mouse Striatum

Brendan Gallagher


Carnegie Mellon University

The Striatum image-stack shows a section of mouse striatum, with the first channel being a nuclear stain, second channel is a label for Tyrosine Hydroxylase, which is a marker for dopamine neurons. The third channel is a marker for presynaptic terminals, and the fourth channel is a marker for a certain type of neurons; what you’re seeing there are projections from the cortex that pass through the striatum and don’t really interact with it, kind of like a highway

The samples were expanded via the ExMicro protocol and then imaged at a 20x magnification. Without expansion, you can see the large axon bundles that are passing through, but often they just look like one large blob. The big use of expansion in this image, however, is the visualization of the presynaptic terminals. Without expansion, it can be very difficult to make these out as the individual points that they are.

 Fluorescent Dyes:

  • Channel 1: DAPI
  • Channel 2: Tyrosine Hydroxylase
  • Channel 3: Synaptophysin
  • Channel 4: Alpha-Internexin (INA)