ConfocalVR: Immersive Visualization for Confocal Microscopy

J Mol Biol. 2018 Oct 19;430(21):4028-4035. doi: 10.1016/j.jmb.2018.06.035. Epub 2018 Jun 24.


ConfocalVR is a virtual reality (VR) application created to improve the ability of researchers to study the complexity of cell architecture. Confocal microscopes take pictures of fluorescently labeled proteins or molecules at different focal planes to create a stack of two-dimensional images throughout the specimen. Current software applications reconstruct the three-dimensional (3D) image and render it as a two-dimensional projection onto a computer screen where users need to rotate the image to expose the full 3D structure. This process is mentally taxing, breaks down if you stop the rotation, and does not take advantage of the eye's full field of view. ConfocalVR exploits consumer-grade VR systems to fully immerse the user in the 3D cellular image. In this virtual environment, the user can (1) adjust image viewing parameters without leaving the virtual space, (2) reach out and grab the image to quickly rotate and scale the image to focus on key features, and (3) interact with other users in a shared virtual space enabling real-time collaborative exploration and discussion. We found that immersive VR technology allows the user to rapidly understand cellular architecture and protein or molecule distribution. We note that it is impossible to understand the value of immersive visualization without experiencing it first hand, so we encourage readers to get access to a VR system, download this software, and evaluate it for yourself. The ConfocalVR software is available for download at, and is free for nonprofits.

Keywords: ImageJ; cellular visualization; confocal microscopy; virtual collaboration; virtual reality.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Databases, Factual
  • Image Processing, Computer-Assisted
  • Imaging, Three-Dimensional
  • Microscopy, Confocal* / methods
  • Software*
  • Virtual Reality*