title: Virtual reality assisted microscopy data visualization and colocalization analysis.
abstract: BACKGROUND
  Confocal microscopes deliver detailed three-dimensional data and are instrumental in biological analysis and research. Usually, this three-dimensional data is rendered as a projection onto a two-dimensional display. We describe a system for rendering such data using a modern virtual reality (VR) headset. Sample manipulation is possible by fully-immersive hand-tracking and also by means of a conventional gamepad. We apply this system to the specific task of colocalization analysis, an important analysis tool in biological microscopy. We evaluate our system by means of a set of user trials.
  
  
  RESULTS
  The user trials show that, despite inaccuracies which still plague the hand tracking, this is the most productive and intuitive interface. The inaccuracies nevertheless lead to a perception among users that productivity is low, resulting in a subjective preference for the gamepad. Fully-immersive manipulation was shown to be particularly effective when defining a region of interest (ROI) for colocalization analysis.
  
  
  CONCLUSIONS
  Virtual reality offers an attractive and powerful means of visualization for microscopy data. Fully immersive interfaces using hand tracking show the highest levels of intuitiveness and consequent productivity. However, current inaccuracies in hand tracking performance still lead to a disproportionately critical user perception.
authors.affiliation: Stellenbosch University, Stellenbosch, 7600, South Africa.
authors.forename: Rensu P
authors.initials: RP
authors.lastname: Theart
authors.affiliation: Stellenbosch University, Stellenbosch, 7600, South Africa.
authors.forename: Ben
authors.initials: B
authors.lastname: Loos
authors.affiliation: Stellenbosch University, Stellenbosch, 7600, South Africa. trn@sun.ac.za.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Niesler
mesh_terms: D000328:Adult; D000818:Animals; D002460:Cell Line; D003198:Computer Simulation; D005260:Female; D006801:Humans; D008297:Male; D051379:Mice; D018613:Microscopy, Confocal; D008875:Middle Aged; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D014584:User-Computer Interface; D055815:Young Adult
keywords: 3D Microscopic reconstruction; Colocalization analysis; Confocal microscopy visualization; Hand tracking; Region of interest selection; Virtual reality; Volume rendering