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Artificial Defocus for Displaying Markers in Microscopy Z-Stacks

Alessandro Giusti, Pierluigi Taddei, Cristina Magli, Giorgio Corani, Luca M. Gambardella, Luca Gianaroli
IEEE Transactions on Visualization and Computer Graphics, 2011. Honorable Mention award recipient

Abstract

As microscopes have a very shallow depth of field, Z-stacks (i.e. sets of images shot at different focal planes) are often acquired to fully capture a thick sample. Such stacks are viewed by users by navigating them through the mouse wheel. We propose a new technique of visualizing 3D point, line or area markers in such focus stacks, by displaying them with a depth-dependent defocus, simulating the microscope's optics; this leverages on the microscopists' ability to continuously twiddle focus, while implicitly performing a shape-from-focus reconstruction of the 3D structure of the sample. User studies confirm that the approach is effective, and can complement more traditional techniques such as color-based cues. We provide two implementations, one of which computes defocus in real time on the GPU, and examples of their application.

Paper

IEEE Xplore link. Preprint PDF.

Bibtex

@article{giusti2011artificial,
  title={Artificial Defocus for Displaying Markers in Microscopy Z-Stacks},
  author={Giusti, Alessandro and Taddei, Pierluigi and Corani, Giorgio and Gambardella, Luca and Magli, Cristina and Gianaroli, Luca},
  journal={Visualization and Computer Graphics, IEEE Transactions on},
  volume={17},
  number={12},
  pages={1757--1764},
  year={2011},
  publisher={IEEE}
}

Software

We provide both software implementations described in the paper. At present, the material below should be considered for research purposes only.

Matlab Prototype

Download - Please read included README

Java+OpenGL Prototype

Download - Please read included README