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 at IEEE VIS.

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

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