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wiki:zstackvis [2014/04/14 19:33]
Alessandro G created
wiki:zstackvis [2014/04/15 01:36] (current)
Alessandro G
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 ====== Artificial Defocus for Displaying Markers in Microscopy Z-Stacks ====== ====== Artificial Defocus for Displaying Markers in Microscopy Z-Stacks ======
-[[wiki:​welcome|Alessandro Giusti]], [[http://​www.pigei.com|Pierluigi Taddei]], Cristina Magli, [[http://​www.idsia.ch/​~corani|Giorgio Corani]], [[http://​www.idsia.ch/​~luca|Luca M. Gambardella]],​ Luca Gianaroli+[[wiki:​welcome|Alessandro Giusti]], [[http://​www.pigei.com|Pierluigi Taddei]], Cristina Magli, [[http://​www.idsia.ch/​~corani|Giorgio Corani]], [[http://​www.idsia.ch/​~luca|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. 
 + 
 +{{ :​wiki:​2011-vis-teaser.png?​nolink&​900 |}} 
 + 
 +===== Paper ===== 
 +IEEE Xplore [[http://​ieeexplore.ieee.org/​xpl/​freeabs_all.jsp?​arnumber=6064938|link]]. Preprint [[http://​www.idsia.ch/​~giusti/​papers/​2011/​vis.pdf|PDF]]. 
 + 
 +===== Bibtex ===== 
 +<​code>​ 
 +@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} 
 +
 +</​code>​ 
 + 
 +===== Software ===== 
 +We provide both software implementations described in the paper. ​ At present, the material below should be considered for research purposes only. 
 +==== Matlab Prototype ==== 
 +[[http://​www.idsia.ch/​~giusti/​papers/​2011/​vis-matlab.zip|Download]] - Please read included README 
 +==== Java+OpenGL Prototype ==== 
 +[[http://​www.idsia.ch/​~giusti/​papers/​2011/​vis-java.zip|Download]] - Please read included README 
 + 
 +===== Random Demonstration Videos ===== 
 +==== Basic interaction techniques ==== 
 +{{youtube>​wIqimGSSfz0?​large}} 
 + 
 +==== Complex interaction techniques: validating & correcting the segmentation of a 4-cell embryo ==== 
 +related: [[wiki:​IN3|image processing for IVF]]). 
 +{{youtube>​k_kecTNV2Mw?​large}} 
 + 
 +==== A ruler and protractor ==== 
 +{{youtube>​8o7L82m5x2E?​large}} 
 + 
 +==== Pointless toys ==== 
 +{{youtube>​5ceQGXOkzz4?​large}}