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Artificial Defocus for Displaying Markers in Microscopy Z-Stacks
Dec. 2011 (vol. 17 no. 12)
pp. 1757-1764
ASCII Text
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Alessandro Giusti, Pierluigi Taddei, Giorgio Corani, Luca Gambardella, Cristina Magli, Luca Gianaroli, "Artificial Defocus for Displaying Markers in Microscopy Z-Stacks," IEEE Transactions on Visualization and Computer Graphics, vol. 17, no. 12, pp. 1757-1764, Dec., 2011.
 
 
BibTex
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@article{ 10.1109/TVCG.2011.168,
author = {Alessandro Giusti and Pierluigi Taddei and Giorgio Corani and Luca Gambardella and Cristina Magli and Luca Gianaroli},
title = {Artificial Defocus for Displaying Markers in Microscopy Z-Stacks},
journal ={IEEE Transactions on Visualization and Computer Graphics},
volume = {17},
number = {12},
issn = {1077-2626},
year = {2011},
pages = {1757-1764},
doi = {http://doi.ieeecomputersociety.org/10.1109/TVCG.2011.168},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE Transactions on Visualization and Computer Graphics
TI - Artificial Defocus for Displaying Markers in Microscopy Z-Stacks
IS - 12
SN - 1077-2626
SP1757
EP1764
EPD - 1757-1764
A1 - Alessandro Giusti,
A1 - Pierluigi Taddei,
A1 - Giorgio Corani,
A1 - Luca Gambardella,
A1 - Cristina Magli,
A1 - Luca Gianaroli,
PY - 2011
KW - Depth of field
KW - Microscopy
KW - Focus stacks.
VL - 17
JA - IEEE Transactions on Visualization and Computer Graphics
ER -
 
Alessandro Giusti, Dalle Molle Institute for Artificial Intelligence, Lugano, Switzerland
Pierluigi Taddei, JRC, Ispra
Giorgio Corani, Dalle Molle Institute for Artificial Intelligence, Lugano, Switzerland
Luca Gambardella, Dalle Molle Institute for Artificial Intelligence, Lugano, Switzerland
Cristina Magli, International Institute of Reproductive Medicine, Lugano, Switzerland
Luca Gianaroli, International Institute of Reproductive Medicine, Lugano, Switzerland
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.

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Index Terms:
Depth of field, Microscopy, Focus stacks.
Citation:
Alessandro Giusti, Pierluigi Taddei, Giorgio Corani, Luca Gambardella, Cristina Magli, Luca Gianaroli, "Artificial Defocus for Displaying Markers in Microscopy Z-Stacks," IEEE Transactions on Visualization and Computer Graphics, vol. 17, no. 12, pp. 1757-1764, Dec. 2011, doi:10.1109/TVCG.2011.168
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