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@article{832398,
author = {Brázdilová, Silvie Luisa and Kozubek, Michal},
article_location = {Oxford},
article_number = {3},
doi = {http://dx.doi.org/10.1111/j.1365-2818.2009.03280.x},
keywords = {automated microscopy; information content analysis; autofocusing; normalized variance},
language = {eng},
issn = {0022-2720},
journal = {Journal of Microscopy},
title = {Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions},
volume = {236},
year = {2009}
}
TY - JOUR
ID - 832398
AU - Brázdilová, Silvie Luisa - Kozubek, Michal
PY - 2009
TI - Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions
JF - Journal of Microscopy
VL - 236
IS - 3
SP - 194-202
EP - 194-202
PB - Blackwell Science
SN - 00222720
KW - automated microscopy
KW - information content analysis
KW - autofocusing
KW - normalized variance
N2 - We present a new algorithm to analyse information content in images acquired using automated fluorescence microscopy. The algorithm belongs to the group of autofocusing methods, but differs from its predecessors in that it can handle thick specimens and operate also in confocal mode. It measures the information content in images using a "content function", which is essentially the same concept as a focus function. Unlike previously presented algorithms, this algorithm tries to find all significant axial positions in cases where the content function applied to real data is not unimodal, which is often the case. This requirement precludes using algorithms that rely on unimodality. Moreover, choosing a content function requires careful consideration, because some functions suppress local maxima. First, we test 19 content functions and evaluate their ability to show local maxima clearly. The results show that only six content functions succeed. To save time, the acquisition procedure needs to vary the step size adaptively, because a wide range of possible axial positions has to be passed so as not to miss a local maximum. The algorithm therefore has to assess the steepness of the content function on-line so that it can decide to use a bigger or smaller step size to acquire the next image. Therefore, the algorithm needs to know about typical behaviour of content functions. We show that for Normalized Variance, one of the most promising content functions, this knowledge can be obtained after normalizing with respect to the theoretical maximum of this function, and using hierarchical clustering. The resulting algorithm is more reliable and efficient than a simple procedure with constant steps.
ER -
BRÁZDILOVÁ, Silvie Luisa and Michal KOZUBEK. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. \textit{Journal of Microscopy}. Oxford: Blackwell Science, 2009, vol.~236, No~3, p.~194-202. ISSN~0022-2720. Available from: https://dx.doi.org/10.1111/j.1365-2818.2009.03280.x.
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