Variational attenuation correction in two-view confocal microscopy (eBook, 2013) [WorldCat.org]
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Variational attenuation correction in two-view confocal microscopy

Author: Thorsten FalkJasmin DürrMargret KeuperThomas BleinKlaus PalmeAll authors
Publisher: Freiburg Universität 2013
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
Abstract: Background<br><br>Absorption and refraction induced signal attenuation can seriously hinder the extraction of quantitative information from confocal microscopic data. This signal attenuation can be estimated and corrected by algorithms that use physical image formation models. Especially in thick heterogeneous samples, current single view based models are unable to solve the underdetermined  Read more...
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Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Thorsten Falk; Jasmin Dürr; Margret Keuper; Thomas Blein; Klaus Palme; Olaf Ronneberger; Albert-Ludwigs-Universität Freiburg Institut für Informatik; Albert-Ludwigs-Universität Freiburg Institut für Biologie II; Albert-Ludwigs-Universität Freiburg Centre for Biological Signalling Studies; Albert-Ludwigs-Universität Freiburg Freiburg Institute of Advanced Studies; FRISYS; Albert-Ludwigs-Universität Freiburg Fakultät für Angewandte Wissenschaften; Albert-Ludwigs-Universität Freiburg Fakultät für Biologie; Albert-Ludwigs-Universität Freiburg
OCLC Number: 1003249523
Notes: BMC Bioinformatics. 14 (2013), 366, DOI 10.1186/1471-2105-14-366, issn: 1471-2105
IN COPYRIGHT http://rightsstatements.org/page/InC/1.0 rs
Description: Online-Ressource

Abstract:

Abstract: Background<br><br>Absorption and refraction induced signal attenuation can seriously hinder the extraction of quantitative information from confocal microscopic data. This signal attenuation can be estimated and corrected by algorithms that use physical image formation models. Especially in thick heterogeneous samples, current single view based models are unable to solve the underdetermined problem of estimating the attenuation-free intensities.<br><br>Results<br><br>We present a variational approach to estimate both, the real intensities and the spatially variant attenuation from two views of the same sample from opposite sides. Assuming noise-free measurements throughout the whole volume and pure absorption, this would in theory allow a perfect reconstruction without further assumptions. To cope with real world data, our approach respects photon noise, estimates apparent bleaching between the two recordings, and constrains the attenuation field to be smooth and sparse to avoid spurious attenuation estimates in regions lacking valid measurements.<br><br>Conclusions<br><br>We quantify the reconstruction quality on simulated data and compare it to the state-of-the art two-view approach and commonly used one-factor-per-slice approaches like the exponential decay model. Additionally we show its real-world applicability on model organisms from zoology (zebrafish) and botany (Arabidopsis). The results from these experiments show that the proposed approach improves the quantification of confocal microscopic data of thick specimen

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