Variational attenuation correction in two-view confocal microscopy
Background
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.
Results
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.
Conclusions
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.
Images and movies
BibTex reference
@Article{SKR13a, author = "T. Schmidt and J. D{\"u}rr and M. Keuper and T. Blein and K. Palme and O. Ronneberger", title = "Variational attenuation correction in two-view confocal microscopy", journal = "BMC Bioinformatics", number = "1", volume = "14", pages = "366", month = "Dec", year = "2013", keywords = "attenuation correction, absorption, confocal microscopy, image restauration, calculus of variations", url = "http://lmb.informatik.uni-freiburg.de/Publications/2013/SKR13a" }