title: Variational attenuation correction in two-view confocal microscopy.
abstract: 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.
authors.affiliation: Department of Computer Science, Albert-Ludwigs-Universität, Georges-Köhler-Allee Geb, 52, 79110 Freiburg, Germany. tschmidt@cs.uni-freiburg.de.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Schmidt
authors.forename: Jasmin
authors.initials: J
authors.lastname: Dürr
authors.forename: Margret
authors.initials: M
authors.lastname: Keuper
authors.forename: Thomas
authors.initials: T
authors.lastname: Blein
authors.forename: Klaus
authors.initials: K
authors.lastname: Palme
authors.forename: Olaf
authors.initials: O
authors.lastname: Ronneberger
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis; D019295:Computational Biology / Q000379:methods; D004734:Energy Metabolism; D005456:Fluorescent Dyes; D014644:Genetic Variation; D007090:Image Interpretation, Computer-Assisted; D018613:Microscopy, Confocal / Q000379:methods; D011381:Programming Languages; D012984:Software; D015027:Zebrafish
chemical_list: D005456:Fluorescent Dyes