title: Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation.
abstract: BACKGROUND
  We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visualize the results of their virtual experiments that are performed in computer simulations, or in silico. The impact of the presented pipeline opens novel avenues for assisting the neuroscientists to build biologically accurate models of the brain. These models result from computer simulations of physical experiments that use fluorescence imaging to understand the structural and functional aspects of the brain. Due to the limited capabilities of the current visualization workflows to handle fluorescent volumetric datasets, we propose a physically-based optical model that can accurately simulate light interaction with fluorescent-tagged scattering media based on the basic principles of geometric optics and Monte Carlo path tracing. We also develop an automated and efficient framework for generating dense fluorescent tissue blocks from a neocortical column model that is composed of approximately 31000 neurons.
  
  
  RESULTS
  Our pipeline is used to visualize a virtual fluorescent tissue block of 50 μm3that is reconstructed from the somatosensory cortex of juvenile rat. The fluorescence optical model is qualitatively analyzed and validated against experimental emission spectra of different fluorescent dyes from the Alexa Fluor family.
  
  
  CONCLUSIONS
  We discussed a scientific visualization pipeline for creating images of synthetic neocortical neuronal models that are tagged virtually with fluorescent labels on a physically-plausible basis. The pipeline is applied to analyze and validate simulation data generated from neuroscientific in silico experiments.
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
authors.forename: Marwan
authors.initials: M
authors.lastname: Abdellah
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Bilgili
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Eilemann
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
authors.forename: Julian
authors.initials: J
authors.lastname: Shillcock
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
authors.forename: Henry
authors.initials: H
authors.lastname: Markram
authors.affiliation: Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland. felix.schuermann@epfl.ch.
authors.forename: Felix
authors.initials: F
authors.lastname: Schürmann
mesh_terms: D000818:Animals; D055592:Biophysical Phenomena; D005456:Fluorescent Dyes; D007091:Image Processing, Computer-Assisted; D008954:Models, Biological; D009010:Monte Carlo Method; D019579:Neocortex / Q000502:physiology*; D051381:Rats; D015203:Reproducibility of Results; D012542:Scattering, Radiation
chemical_list: D005456:Fluorescent Dyes
keywords: Fluorescence rendering and visualization; Highly scattering volumes; In silico neuroscience; Modeling and simulation; Neocortical brain models