title: Visualizing in vivo brain neural structures using volume rendered feature spaces.
abstract: BACKGROUND
  Dendrites of cortical neurons are widely spread across several layers of the cortex. Recently developed two-photon microscopy systems are capable of visualizing the morphology of neurons within deeper layers of the brain and generate large amounts of volumetric imaging data from living tissue.
  
  
  METHODS
  For visual exploration of the three-dimensional (3D) structure of dendrites and the connectivity among neurons in the brain, we propose a visualization software and interface for 3D images based on a new transfer function design using volume rendered feature spaces. This software enables the visualization of multidimensional descriptors of shape and texture extracted from imaging data to characterize tissue. It also allows the efficient analysis and visualization of large data sets.
  
  
  RESULTS
  We apply and demonstrate the software to two-photon microscopy images of a living mouse brain. By applying the developed visualization software and algorithms to two-photon microscope images of the mouse brain, we identified a set of feature values that distinguish characteristic structures such as soma, dendrites and apical dendrites in mouse brain. Also, the visualization interface was compared to conventional 1D/2D transfer function system.
  
  
  CONCLUSIONS
  We have developed a visualization tool and interface that can represent 3D feature values as textures and shapes. This visualization system allows the analysis and characterization of the higher-dimensional feature values of living tissues at the micron level and will contribute to new discoveries in basic biology and clinical medicine.
authors.affiliation: Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto, Japan. Electronic address: megumi@i.kyoto-u.ac.jp.
authors.forename: Megumi
authors.initials: M
authors.lastname: Nakao
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, Japan.
authors.forename: Kosuke
authors.initials: K
authors.lastname: Kurebayashi
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, Japan.
authors.forename: Tadao
authors.initials: T
authors.lastname: Sugiura
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Sato
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan.
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Sawada
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan; Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Kawakami
authors.affiliation: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan; Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Nemoto
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, Japan.
authors.forename: Kotaro
authors.initials: K
authors.lastname: Minato
authors.affiliation: Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Matsuda
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D021621:Imaging, Three-Dimensional / Q000379:methods; D051379:Mice; D008822:Mice, Transgenic; D059906:Neuroimaging / Q000379:methods*; D061848:Optical Imaging / Q000379:methods*
keywords: Feature analysis; Neural structures; Two-photon microscopy; Volume visualization