Share Email Print

Proceedings Paper

Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy
Author(s): Philip Julian Broser; Roland Schulte; A. Roth; Fritjof Helmchen; Jack Waters; Stefan Lang; Bert Julian Sakmann; Gabriel Wittum
Format Member Price Non-Member Price
PDF $17.00 $21.00

Paper Abstract

Two-photon microscopy in combination with novel fluorescent labeling techniques enables imaging of three-dimensional neuronal morphologies in intact brain tissue. In principle it is now possible to automatically reconstruct the dendritic branching patterns of neurons from 3D fluorescence image stacks. In practice however, the signal-to-noise ratio can be low, in particular in the case of thin dendrites or axons imaged relatively deep in the tissue. Here we present a nonlinear anisotropic diffusion filter that enhances the signal-to-noise ratio while preserving the original dimensions of the structural elements. The key idea is to use structural information in the raw data -- the local moments of inertia -- to locally control the strength and direction of diffusion filtering. A cylindrical dendrite, for example, is effectively smoothed only parallel to its longitudinal axis, not perpendicular to it. This is demonstrated for artificial data as well as for in vivo 2-photon microscopic data from pyramidal neurons of rat neocortex. In both cases noise is averaged out along the dendrites, leading to bridging of apparent gaps, while dendritic diameters are not affected. The filter is a valuable general tool for smoothing cellular processes and is well suited for preparing data for subsequent image segmentation and neuron reconstruction.

Paper Details

Date Published: 1 March 2005
PDF: 26 pages
Proc. SPIE 5672, Image Processing: Algorithms and Systems IV, (1 March 2005); doi: 10.1117/12.593376
Show Author Affiliations
Philip Julian Broser, Max-Planck-Institut fur Medizinische Forschung (Germany)
Ruprecht-Karls-Univ. Heidelberg (Germany)
Roland Schulte, Ruprecht-Karls-Univ. Heidelberg (Germany)
A. Roth, Max-Planck-Institut fur Medizinische Forschung (Germany)
Fritjof Helmchen, Max-Planck-Institut fur Medizinische Forschung (Germany)
Jack Waters, Max-Planck-Institut fur Medizinische Forschung (Germany)
Stefan Lang, Ruprecht-Karls-Univ. Heidelberg (Germany)
Bert Julian Sakmann, Max-Planck-Institut fur Medizinische Forschung (Germany)
Gabriel Wittum, Ruprecht-Karls-Univ. Heidelberg (Germany)

Published in SPIE Proceedings Vol. 5672:
Image Processing: Algorithms and Systems IV
Edward R. Dougherty; Jaakko T. Astola; Karen O. Egiazarian, Editor(s)

© SPIE. Terms of Use
Back to Top
Sign in to read the full article
Create a free SPIE account to get access to
premium articles and original research
Forgot your username?