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  Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy

Broser, P. J., Schulte, R., Lang, S., Roth, A., Helmchen, F., Waters, D. J., et al. (2004). Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy. Journal of Biomedical Optics, 9(6), 1253-1264. doi:10.1117/1.1806832.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-1508-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-150B-2
Genre: Journal Article
Alternative Title : Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy

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JBiomedicalOpt_9_2004_1253.pdf (Any fulltext), 487KB
 
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 Creators:
Broser, Philip Julian1, Author              
Schulte, Roland, Author
Lang, Stefan1, Author              
Roth, Arnd1, Author              
Helmchen, Fritjof1, Author              
Waters, David Jack1, Author              
Sakmann, Bert1, Author              
Wittum, Gabriel, Author
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1Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society, ou_1497701              

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Free keywords: filters; diffusion; nonlinear; anisotropic; two-photon imaging; neural morphology; reconstruction
 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 3-D 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 two-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.

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Language(s): eng - English
 Dates: 2004-01-272004-05-102004-11-222004-11-01
 Publication Status: Published in print
 Pages: 12
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Degree: -

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Title: Journal of Biomedical Optics
Source Genre: Journal
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Publ. Info: Bellingham, WA : Published by SPIE--the International Society for Optical Engineering in cooperation with International Biomedical Optics Society
Pages: - Volume / Issue: 9 (6) Sequence Number: - Start / End Page: 1253 - 1264 Identifier: ISSN: 1083-3668
CoNE: https://pure.mpg.de/cone/journals/resource/954925607859