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Journal Article

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

MPS-Authors
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Broser,  Philip Julian
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Lang,  Stefan
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Roth,  Arnd
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Helmchen,  Fritjof
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Waters,  David Jack
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Sakmann,  Bert
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Citation

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.


Cite as: https://hdl.handle.net/11858/00-001M-0000-002A-1508-8
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.