Extracting generalized cylinder models of dendritic trees from 3D image stacks

Fenglian Xu; Paul H. Lewis; John E. Chad; Howard V. Wheal

doi:10.1117/12.310548

9 June 1998 Extracting generalized cylinder models of dendritic trees from 3D image stacks

Fenglian Xu, Paul H. Lewis, John E. Chad, Howard V. Wheal

Proceedings Volume 3261, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing V; (1998) https://doi.org/10.1117/12.310548
Event: BiOS '98 International Biomedical Optics Symposium, 1998, San Jose, CA, United States

Abstract

The automatic reconstruction of 3D structures from stacks of 2D images is an important problem in medical image analysis. In neuroscience, in particular, the availability of explicit 3D models of the dendritic tree structure of a neuron can be a valuable tool for understanding the complexity of neuronal function and neuronal morphology In this work, the dendritic tree structure is imaged at different levels through the tissue using a laser scanning confocal microscope. The aim of the software is to deliver an explicit representation of the tree as a generalized cylinder model. Automatic techniques often fail to produce a continuous 3D model and manual or semi-automatic techniques can be particularly labor intensive.In this paper we describe algorithms which lead to a continuous 3D cylinder model representation of the dendritic tree with a minimum of user involvement. The initial stage of the approach involves the identification of voxels with a high probability of being on the center-lines of the dendritic structure. These points are linked to form a skeleton using cost minimization techniques. In the final stage the full 3D structure is extracted around the center- lines and represented by generalized cylinders. This paper provides details of the algorithms in each of the stages together with some of the results of using the method on both synthetic and real data sets.

Citation Download Citation

Fenglian Xu, Paul H. Lewis, John E. Chad, and Howard V. Wheal "Extracting generalized cylinder models of dendritic trees from 3D image stacks", Proc. SPIE 3261, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing V, (9 June 1998); https://doi.org/10.1117/12.310548

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