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New Methods for the Computer-Assisted 3D Reconstruction of Neurons from Confocal Image Stacks
Citation key Schmitt2004
Author Schmitt, S. and Evers, J.-F. and Duch, C. and Scholz, M. and Obermayer, K.
Pages 1283 – 1298
Year 2004
DOI doi:10.1016/j.neuroimage.2004.06.047
Journal Neuroimage
Volume 23
Number 4
Publisher Elsevier
Abstract Exact geometrical reconstructions of neuronal architecture are indispensable for the investigation of neuronal function. Neuronal shape is important for the wiring of networks, and dendritic architecture strongly affects neuronal integration and firing properties as demonstrated by modeling approaches. Confocal microscopy allows to scan neurons with submicron resolution. However, it is still a tedious task to reconstruct complex dendritic trees with fine structures just above voxel resolution. We present a framework assisting the reconstruction. User time investment is strongly reduced by automatic methods which fit a skeleton and a surface to the data, while the user can interact, and thus, keeps full control to ensure a high quality reconstruction. The reconstruction process comprises a successive gain of metric parameters. First a structural description of the neuron is built, including the topology and the exact dendritic lengths and diameters. We use generalized cylinders with circular cross-sections. The user provides a rough initialization by marking the branching points. The axes and radii are fitted to the data by minimizing an energy-functional which is regularized by a smoothness constraint. The investigation of proximity to other structures throughout dendritic trees requires a precise surface reconstruction. In order to achieve accuracy of 0.1 micron and below, we additionally implemented a segmentation algorithm based on geodesic active contours which allows for arbitrary cross-sections and uses locally adapted thresholds. In summary, this new reconstruction tool saves time and increases quality as compared to other methods which have previously been applied to real neurons.
Bibtex Type of Publication Selected:main selected:3dimages selected:publications
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