NDLI: Automated three-dimensional tracing of neurons in confocal and brightfield images.

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Automated three-dimensional tracing of neurons in confocal and brightfield images.

Content Provider	Semantic Scholar
Author	He, Wenyun Hamilton, Thomas A. Cohen, Andrew R. Roysam, Badrinath
Copyright Year	2003
Abstract	Automated three-dimensional (3-D) image analysis methods are presented for tracing of dye-injected neurons imaged by fluorescence confocal microscopy and HRP-stained neurons imaged by transmitted-light brightfield microscopy. An improved algorithm for adaptive 3-D skeletonization of noisy images enables the tracing. This algorithm operates by performing connectivity testing over large N x N x N voxel neighborhoods exploiting the sparseness of the structures of interest, robust surface detection that improves upon classical vacant neighbor schemes, improved handling of process ends or tips based on shape collapse prevention, and thickness-adaptive thinning. The confocal image stacks were skeletonized directly. The brightfield stacks required 3-D deconvolution. The results of skeletonization were analyzed to extract a graph representation. Topological and metric analyses can be carried out using this representation. A semiautomatic method was developed for reconnection of dendritic fragments that are disconnected due to insufficient dye penetration, an imaging deficiency, or skeletonization errors.
Starting Page	296
Ending Page	310
Page Count	15
File Format	PDF HTM / HTML
Alternate Webpage(s)	http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=E9B1C74308225B71D316E3C210CFA94A?doi=10.1.1.84.1211&rep=rep1&type=pdf
Alternate Webpage(s)	http://www.ecse.rpi.edu/~roysam/PDF/J35.pdf
PubMed reference number	12901764v1
Volume Number	9
Issue Number	4
Journal	Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
Language	English
Access Restriction	Open
Subject Keyword	Brightfield Microscopy Dyes Fluorescence Graph - visual representation Handling (Psychology) Horseradish Peroxidase Inborn Errors of Metabolism Microscopy, Confocal algorithm disease transmission
Content Type	Text
Resource Type	Article

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