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          Institute: MPI für Neurobiologie     Collection: Systems and Computational Neurobiology     Display Documents



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ID: 400795.0, MPI für Neurobiologie / Systems and Computational Neurobiology
Contour-propagation algorithms for semi-automated reconstruction of neural processes
Authors:Macke, J. H.; Maack, N.; Gupta, R.; Denk, W.; Schölkopf, B.; Borst, A.
Language:English
Date of Publication (YYYY-MM-DD):2008-01-30
Title of Journal:Journal of Neuroscience Methods
Journal Abbrev.:J. Neurosci. Methods
Volume:167
Issue / Number:2
Start Page:349
End Page:357
Review Status:Peer-review
Audience:Not Specified
Abstract / Description:A new technique, "serial block face scanning electron microscopy" (SBFSEM), allows for automatic sectioning and imaging of biological tissue with a scanning electron microscope. Image stacks generated with this technology have a resolution sufficient to distinguish different cellular compartments, including synaptic structures, which should make it possible to obtain detailed anatomical knowledge of complete neuronal circuits. Such an image stack contains several thousands of images and is recorded with a minimal voxel size of 10-20 nm in the x- and y-direction and 30 mu in Z-direction. Consequently, a tissue block of 1 mm(3) (the approximate volume of the Calliphora vicina brain) will produce several hundred terabytes of data. Therefore, highly automated 3D reconstruction algorithms are needed. As a first step in this direction we have developed semi-automated segmentation algorithms for a precise contour tracing of cell membranes. These algorithms were embedded into an easy-to-operate user interface, which allows direct 3D observation of the extracted objects during the segmentation of image stacks. Compared to purely manual tracing, processing time is greatly accelerated. (c) 2007 Elsevier B.V. All rights reserved.
Free Keywords:circuit reconstruction software; contour detection; algorithm; image segmentation; serial block-face scanning electron microscopy; neural circuits; fly visual system
External Publication Status:published
Document Type:Article
Affiliations:MPI für Neurobiologie/Systems and Computational Neurobiology (Borst)
MPI für biologische Kybernetik/Empirical Inference (Dept. Schölkopf)
MPI für medizinische Forschung/Abteilung Biomedizinische Optik
External Affiliations:Indian Inst Technol, Dept Elect Engn, Kanpur 208016, Uttar Pradesh, India
Identifiers:ISI:000252938400026 [ID No:1]
ISSN:0165-0270 [ID No:2]
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