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          Institute: MPI für biologische Kybernetik     Collection: Biologische Kybernetik     Display Documents

ID: 419921.0, MPI für biologische Kybernetik / Biologische Kybernetik
Contour-propagation Algorithms for Semi-automated Reconstruction of Neural Processes
Authors:Macke, J.H.; Maack, N.; Gupta, R.; Denk, W.; Schölkopf, B.; Borst, A.
Date of Publication (YYYY-MM-DD):2008-01
Title of Journal:Journal of Neuroscience Methods
Issue / Number:2
Start Page:349
End Page:357
Audience:Not Specified
Intended Educational Use:No
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 10-20nm in the x and y- and 30nm
in z-direction. Consequently, a tissue block of 1mm3 (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 semiautomated
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.
External Publication Status:published
Document Type:Article
Communicated by:Holger Fischer
Affiliations:MPI f�r biologische Kybernetik/Empirical Inference (Dept. Sch�lkopf)
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