Contour-propagation algorithms for semi-automated reconstruction of neural processes

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, i...

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Bibliographic Details
Published in:Journal of neuroscience methods Vol. 167; no. 2; pp. 349 - 357
Main Authors: Macke, Jakob H., Maack, Nina, Gupta, Rocky, Denk, Winfried, Schölkopf, Bernhard, Borst, Alexander
Format: Journal Article
Language:English
Published: Netherlands Elsevier B.V 30.01.2008
Subjects:
Algorithm
Algorithms
Animals
Automatic Data Processing - methods
Brain - cytology
Brain - ultrastructure
Circuit reconstruction software
Contour detection
Fly visual system
Image Processing, Computer-Assisted
Image segmentation
Insecta
Microscopy, Electron, Scanning - instrumentation
Neural circuits
Neurons - ultrastructure
Serial block-face scanning electron microscopy
Image segmentation
Neural circuits
Contour detection
Fly visual system
Circuit reconstruction software
Serial block-face scanning electron microscopy
Algorithm
ISSN:0165-0270, 1872-678X
Online Access:Get full text
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Summary: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 nm 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.
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ISSN:0165-0270
1872-678X
DOI:10.1016/j.jneumeth.2007.07.021