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  3D Reconstruction of Neural Circuits from Serial EM Images

Maack, N., Kapfer, C., Macke, J., Schölkopf, B., Denk, W., & Borst, A. (2007). 3D Reconstruction of Neural Circuits from Serial EM Images. Poster presented at 7th Meeting of the German Neuroscience Society, 31st Göttingen Neurobiology Conference, Göttingen, Germany.

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Maack, N, Author
Kapfer, C, Author
Macke, JH1, 2, Author           
Schölkopf, B2, 3, Author           
Denk, W, Author
Borst, A, Author           
1Research Group Computational Vision and Neuroscience, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497805              
2Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497794              
3Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              


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 Abstract: The neural processing of visual motion is of essential importance for course control. A basic model suggesting a possible mechanism of how such a computation could be implemented in the fly visual system is the so called "correlation-type motion detector" proposed by Reichardt and Hassenstein in the 1950s. The basic requirement to reconstruct the neural circuit underlying this computation is the availability of electron microscopic 3D data sets of whole ensembles of neurons constituting the fly visual ganglia. We apply a new technique,"Serial Block Face Scanning Electron Microscopy" (SBFSEM), that allows for an automatic sectioning and imaging of biological tissue with a scanning electron microscope [Denk, Horstman (2004) Serial block face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLOS Biology 2: 1900-1909]. Image Stacks generated with this technology have a resolution sufficient to distinguish different cellular compartments, especially synaptic structures. Consequently detailed anatomical knowledge of complete neuronal circuits can be obtained. Such an image stack contains several thousands of images and is recorded with a minimal voxel size of 25nm in x and y and 30nm in z direction. Consequently a tissue block of 1mm³ (volume of the Calliphora vicina brain) produces several hundreds terabyte of data. Therefore new concepts for managing large data sets and for automated 3D reconstruction algorithms need to be developed. We developed an automated image segmentation and 3D reconstruction software, which allows a precise contour tracing of cell membranes and simultaneously displays the resulting 3D structure. In detail, the software contains two stand-alone packages: Neuron2D and Neuron3D, both offer an easy-to-operate Graphical-User-Interface. Neuron2D software provides the following image processing functions: • Image Viewer: Display image stacks in single or movie mode and optional calculates intensity distribution of each image. • Image Preprocessing: Filter process of image stacks. Implemented filters are a Gaussian 2D and a Non-Linear-Diffusion Filter. The filter step enhances the contrast between contour lines and image background, leading to an enhanced signal to noise ratio which further improves detection of membrane structures. • Image Segmentation: The implemented algorithm extracts contour lines from the preceding image and automatically traces the contour lines in the following images (z-direction), taking into account the previous image segmentation. In addition, a manual interaction is possible. To visualize 3D structures of neuronal circuits the additional software Neuron3D was developed. The reconstruction of neuronal surfaces from contour lines, obtained in Neuron2D, is implemented as a graph theory approach. The reconstructed anatomical data can further provide a subset for computational models of neuronal circuits in the fly visual system.


 Dates: 2007-02
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: BibTex Citekey: 4347
 Degree: -


Title: 7th Meeting of the German Neuroscience Society, 31st Göttingen Neurobiology Conference
Place of Event: Göttingen, Germany
Start-/End Date: 2007-03-29 - 2007-04-01

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Title: Neuroforum
Source Genre: Journal
Hoffmann, K-P, Editor
Krieglstein , K, Editor
Publ. Info: -
Pages: - Volume / Issue: 13 (Supplement) Sequence Number: T37-3C Start / End Page: 1195 Identifier: ISSN: 0947-0875
CoNE: https://pure.mpg.de/cone/journals/resource/110978984249776