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• W1566652377 abstract "A basic requirement for reconstructing and understanding complete circuit diagrams ofneuronal processing units is the availability of electron microscopic 3D data sets of largeensembles of neurons. A recently developed technique, Serial Block Face Scanning ElectronMicroscopy (SBFSEM, Denk and Horstmann 2004) allows automatic sectioning andimaging of biological tissue inside the vacuum chamber of a scanning electron microscope.Image stacks generated with this technology have a resolution sucient to distinguish differentcellular compartments, including synaptic structures. Such an image stack containsthousands of images and is recorded with a voxel size of 23 nm in the x- and y-directionsand 30 nm in the z-direction. Consequently a tissue block of 1 mm3 produces 63 terabytesof data.Therefore new concepts for managing large data sets and automated image processingare required. I developed an image segmentation and 3D reconstruction software, whichallows precise contour tracing of cell membranes and simultaneously displays the resulting3D structure. The software contains two stand-alone packages: Neuron2D and Neuron3D,both oering an easy-to-operate graphical user interface (GUI).The software package Neuron2D provides the following image processing functions:• Image Registration: Combination of multiple SBFSEM image tiles.• Image Preprocessing: Filtering of image stacks. Implemented are Gaussian andNon-Linear-Diusion lters in 2D and 3D. This step enhances the contrast betweencontour lines and image background, leading to a higher signal-to-noise ratio, thusfurther improving detection of membrane borders.• Image Segmentation: The implemented algorithms extract contour lines from thepreceding image and automatically trace the contour lines in the following images(z-direction), taking into account the previous image segmentation. They also permitimage segmentation starting at any position in the image stack. In addition, manualinteraction is possible.To visualize 3D structures of neuronal circuits the additional software Neuron3D wasdeveloped. The program relies on the contour line information provided by Neuron2D toimplement a surface reconstruction algorithm based on dynamic time warping. Additionalrendering techniques, such as shading and texture mapping, are provided.The detailed anatomical reconstruction provides a framework for computational modelsof neuronal circuits. For example in ies, where moving retinal images lead to appropriatecourse control signals, the circuit reconstruction of motion-sensitive neurons can help tofurther understand the neural processing of visual motion in ies." @default.
• W1566652377 created "2016-06-24" @default.
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• W1566652377 date "2007-04-01" @default.
• W1566652377 modified "2023-09-26" @default.
• W1566652377 title "3D Reconstruction of Neural Circuits from Serial EM Images" @default.
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