File Loader
• Imaris 3, Imaris Classic
• Carl Zeiss LSM 310 - 510
• Leica 3D formats
• More formats can be processed by loading files into Imaris first and converting them to the Imaris 3 format
Filtering
• Gaussian filter
• Line filter
• Thresholding using intensity and connectivity
Segmentation
• Automatic neurite tracking using 3D isotropic dilatation
• Conversion of segmented skeleton into graph
• Visual segmentation control by visual overlaying microscopy slice with graph
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Graph Operations
• Various functions to select segments
• Delete side branches shorter than specified length
• Automatic measurement of segment length (individual and in total)
• Show/hide branch points
• Insert branch points
• Join segments manually
Measurements
• Measure individual segments
• Measure total length of selected segments
• Measure segments by branch level
Application
• Wizard-style user interface
• Export measurements in tabular format
• Export graph as inventor file, conversion to VRML using SGI tools
• NeuronTracer only runs on Irix.
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