Parameter

Description

Channel

Sets the processing and analysis target channels.

Method

Sets the method for tracing neurons. Each has a set of settings which need to be properly adjusted to get the best result.

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Threshold-based Reconstructor

This method uses a threshold to separate the foreground from the background. The foreground is searched for connected pixels. These connected pixels are formed into paths and only paths that form a neuron skeleton structure will be kept and used to create a complete trace.

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Probabilistic Reconstructor

This method calculates the local tubularity of the image data. This tubularity map is searched for seed points. Starting from seed points, using a probability function (Monte-Carlo), trace parts are detected. These trace parts are then merge together to create the complete trace.

Threshold

Sets threshold value as the minimum intensity level of the tubular structures vs. the background.
Note: You can use the Picker or Calculator to determine the value.

Min. terminal section length

Sets the minimum branch length to be considered. Any structure smaller than this value will not be segmented.