Before setting the Neuron Tracer parameters, run the Blob Finder operation.

Parameter

Description

Channel

Sets the processing and analysis target channels.

Cell body

Sets the output of another operation as an input. It is recommended to select the Output of the Blob Finder operation as input.

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 the threshold values accordingly to the image dynamic range.
Note: You can use the Picker or Calculator to determine the value.

Keep only neurites connected to a cell body

Sets that all traces that are not connected to a cell body should be filtered out.

Min. terminal section length

Sets the minimum length of a trace's terminal sections. Any terminal section with a length smaller than this value will be filtered out.