The following operations are part of the pipeline.
Pipeline operations layout
Input ROI
This operation allows to select the region of interest (ROI). ROI defines the dataset subarea that will be processed and analyzed by the pipeline.
Blob Finder
Automatic objects detection algorithm. It works on small and roundish structures, and it is used to segment the neuron cell body.
Neuron Tracer
Sets threshold value as the minimum intensity level of the tubular structures vs. the background.
Neuron Trace parameters
Before setting the Neuron Tracer parameters, run the Blob Finder operation.
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Parameter |
Description |
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Channel |
Sets the processing and analysis target channels. |
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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. |
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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. |
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Threshold |
Sets the threshold values accordingly to the image dynamic range. |
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Keep only neurites connected to a cell body |
Sets that all traces that are not connected to a cell body should be filtered out. |
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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. |
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Store Objects
Store the detected segments (tag) in the active dataset.