Axons#

Expert axon image processing pipeline.

This module provides the basic routines for processing axon data. The routines are used in the ClearMap.Scripts.AxonMap pipeline.

binary_statistics(source)[source]#

Counts the binarization types.

Arguments

sourcearray: The status array of the binarization process.

Returns

statisticsdict: A dict with entires {description : count}.

clip(source, clip_range, norm, dtype)[source]#: Clips lower and rescales to higher clip range

deconvolve(source, binarized, sigma=10)[source]#

equalize(source, percentile=(0.5, 0.95), max_value=1.5, selem=(200, 200, 5), spacing=(50, 50, 5), interpolate=1, mask=None)[source]#

preprocess(source, sink=None, parameter=None, processing_parameter=None)[source]#

preprocess_block(source, sink, parameter)[source]#: Preprocess a Block.

status_to_description(status)[source]#

Converts a status int to its description.

Arguments

statusint: The status.

Returns

descriptionstr: The description corresponding to the status.

threshold_adaptive(source, function=<function threshold_isodata>, selem=(100, 100, 3), spacing=(25, 25, 3), interpolate=1, mask=None, step=None)[source]#

threshold_isodata(source)[source]#

tubify(source, sigma=1.0, gamma12=1.0, gamma23=1.0, alpha=0.25)[source]#