Quick and easy analysis

The neurom.ezy module

The neurom.ezy module brings together various neurom components and helper functions to simplify loading neuron morphologies from files into neurom data structures and obtaining morphometrics, either from single or multiple neurons. The functionality is limited, but it is hoped that it will suffice for most analyses.

These are some of the properties can be obtained for a single neurite type or for all neurites regardless of type via the neurom.ezy.get function:

  • Segment lengths
  • Section lengths
  • Segment radii
  • Number of sections
  • Number of sections per neurite
  • Number of neurites
  • Number of segments
  • Local and remote bifurcation angles
  • Section path distances
  • Section radial distances
  • Section branch orders
  • Total neurite length

This function also allows obtaining the soma radius and surface area.

There are also helper functions to plot a neuron in 2 and 3 dimensions.

See also

The neurom.ezy documentation for more details and examples.

Data checking applications

There are two user-friendly data checking applications. raw_data_check checks for basic consistency of raw data, and morph_check applies some further semantic checks to the data in order to determine whether it is suitable to construct a neuron structure and whether certain defects within the structure are detected. Both can be invoked from the command line, and take as main argument the path to either a single file or a directory of morphology files.

For example,

$ morph_check test_data/swc/Neuron.swc # single file
INFO: ========================================
INFO: Check file test_data/swc/Neuron.swc...
INFO:                     Has valid soma? PASS
INFO:               All points connected? PASS
INFO:                 Has basal dendrite? PASS
INFO:                           Has axon? PASS
INFO:                Has apical dendrite? PASS
INFO:            Nonzero segment lengths? PASS
INFO:            Nonzero section lengths? PASS
INFO:              Nonzero neurite radii? PASS
INFO:                       Check result: PASS
INFO: ========================================

$ morph_check test_data/swc # all files in directory
# loops over all morphology files found in test_data/swc

For more information, use the help option:

$ morph_check --help
....

$ raw_data_check --help
....