Morphology parsers

BsbParser

This is the default parser. It only parses SWC files, but it allows you to create as many different SWC tags as you want, and can assign labels based on these tags. This allows you to create a rich annotation system on top of the SWC format to denote dendritic spines, axonal myelination with saltatory conduction, or any other morphological feature.

PYTHON

from bsb.morphologies.parsers.parser import BsbParser

BsbParser(
  cls='builtins.str',
  branch_cls='builtins.str',
  parser='bsb',
  tags={},
  skip_boundary_labels=[],
)

JSON

{
    "cls": "builtins.str",
    "branch_cls": "builtins.str",
    "parser": "bsb",
    "tags": {},
    "skip_boundary_labels": []
}

YAML

branch_cls: builtins.str
cls: builtins.str
parser: bsb
skip_boundary_labels: []
tags: {}

The default SWC tags are 1 for soma, 2 for axon, and 3 for dendrites. You can add/overwrite tags by setting the tags attribute:

{
  "parser": "bsb",
  "tags": {
    4: ["dendrites", "apical_dendrites"],
    5: ["dendrites", "basal_dendrites"],
    6: ["axon", "axon_initial_segment"],
    7: ["axon", "axon_hillock"],
    8: ["axon", "myelin"],
    9: ["axon", "myelin", "node_of_ranvier"]
  }
}

The soma is usually approximated as a stack of cylinders, this means that

MorphIOParser

PYTHON

from bsb.morphologies.parsers.parser import MorphIOParser

MorphIOParser(
  cls='builtins.str',
  branch_cls='builtins.str',
  parser='bsb',
  flags=[],
)

JSON

{
    "cls": "builtins.str",
    "branch_cls": "builtins.str",
    "parser": "bsb",
    "flags": []
}

YAML

branch_cls: builtins.str
cls: builtins.str
flags: []
parser: bsb