SWC

SWC#

SWC is the most widely used morphology format: a plain-text table where each row is a sample point with an id, a structure type, (x, y, z) coordinates, a radius, and a parent id. It is the default export of most reconstruction tools and the primary download format on NeuroMorpho.Org.

Loading#

import braincell

morpho = braincell.Morphology.from_swc("neuron.swc")

from_swc accepts:

  • path — the file to read.

  • options — a SwcReadOptions controlling validation.

  • mode — a named validation preset.

  • return_report — when True, also return an SwcReport.

morpho, report = braincell.Morphology.from_swc("neuron.swc", return_report=True)

Structure types#

SWC structure identifiers map onto braincell’s typed branches:

SWC id

Structure

braincell type

1

soma

Soma

2

axon

Axon

3

(basal) dendrite

BasalDendrite

4

apical dendrite

ApicalDendrite

other

custom

CustomBranch

So once an SWC file is loaded, region selectors like branch_in("type", "soma") work immediately (see Regions & Locsets).

Validation options#

SwcReadOptions controls how forgiving the reader is:

from braincell.io import SwcReadOptions

opts = SwcReadOptions(
    standardize_safe_fixes=True,   # apply safe automatic corrections
    unknown_type_as_custom=True,   # don't error on unknown structure ids
    require_root_type_soma=False,  # allow non-soma roots
)
morpho = braincell.Morphology.from_swc("neuron.swc", options=opts)

The lower-level reader#

Morphology.from_swc is a convenience wrapper over braincell.io.SwcReader, which you can use directly when you want to check a file without building a morphology:

from braincell.io import SwcReader

reader = SwcReader()
report = reader.check("neuron.swc")   # validate only
morpho = reader.read("neuron.swc")    # parse to a Morphology

See braincell.io module for the full reader, options, and report API.