IO Overview

IO Overview#

Loading a morphology is almost always a one-liner using a Morphology.from_* constructor. Each reader parses a file (or a downloaded record), validates it, and returns a braincell.Morphology ready to wrap in a Cell.

import braincell

morpho = braincell.Morphology.from_swc("neuron.swc")
morpho = braincell.Morphology.from_asc("neuron.asc")
morpho = braincell.Morphology.from_neuromorpho(12345)   # NeuroMorpho.Org neuron id

Validation reports#

Reconstructions are messy: disconnected points, missing soma, unknown structure identifiers. Instead of failing on the first problem (or silently guessing), the SWC reader can hand back a report describing what it found and fixed. Pass return_report=True:

morpho, report = braincell.Morphology.from_swc("messy.swc", return_report=True)
print(report)        # SwcReport: issues, fixes applied, summary

The report types (SwcReport, SwcIssue, and the ASC equivalents) let you decide programmatically whether a reconstruction is clean enough to trust.

Reader options#

Readers accept an options object to control validation strictness. For SWC, SwcReadOptions controls things like:

  • standardize_safe_fixes — automatically apply safe corrections;

  • unknown_type_as_custom — map unrecognized structure ids to CustomBranch instead of erroring;

  • require_root_type_soma — enforce that the root is a soma.

from braincell.io import SwcReadOptions

opts = SwcReadOptions(unknown_type_as_custom=True)
morpho = braincell.Morphology.from_swc("neuron.swc", options=opts)

Saving and reloading#

To persist a braincell morphology (after editing, say) and reload it later, use the checkpoint helpers — see Checkpointing.

Where to go next#