Checkpointing

Once you have loaded and possibly edited a morphology, you can persist it to disk and reload it later without re-parsing the original reconstruction. This is useful for caching a cleaned-up morphology or sharing a processed cell.

Saving and loading a morphology

import braincell
import braincell.io as io

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

path = io.save_morpho(morpho, "neuron.bcm")   # returns the written Path
morpho = io.load_morpho("neuron.bcm")

For a single branch there are matching helpers:

io.save_branch(branch, "branch.bcb")
branch = io.load_branch("branch.bcb")

Versioning and errors

Checkpoints are versioned. If you load a file written by an incompatible version, the loaders raise a clear error:

• CheckpointError — a checkpoint could not be read.

• CheckpointVersionError — the checkpoint’s format version is not supported by the installed braincell.

from braincell.io import CheckpointVersionError

try:
    morpho = io.load_morpho("old.bcm")
except CheckpointVersionError as e:
    print("Re-export from the source file:", e)

See also

• IO Overview — loading from the original formats.

• braincell.io module — the full checkpoint API.