CLI Task Guide#

This page groups the current CLI command surface by task.

It is a quick practical companion to the full CLI Reference.

Inspect one file#

swcstudio check ./data/single-soma.swc
swcstudio validate ./data/single-soma.swc
swcstudio rule-guide

Repair one file#

Validation-oriented edits:

swcstudio auto-fix ./data/single-soma.swc
swcstudio auto-label ./data/single-soma.swc
swcstudio radii-clean ./data/single-soma.swc
swcstudio index-clean ./data/single-soma.swc

Morphology edits:

swcstudio set-type ./data/single-soma.swc --node-id 14169 --new-type 3
swcstudio dendrogram-edit ./data/single-soma.swc --node-id 42 --new-type 3
swcstudio set-radius ./data/single-soma.swc --node-id 42 --radius 0.75

Geometry edits:

swcstudio simplify ./data/single-soma.swc
swcstudio connect ./data/single-soma.swc --start-id 10 --end-id 22
swcstudio disconnect ./data/single-soma.swc --start-id 10 --end-id 22
swcstudio move-subtree ./data/single-soma.swc --root-id 40 --x 100 --y 120 --z 5

Current single-file edit behavior:

  • the updated SWC is written automatically

  • the matching log is written automatically

  • both go into the source file’s *_swc_studio_output directory

Process a folder#

swcstudio validate ./data
swcstudio split ./data
swcstudio auto-typing ./data --soma --axon --basal
swcstudio radii-clean ./data
swcstudio simplify ./data
swcstudio index-clean ./data

Use temporary config overrides#

swcstudio validate ./data/single-soma.swc --config-json '{"checks":{"has_soma":{"enabled":true,"severity":"warning","params":{}}}}'