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 cell.swc
swcstudio validate cell.swc
swcstudio rule-guide

Repair one file#

Validation-oriented edits:

swcstudio auto-fix cell.swc
swcstudio auto-label cell.swc
swcstudio radii-clean cell.swc
swcstudio index-clean cell.swc

Morphology edits:

swcstudio set-type cell.swc --node-id 14169 --new-type 3
swcstudio dendrogram-edit cell.swc --node-id 42 --new-type 3
swcstudio set-radius cell.swc --node-id 42 --radius 0.75

Geometry edits:

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

Current single-file edit behavior:

  • auto-label always applies soma, axon, and basal labeling

  • apical labeling is detected automatically when appropriate

  • --cell-type pyramidal / --cell-type interneuron bypasses Stage 1 when the user already knows the cell type

  • flag scoring is enabled by default; --flag-strictness tunes loose vs conservative flagging and --no-flag disables it

  • the source SWC is updated automatically

  • the operation is recorded in <stem>_history.swcstudio

  • SWC/SWC+ comment headers are preserved while # @PROV pointers are updated

Process a folder#

swcstudio validate ./swc-folder
swcstudio split ./swc-folder
swcstudio auto-typing ./swc-folder
swcstudio radii-clean ./swc-folder
swcstudio simplify ./swc-folder
swcstudio index-clean ./swc-folder

Use temporary config overrides#

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