CLI Tutorial#

This tutorial walks through the current command-line workflow for inspecting a file, applying edits, and reviewing the generated outputs.

Before you start#

Note

You need a working CLI install and one or more SWC files. If the command is not on your path, use module mode from Getting Started.

The examples below use macOS or Linux path style. On Windows, replace ./data/... with .\data\....

Step 1: Verify the CLI#

swcstudio --help

Module-mode fallback:

python -m swcstudio.cli.cli --help

Step 2: Inspect one file with check#

Start with the combined issue view:

swcstudio check ./data/single-soma.swc

This command prints the same shared issue list logic used by the GUI. It is the fastest way to see:

  • validation findings

  • suspicious radii suggestions

  • likely wrong-label suggestions

  • simplification suggestions

Step 3: Run grouped validation#

swcstudio validate ./data/single-soma.swc

Use this when you want the full grouped validation report rather than the broader issue summary from check.

If you only want the validation guide:

swcstudio rule-guide

Step 4: Apply a targeted edit#

Choose the command that matches the issue you want to fix.

Examples:

swcstudio index-clean ./data/single-soma.swc
swcstudio auto-fix ./data/single-soma.swc
swcstudio auto-label ./data/single-soma.swc
swcstudio set-type ./data/single-soma.swc --node-id 14169 --new-type 3
swcstudio set-radius ./data/single-soma.swc --node-id 42 --radius 0.75
swcstudio connect ./data/single-soma.swc --start-id 10 --end-id 22

Single-file edit commands automatically write:

  • the updated SWC file

  • the matching operation log

to the default *_swc_studio_output directory for the source file.

Step 5: Use batch commands for folders#

When you need the same operation across many files, use folder commands.

Examples:

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

Step 6: Use temporary config overrides#

Most commands accept --config-json so you can override parameters for one run without editing the default config files.

Example:

swcstudio simplify ./data/single-soma.swc --config-json '{"thresholds":{"epsilon":1.2,"radius_tolerance":0.35}}'

Step 7: Review outputs and logs#

For single-file edits, open the source file’s default output folder:

  • <stem>_swc_studio_output

Typical files there include:

  • edited SWC copies

  • validation reports

  • per-operation text logs