Simplification Tutorial#

Simplification reduces redundant SWC geometry while preserving the main tree structure.

This page keeps the older filename for compatibility, but the current feature name in the app is Simplification.

Backend and config#

Current implementation path:

  • swcstudio.tools.morphology_editing.features.simplification

Current config file:

  • swcstudio/tools/morphology_editing/configs/simplification.json

Main parameters#

  • thresholds.epsilon

  • thresholds.radius_tolerance

  • flags.keep_tips

  • flags.keep_bifurcations

  • flags.keep_roots

Parameter guidance#

  • lower epsilon

    • keeps more geometry detail

  • higher epsilon

    • removes more intermediate points

  • lower radius_tolerance

    • protects more radius-sensitive nodes

  • higher radius_tolerance

    • allows stronger decimation around radius variation

CLI usage#

Run simplification on one file:

swcstudio simplify cell.swc

Use temporary overrides for one run:

swcstudio simplify cell.swc --config-json '{"thresholds":{"epsilon":1.2,"radius_tolerance":0.35},"flags":{"keep_tips":true,"keep_bifurcations":true}}'

Current single-file behavior:

  • 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

GUI usage#

In Geometry Editing -> Simplification:

  1. open the source SWC

  2. adjust the JSON config if needed

  3. run simplification

  4. review the updated morphology

  5. save or close the document to keep the source SWC updated and record the operation in history