GUI Tutorial#

This tutorial walks through the main desktop workflow for reviewing one SWC file, letting issues guide the repair process, and saving the result.

Before you start#

Note

You need a working GUI install and at least one SWC file. If needed, start with Getting Started.

Start the application:

swcstudio-gui

Step 1: Open a file#

Open an SWC file from the File menu.

After loading:

  • the file appears in the central workspace

  • the left-side Issues and SWC File panels are populated for the active document

  • validation is triggered automatically for a normal editable document when no prior validation report exists

Step 2: Review the issue list#

The Issues panel is the center of the desktop workflow.

It can include:

  • validation findings

  • blocked prerequisite summaries

  • suspicious radii suggestions

  • likely wrong-label suggestions

  • a simplification suggestion

This means the panel acts as a guided repair queue, not only as a validation dump.

Step 3: Select one issue#

When you click an issue, the GUI:

  1. focuses the relevant nodes in the active document

  2. updates the inspector with the issue description and suggested solution

  3. routes the right-side controls to the matching repair tool when appropriate

Examples:

  • index issues route to Validation -> Index Clean

  • label issues route to Morphology Editing

  • radii issues route to radii editing controls

  • topology issues route to geometry editing

Step 4: Apply a repair#

Use the routed tool to apply the fix.

Common repair paths:

  • Index Clean

  • Manual Label Editing

  • Auto Label Editing — runs the auto-typing engine. The bundled model files work out of the box, so just click Run. To use custom-trained models, use the Browse… button next to the Model dir field. The green/red status indicator next to the field tells you whether the engine can run with the current selection. Use the cell-type selector when you already know whether the cell is pyramidal or interneuron; leave it unknown to run Stage 1. The flag strictness slider controls how conservatively the bad-label flagger marks a cell.

  • Manual Radii Editing

  • Auto Radii Editing

  • Geometry Editing

  • Simplification

Step 5: Define custom types when needed#

If your file uses custom SWC type IDs, define them from the dendrogram editing controls with Add/Edit Types.

Each custom type can store:

  • type ID

  • name

  • color

  • notes

These definitions persist across restarts, so once they are saved they remain available the next time you open the app.

Step 6: Rerun validation#

After a repair, rerun validation and review the refreshed issue list.

This is the main loop:

  1. inspect

  2. route

  3. repair

  4. validate again

Continue until the important issues are resolved or reduced to acceptable warnings for your workflow.

Step 7: Save and review outputs#

Save the document or close the tab.

The GUI keeps:

  • the source SWC updated with the current state

  • an encrypted history archive next to the SWC

Open the History Browser to review operation summaries and expandable node-level old/new values. Use Commit History only when you need the exact internal version ID for technical review.

Selecting an operation and choosing Undo selected and later operations restores the document to immediately before that operation. The selected operation and all later operations are removed from the current state, but remain recoverable in history. Commit History instead restores the exact selected saved state.