# SNT Tips -- common to both Traditional and Stream mode
# Lines starting with # are comments and will be ignored
# Tips are plain text, not HTML: '&', '<', '>' are escaped automatically
# 'ctrlKey()'' will be replaced by 'Cmd' on macOS; 'Ctrl' on linux/Windows
# 'mCrop()' will be replaced by 'Materialized crop — ' when in stream mode

# Navigation & Basic Shortcuts
mCrop() Press G to grab the path nearest to the cursor
mCrop() Hold Shift+G to grab multiple paths to your selection
mCrop() Press O to temporarily show path orientations (start→end direction)
Press H to temporarily hide all paths while held down
Use the Command Palette (ctrlKey()+Shift+P) to quickly find any action
mCrop() Press Enter to shuttle focus between the tracing image and the SNT window
Double-click on a bookmark to navigate directly to that location
Most shortcuts are single keystrokes and are highlighted in menus/dialogs
mCrop() Hold Spacebar or middle-click (scroll wheel button) to pan the canvas without changing tools
Press Z to undo the last traced segment or the last edit operation

# Tracing
mCrop() Enable cursor snapping (S) to auto-snap to the brightest nearby voxel
mCrop() Press V to auto-click on the brightest voxel above/below the cursor
Use Alt+Click on an existing path to fork a branch from the nearest node
mCrop() Use Ctrl+mouse wheel to assign diameters to paths being traced

# Path Editing
mCrop() Press Shift+E to enter Edit Mode
mCrop() In Edit Mode: D deletes, M moves, I inserts, and B brings nodes to the current Z-plane
mCrop() In Edit Mode: Alt+drag a node to reposition it
mCrop() Press R in Edit Mode to change the radius of the active node
mCrop() Press L in Edit Mode to lock a node and prevent accidental changes
mCrop() Press X in Edit Mode to split a tree at the active node
mCrop() Press C in Edit Mode to connect the active node to a nearby path
mCrop() Press T in Edit Mode to tag the active node with a color label
mCrop() Press P in Edit Mode to toggle Paint Mode for brush editing
mCrop() In Paint Mode: drag to move nodes with a Gaussian brush; Alt+drag to blend radii from the center node
mCrop() In Paint Mode: use Ctrl+mouse wheel to adjust the brush radius

# Analysis
Use Quick Measurements for instant metrics without prompts
Color-code paths by morphometric properties via Path Manager→Analyze→Color Mapping
mCrop() Run Sholl Analysis from any node using Alt+Shift+A
Create dendrograms using Analysis→Utilities→Create Dendrogram
Use Path Profiler to visualize intensity gradients along traced neurites
Compare cell groups statistically via Analysis→Utilities→Compare Reconstructions...

# Visualization
mCrop() Press 1/2/3 to toggle visibility filters for paths (Main tab)
Use the Reconstruction Viewer (3D tab) for interactive 3D visualization of tracings
Export publication-quality figures via Reconstruction Plotter (supports PDF/SVG)
Use Create Figure to generate multi-panel montages of reconstructions
Use sciview (3D tab) for immersive 3D visualization powered by the scenery rendering engine

# Data Management
Save tracings with ctrlKey()+S; use ctrlKey()+Shift+S for a timestamped backup
Use File→Revert to Backup... to restore from previous saves
Drag and drop SWC/TRACES files directly into the Path Manager to import them
Use the Script Recorder (Scripts menu) to generate code from GUI actions

# REPL & Scripting (since v5.0.3)
The REPL now features syntax highlighting for easier interactive scripting

# Reconstruction Viewer (since v5.0.4)
Rec. Viewer: Double-click to auto-rotate the scene; Shift+double-click forces Z-axis rotation
Rec. Viewer: Use 'Ping-pong' animation mode (Settings→Animation Type) for a gentle back-and-forth tilt instead of full 360° spins
Rec. Viewer: Use 'Anatomical Mapping...' (Scene Controls→Axes) to label scene axes with anatomical orientations
Rec. Viewer: Choose between Simple Lines, Pseudo-Lighting, or Shaded Tubes to render neurites (Settings→Neurite Style)
Rec. Viewer: Enable Path Smoothing (Settings) to apply Catmull-Rom interpolation and reduce kinks at line joints
Rec. Viewer: Enable Depth Perception (Settings) to fade distant neurites toward the background for depth cues
Rec. Viewer: Add a scale bar overlay to the 3D scene via Scene Controls→Scale Bar
Rec. Viewer: Mesh rendering supports Smooth Shading for per-fragment Phong lighting (Settings→Mesh Style)
Rec. Viewer: Use 'Align View to Tree' to snap the camera to a cell's bounding box orientation

# Curation & Proofreading (since v5.0.X)
Use the Peripath Detector (Analysis→Spines/Varicosities) to detect spines and varicosities along paths
Use the AlongPath Detector (Analysis→Spines/Varicosities) to detect enlargements (blebs/boutons/varicosities) along paths
The Spacing Analysis template script quantifies inter-spine or inter-varicosity distances

# Curation Assistant (since v5.0.X)
Use the Curation Assistant to flag statistical outliers—potential tracing errors—across your reconstructions
Curation parameters persist across sessions, so calibrated thresholds carry over to future work
Use the Plausibility Calibrator in the Curation Assistant to derive curation thresholds from trusted reference cells
