UI Tour

Every panel and button in LEAF, mapped. Use this when you can't find a setting or aren't sure what something does.

[Screenshot: full LEAF window with regions labeled — top bar, sidebar, main content, floating action button]

Top action bar

Always visible. Spans the full width.

Element	What it does
LEAF logo (left)	Returns to the home page
View tabs	Switch between Extract, Peak Picking, Untargeted, Visualize
Visualize dropdown	Open a statistical chart (PCA, heatmap, volcano, ...)
Download button	Open the export dialog (.msd / .csv)
Settings gear	Storage paths, theme, advanced options

Floating action button

Bottom-right corner. Appears whenever a job is running.

Color	State	Click action
Blue + spinner	Job in progress	Open jobs panel for progress details
Green + checkmark	Job done	Open jobs panel — Download or Open results
Red + warning	Job failed	Open jobs panel for error details

Extract view

The landing page after loading. Use this to launch new analyses.

[Screenshot: Extract view fully labeled]

Region	Element	What it does
Top	Targeted / Untargeted toggle	Switch the page mode
Top-left	Folder selector	Pick the folder of RAW files
Center	Compound list editor	Upload, edit, validate the metabolite CSV (targeted only)
Right (top)	Parameters sidebar	Polarity, mass tolerance, RT window, peak picking, scoring
Right (bottom)	Tracing editor	Configure isotopologues
Bottom-right	Start Processing	Launch the run (turns blue when ready)

Peak Picking view (Charts tab)

Where you inspect targeted results. Loads after extraction or when you open a .msd.

[Screenshot: Peak Picking view fully labeled]

Region	Panel	What it does
Left sidebar	Sample selector	Toggle samples, group them, switch pick mode
Top-left	Metabolite table	Pick a compound — drives all other panels
Top-right	EIC chart	Chromatogram overlay across selected samples
Top-right (tab 2)	RT check	Manual vs auto-detected RT scatter + outlier table
Bottom-left	Isotopologue bars	M+0, M+1, ... distribution
Bottom-right	Quality info	Verdict (good/warning/poor) + warnings

Sample selector (left sidebar)

Element	What it does
Sample checkbox	Toggle whether the sample appears on charts
Lightning-bolt icon	Auto-group by sample-name prefix
Group color swatches	Show / change group colors
Pick mode toggle	Area Top (apex) ↔ Area Sum (integrated area)

Untargeted view

Loads after an untargeted extraction or when you open a .usd.

Panel	What it does
Feature table	Every detected feature with m/z, RT, detection rate
EIC chart	Chromatogram for the selected feature
Alignment panel	RT alignment quality across samples
Gap-group panel	Features that should align but don't
Stats panel	Per-feature group comparisons
Results panel	Filter, tag, export

Visualize views

Each chart has the same shell:

Region	What it does
Center	Plotly chart — interactive (zoom, hover, pan)
Right sidebar (collapsible)	Chart-specific settings (normalization, clustering, thresholds)
Top-right of chart	Plotly toolbar — download PNG, zoom, reset

Job panel (slide-out)

Click the floating action button to open. Lists every job from the current session.

Element	What it does
Job row	Status badge + sample count + filename
Progress bar	% complete (live during runs)
Download	Open the export dialog with this job's data preselected
Open	Load the result into Peak Picking / Untargeted view
Cancel	Stop a running job

Settings (gear icon)

Tab	Contains
Storage	Where LEAF saves intermediate files and results
Display	Theme (light/dark), chart defaults
Advanced	Backend selection (Rust / Python), worker count

Keyboard shortcuts

Key	Action
↑ / ↓ (in metabolite table)	Move to previous / next compound
Cmd/Ctrl + F	Focus search in tables
Esc	Close modals and dropdowns

Next

→ Troubleshooting — when things don't work → FAQ — quick answers → Glossary — what does "ppm" mean?