UI Tour
This page maps the visible controls in the targeted LEAF workflow.
[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 |
| Page selector | Switch between Extract, Quick Check, and Analysis |
| Visualize dropdown | Open a statistical chart from the Analysis view |
| 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 |
|---|---|---|
| Left sidebar | Folder selector | Pick the folder of LC-MS files |
| Left sidebar | Parameters | RT window, peak picking, grouping, instrument settings, backend |
| Center | Compound list editor | Upload, edit, validate the metabolite CSV (targeted only) |
| Right | Tracing editor | Configure isotopologues |
| Bottom-right | Start Processing | Launch the run (turns blue when ready) |
Peak Picking view (Charts tab)
Interface for inspecting targeted results. Loads after extraction or when a .msd archive is opened.
[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) |
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 the Peak Picking view |
| Cancel | Stop a running job |
Settings (gear icon)
| Tab | Contains |
|---|---|
| Storage | Where LEAF saves intermediate files and results |
| Display | Theme and chart defaults |
| Advanced | Backend selection and 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 — common installation and analysis problems → FAQ — quick answers → Glossary — what does "ppm" mean?