Quick tour (60 seconds)#

Audience: first-time users (wet lab + computational)
Time: 1–3 minutes
What you’ll do: load → move → color → keep a snapshot → highlight → export/save

Tip

If you prefer to learn by definition-first, read a_orientation/04_ui_glossary_terminology before this tour.

Fast path (click-by-click)#

1) Load a dataset (demo is fine)#

  1. Open the Session accordion.

  2. Under Sample datasets, choose any dataset.

  3. Wait for the dataset info panel to populate (Cells/Genes/Obs fields).

What success looks like

  • The canvas shows points (usually on a grid background).

  • The dataset info panel shows non‑zero counts.

Note

You can also load your own data from Local data (H5AD/Zarr/Prepared) or from a Remote server, but those workflows are documented in b_data_loading/index.

2) Move the camera (don’t skip this)#

  1. Open Compare Views → Navigation.

  2. Keep the default mode: Orbit.

  3. Try:

    • click‑drag to rotate,

    • mouse wheel / trackpad scroll to zoom,

    • right‑drag (or Shift‑drag) to pan.

If you are on a trackpad and the interaction feels “wrong”, try Planar mode (best for 2D embeddings).

3) Color by a field (metadata or gene expression)#

  1. Open Coloring & Filtering.

  2. Pick one:

    • Categorical obs (clusters, batch, sample), or

    • Continuous obs (QC metrics, scores).

  3. Look for the legend changing on the left.

What success looks like

  • The points change color.

  • A legend appears/updates (categories or a color scale).

4) Keep a snapshot (small multiple)#

  1. Open Compare Views → Multiview.

  2. Click Keep view.

  3. You should see a new numbered badge/panel.

This is how you compare hypotheses side‑by‑side without losing your current view.

5) Make a highlight (selection)#

  1. Open Highlighting.

  2. Choose a mode (e.g., Lasso).

  3. Draw a selection; a highlight group should appear in the highlight list.

If you want a keyboard-first workflow, the UI supports:

  • Alt + drag for area selection (and other shortcuts; see the in‑app “Keyboard Shortcuts” accordion).

6) Export or save what you did#

Pick one:

  • Save State (Session accordion) to download a .cellucid-session bundle you can reopen later.

  • Figure Export to export a publication‑ready figure of the current view(s).

Troubleshooting (quick tour blockers)#

“The canvas is blank” / “WebGL2 required”#

Go to a_orientation/02_system_requirements.

“I can’t rotate/zoom/pan”#

Go to c_core_interactions/06_troubleshooting_core_interactions (focus, pointer lock, nav mode confusion).

“Keep view does nothing”#

You are likely in smoke mode (multiview is points‑only). See c_core_interactions/04_view_layout_live_snapshots_small_multiples.

Next steps#

  • Learn navigation + multiview properly: c_core_interactions/index

  • Learn the language of the UI: a_orientation/04_ui_glossary_terminology