UI glossary (terminology)#

Audience: everyone (this is the shared vocabulary)
Time: 10–20 minutes (skim now, return later)
What you’ll get: exact meanings of UI terms so the rest of the docs feel predictable

How to use this page#

If you’re new: read the bold terms only.
If you’re debugging something subtle: read the “Scope / persistence” notes under each section.

Tip

This glossary is written to match the app UI language, even when a “technical” term might be more precise. The goal is: when the docs say “view” or “snapshot”, you know exactly what screen element/state is meant.

UI map (one screenshot you’ll reuse everywhere)#

Cellucid UI overview: the left sidebar controls state; the canvas renders the active view(s).#

Data model terms#

Dataset: the loaded data bundle (points + metadata + optional gene expression + optional connectivities/vector fields).
Cell / point: one row/observation rendered as a point. (The UI often says “points” because the viewer is generic.)
Gene / feature: one variable/feature; used for gene expression coloring and some analyses.
Embedding: coordinates for points in 1D/2D/3D (UMAP/tSNE/PCA/etc).
Dimension (1D / 2D / 3D): which embedding dimensionality you are currently viewing for a given view.
- 4D: present in some UI lists as “reserved”; not currently supported.
Connectivity: a neighbor graph (edges). When enabled, edges are drawn between visible points only.
Vector field / velocity overlay: an optional overlay that visualizes per-cell vectors (dimension-specific).

Fields, coloring, and legends#

Field: something you can color by.
- Categorical obs: discrete labels (clusters, batch, sample).
- Continuous obs: numeric values (QC metrics, scores).
- Gene expression / var: expression of a selected gene/feature.
Active field: the currently selected field that drives coloring (per view).
Legend: the UI element that explains the current coloring.
- Categorical legend shows categories and their colors.
- Continuous legend shows a numeric color scale.
Color-by: the act of selecting a field to drive coloring.

Scope note:

In multiview, the “active field” is typically per view (each view can show a different coloring).

Views, snapshots, and “small multiples”#

These terms are the most important for understanding Cellucid.

View: one panel that renders the dataset with its own state (camera, dimension, coloring, filters, highlights).
Live view: your default working view (often labeled “All cells” in the view badges).
Snapshot view (also “kept view”): a view created by clicking Keep view; used to compare multiple states side-by-side.
Multiview: the overall feature of having multiple views/snapshots.
View layout
- Grid compare: shows all views in a grid.
- Edit selected view: shows only the active view so you can edit it precisely.
Active view: the view you are editing/configuring (the one selected in the view badges).
Focused view: in grid mode, the view under your last click; this determines which view the camera controls target.
View badge: the clickable pill/row representing a view (with indicators like 3D, Orb/Pan/Fly).
Cameras locked: all views share one camera (navigation is synchronized).
Cameras unlocked: each view has its own camera and navigation mode; badges show per-view navigation indicators.

Scope note:

When cameras are unlocked, Cellucid stores camera state per view and switches it when you focus a different view.

Navigation and camera terms#

Orbit: rotate around an anchor (best for 3D).
Planar: pan/zoom as if looking at a flat map (best for 2D).
Free-fly: first-person navigation (immersive; supports pointer lock).
Pointer lock / Capture pointer: a browser feature that hides the cursor and reports raw mouse movement (needed for FPS-style looking).
Orbit anchor: a visual compass/anchor indicator shown in orbit mode (optional).
Reset Camera: returns the camera to a default framing (and can reset related UI controls depending on how you trigger it).

Highlighting and selection terms#

Highlight mode: the active interaction tool for selecting points (e.g., lasso).
Highlight group: a named set of highlighted cells (used for comparison/analysis).
Highlight page: a collection of highlight groups (useful when you want multiple “sets” of groups).

Scope note:

Highlights can be global or per-view depending on the feature; always check the page you’re using (highlighting is documented under f_highlighting_selection/index).

Analysis and export terms#

Analysis: computations driven by the current dataset state (often highlights/groups).
Figure Export: export an image/vector figure of the current view(s) suitable for papers.
Save State / Load State: save/restore a .cellucid-session bundle that captures the application state.

Scope & persistence vocabulary (used throughout the docs)#

Global: one value shared across the entire app/dataset (not specific to a view).
Per view: stored separately for each view/snapshot.
Session bundle: a saved .cellucid-session file (explicit user action).
Local storage: persistent browser storage used for small preferences (e.g., theme/background).
Session storage: storage that is cleared when the tab closes (used for sensitive tokens like GitHub OAuth in community annotation).

Next steps#

Choose a workflow: a_orientation/05_which_workflow_is_for_me_decision_tree
Learn navigation + multiview: c_core_interactions/index