Should I Choose a Single-Sample or Multi-Sample Session?

CartoScope offers two session modes tailored to different exploration goals.

Choosing between a Single-Sample Session and a Multi-Sample Session depends on whether you are focusing on an in-depth analysis of one tissue section or comparing spatial patterns across a cohort of samples.

1. Benefits, Use Cases & Requirements

Aspect	Single-Sample Session	Multi-Sample Session
Requirements	Any single dataset (catalog.yaml or public catalog item). No special setup required.	Joint multi-sample analysis required (multi-catalog.yaml). Samples must have been processed together in a joint pipeline.
Primary Goals	In-depth exploration of a single tissue slide at maximum spatial resolution.	Side-by-side comparative spatial analysis across an experimental cohort.
Use Cases	Examining fine cell boundaries, subcellular transcript distributions, or aligning morphology images for one section.	Comparing Control vs. Treated samples, disease progression time-series, or biological replicates.
Key Benefits	Maximum detail, full individual layer customization, lighter memory footprint, and fast loading.	Synchronized camera navigation across slides, group-level statistical testing, and volcano plot screening.

Tip

For the datasets that were analyzed using multi-sample analysis in cartloader, you also also load individual datasets as single-sample sessions as well.

2. Shared Features & Capabilities

Both session modes share core CartoScope functionality, including:

• Multi-Layer Visualization: Overlay morphology images, gene expression, and factor layers.
• Gene & Factor Drawers: Search, filter, inspect marker genes, and explore UMAP plots.
• ROI Analysis: Draw, refine, load, and analyze custom Regions of Interest.
• Spot & Cell Inspection: Hover and click inspection for molecular metrics and confidence scores.
• Code Filter: Write multi-condition logical expressions to filter data tables.
• Sharing & Bookmarks: Save workspace configurations and generate shareable links.
• Data & Image Export: Download high-resolution PNG/PDF maps and tabular data matrices.

3. Features & Capabilities Differences

Feature / Capability	Single-Sample Session	Multi-Sample Session
Grid Canvas & Dragging	Single \(1 \times 1\) viewport canvas.	\(N \times M\) grid canvas with drag-and-drop slot reordering handles.
Camera Synchronization	N/A (independent viewport controls).	Exclusive: Synchronized panning and zooming with camera locking across slots.
Sample Group Labeling	N/A	Exclusive: Assign custom biological condition labels (e.g. Group 1 vs. Group 2) in Sample Drawer.
Cohort Sample Comparison	N/A (ROI differential analysis only).	Exclusive: Run Chi-squared tests and DESeq2-inspired statistical models across sample groups.
Volcano Plot Analysis	N/A	Exclusive: Interactive volcano plots displaying log2 fold changes and p-values in Sample Drawer.
Layer Management Scope	Full individual layer styling and stack ordering.	Shared layer stack overlaid uniformly across all grid slots with slot-specific toggles.
Performance & Hardware	Lightweight browser memory footprint.	Higher RAM and GPU requirements due to rendering multi-tile viewports simultaneously.

---

Related Pages

Concepts

• Multi-Sample View Modes
• Multi-Sample Analysis
• DESeq2-inspired Model

Manual Pages

• Central Map View (Multi-Sample)
• Sample Drawer
• Set Up a Multi-Sample Session

How-to Guides

• How to Compare Samples
• How to Link Sample Views