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Set Up a Multi-Sample Session

Multi-Sample Session Specific

This feature is only available in multi-sample sessions.

CartoScope supports the Set Up a Multi-Sample Session dialog to assemble, preview, and configure multi-sample spatial transcriptomics sessions from various input sources prior to launching the workspace.

Interface

The setup dialog allows you to define basic session parameters, select participating sample slots from four input tabs, customize grid layout parameters, and verify dataset metadata prior to launching the workspace.

1. Define Session

Define global session parameters and viewport layout settings:

  • Session Title: Enter a custom title for your multi-sample study.
  • Grid Setup:
    • Grid Layout: Set the number of Rows and Columns for the multi-tile map layout grid.
    • Layout Direction: Choose between Row-first or Column-first ordering for sample slot placement.
    • Equal Size: If checked, all grid viewports will have identical square dimensions. Otherwise, individual slot sizes adapt to actual dataset physical boundaries.
  • Options:
    • Load Background ROI Layers: Toggle whether to preload background histology staining images and ROI annotations across all grid slots.
    • Grid: Toggle grid borders separating sample tiles in the workspace.
    • Overview Size: Set the display size of overview mini-maps per slot.

2. Datasets and Metadata

The Datasets and Metadata panel provides four interactive tabs to select datasets, inspect metadata, verify spatial layer compatibility, and configure grid slot placements.

Feature Comparison Summary

Feature / Task Gallery Tab Metadata Tab Layer Tab URL Tab
Description Visual thumbnail cards for candidate datasets Tabular view of biological and technical metadata Matrix of pre-calculated spatial layer availability External dataset URLs, shared links, and YAML config
Select Datasets Click datasets from Available panel into Selected Grid Toggle selection checkboxes or assign numeric ranks N/A (read-only layer matrix) Input external catalog.yaml links or paste session YAML
Grid Arrangement Drag thumbnail cards directly within Selected Grid Automatically ordered by the Rank column N/A N/A
Rename Datasets Edit the text field at the bottom of any thumbnail card Edit custom sample labels in the Name column N/A Edit dataset label or URL entries

Launch Session

Click the Launch Multi-Sample Session button to initialize the synchronized Map (Multi-Sample) workspace.

Related Pages

Concepts

Manual Pages