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Map (Multi-Sample)

Multi-Sample Session Specific

This feature is only available in multi-sample sessions.

The Multi-Sample Map View serves as the central interactive canvas for exploring multiple datasets in a synchronized N × M grid layout.

Interface

The multi-sample map interface provides interactive floating toolkits, tile slot controls, and layout modes:

1. Map Toolkit

The floating map toolkit sidebar contains four action button groups arranged sequentially from top to bottom:

1.1 Layout & Viewport Group (Top)

Located at the top of the floating toolkit sidebar:

  • Layout Mode Switcher: Click to open the layout menu and switch between Gallery Mode (Grid View), Single-Focus Mode, and Dual-Focus Mode (see Multi-Sample View Modes).
  • Show / Hide Grid: Toggle grid lines separating individual tile viewports in the workspace.
  • Left Drawer Map Shift: Enable or disable automatic map canvas shifting when opening the left sidebar drawer.
  • Right Drawer Map Shift: Enable or disable automatic map canvas shifting when opening the right sidebar drawer.

1.2 Slot Selection & Grouping Board (Second Group)

Provides tools to select, link, replace, and reorder grid slots:

  • Select All Slots: Select all slots across the grid simultaneously (or use Cmd + Click on Mac or Ctrl + Click on Windows to select individual slots).
  • Deselect All Slots: Clear selection for all currently selected slots.
  • Change Dataset: Open the dataset chooser dialog to replace the dataset in the currently selected slot.
  • Link / Unlink Selected Views: Link or unlink camera panning and zooming synchronization across two or more selected slots.
  • Reorder Slots Mode: Toggle interactive drag-and-drop slot reordering mode across the grid.

1.3 Zoom, Scale & Orientation Group (Third Group)

Adjust map scaling, orientation, and physical scale bar settings:

  • Fit to View: Auto-zoom to fit the Spatial Gene Expression density extent across all active slots.
  • Zoom In (+): Increase zoom level.
  • Zoom Out (-): Decrease zoom level.
  • Scale Bar Settings: Open the Scale Bar popover to toggle visibility, choose automatic/custom scale lengths (e.g. 500 µm, 50 µm), and apply settings globally across all slots.
  • Reset North: Reset compass bearing to North orientation.
  • Rotate Clockwise (90°): Rotate map views 90 degrees clockwise.
  • Flip Horizontal: Toggle horizontal flip across map viewports.
  • Reset Orientation: Reset rotation and horizontal flip to their default states.

1.4 ROI Drawing Group (Bottom)

Tools for spatial Region of Interest (ROI) polygon analysis:

  • Draw ROI Polygon: Toggle polygon drawing mode to define custom spatial ROIs on the map.
  • Delete Selected Polygon: Remove the currently selected ROI polygon shape.

2. Slot Types

CartoScope utilizes two slot types to support interactive multi-sample layouts:

2.1 Standard Slot

The primary canvas slot for interactive spatial dataset exploration:

  • Main Map: Interactive canvas rendering spatial layer visualizations.
  • Expandable Map View Summary: Located at the bottom-left corner of each slot, providing real-time readouts for zoom level, subsampling rate, rotation, pitch, flip status, and bounding box coordinates (see Map View Summary).
  • Overview Mini-Map: Miniature dataset map displaying current viewport bounds.
  • Index and Name: Displays grid slot coordinates (e.g. R1 C1) and the dataset name.
  • Scale Bar: Located at the bottom-right corner, displaying physical spatial distance (e.g. 500 µm).

2.2 Mini Slot

Compact preview slots displayed in Focus and Dual-Focus modes:

  • Focus Buttons: Features a Focus button (in Focus mode) or Focus-Left / Focus-Right buttons (in Dual-Focus mode) on the top-left to swap slides into the main viewports.
  • Map Preview: Displays a compact thumbnail preview of the sample dataset.

3. Layout Modes

CartoScope supports three synchronized multi-sample layout modes:

In Gallery mode, all datasets are displayed as standard slots in an \(N \times M\) grid layout.

3.2 Focus Mode

In Focus mode, the active sample occupies the entire main canvas as a standard slot, while all other samples are displayed as mini-slots along the bottom bar. Click the Focus button on any mini-slot to focus on a different sample.

3.3 Dual-Focus Mode

In Dual-Focus mode, two selected samples are displayed side-by-side as standard slots occupying the left and right halves of the canvas, while remaining samples are displayed as mini-slots along the bottom bar. Click Focus-Left or Focus-Right on any mini-slot to assign samples to comparison panes.

Related Pages

Concepts

Manual Pages