Map Viewer

Core Feature

This feature is available in all MATISSE Explorer deployments.

The Map Viewer is the primary visualization component in MATISSE Explorer. It displays your spatial transcriptomics data as an interactive map, allowing you to explore tissue images overlaid with data points.

Interface Components

Toolbar

The toolbar at the top of the map viewer provides access to essential controls:

Control	Description
Pan (Hand icon)	Navigate the map by clicking and dragging
Selection (Lasso icon)	Draw selections to highlight regions of interest
Items dropdown	Shows count of visible/filtered items with additional options

Map Area

The central map area displays:

• Background image - Tissue image (if available)
• Data points - Individual cells or spots colored by the selected annotation
• Selection overlay - Highlighted region when using lasso selection

Legend

The legend shows the color mapping for the current annotation:

• Categorical annotations - List of categories with their colors
• Continuous annotations - Color gradient with min/max values

Hover over legend items to highlight corresponding points on the map.

Filter Panel

Click the filter button to open the Filter Panel. See Filter for details.

Interaction Modes

Pan Mode

Pan mode is the default interaction mode for navigating the map.

Controls:

Action	Mouse	Result
Pan	Click + drag	Move the map view
Zoom in	Scroll up / Double-click	Zoom into the map
Zoom out	Scroll down	Zoom out of the map

Selection Mode

Selection mode allows you to draw lasso selections to highlight specific regions.

How to use:

1. Click the Selection button (Lasso icon) in the toolbar
2. Click and drag on the map to draw a closed shape
3. Release to complete the selection
4. The toolbar shows the count of selected items

After selecting:

Click the Items dropdown to access options:

• Add selection to filter - Save the lasso as a filter condition

Projection Modes

Switch between different coordinate systems to view your data from multiple perspectives.

Available Projections

Mode	Description
Spatial	Original tissue coordinates (default)
UMAP	UMAP dimensionality reduction coordinates
t-SNE	t-SNE dimensionality reduction coordinates

Switching Projections

1. Locate the projection selector in the toolbar or sidebar
2. Click to open the dropdown menu
3. Select the desired projection mode
4. The map view updates to show the new coordinates

Lasso selections made in embedding space (UMAP/t-SNE) can be saved and reused in filters.

Supported Image Formats

The Map Viewer supports multiple image formats for background tissue images:

Format	Description	Best For
GeoTIFF	Cloud Optimized GeoTIFF	Large images, streaming
Static	PNG, JPEG	Small to medium images
Tiles	Multi-resolution tile pyramid	Very large images

The appropriate format is determined by your data configuration and loaded automatically.

Tooltip

Hover over data points to see detailed information:

The tooltip displays:

• Current annotation value for the hovered point
• Point index or identifier
• Additional metadata (if configured)

Performance Tips

Large Datasets

For datasets with millions of points:

• Use tile-based images when available
• Allow time for initial rendering
• Zoom into regions of interest for smoother interaction
• Consider using filters to reduce visible points

Smooth Navigation

• Avoid rapid zoom changes
• Wait for rendering to complete before making new selections
• Use Pan mode for general navigation, switch to Selection only when needed

Related Topics

• Navigation & Zoom - Detailed navigation controls
• Lasso Selection - Complete lasso selection guide
• Color Mapping - Configure data point colors
• Layer Settings - Adjust point size and opacity