Navigation & Zoom

Core Feature

This feature is available in all MATISSE Explorer deployments.

Learn how to navigate the map viewer efficiently using mouse controls and projection modes.

Mouse Controls

Pan Mode (Default)

In Pan mode, use your mouse to move around the map:

Action	Mouse Control	Result
Pan	Click + drag	Move the view in any direction
Zoom in	Scroll wheel up	Zoom into the map
Zoom out	Scroll wheel down	Zoom out of the map
Quick zoom in	Double-click	Zoom in on clicked location

Selection Mode

In Selection mode, mouse behavior changes:

Action	Mouse Control	Result
Draw lasso	Click + drag	Draw selection boundary
Complete selection	Release	Close and apply selection

See Lasso Selection for details.

Zoom Controls

Zoom Levels

The map supports multiple zoom levels:

• Zoomed out - See the entire tissue/sample
• Zoomed in - See individual data points in detail

Zoom to Fit

Reset the view to show all data:

1. Look for the Reset button in the bottom-left corner of the map viewer
2. Click to reset zoom and position
3. The view adjusts to show the entire dataset

Projection Modes

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

Available Projections

Available projections depend on your project data. Common examples include:

Mode	Description	Use For
Spatial	Original tissue coordinates	Anatomical context
UMAP	UMAP embedding	Transcriptional similarity
t-SNE	t-SNE embedding	Cluster visualization
PCA	PCA embedding	Variance analysis

Your project may include additional or different projections based on the analysis performed during data preparation.

Switching Projections

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

What Changes

When you switch projections:

• Point positions update to new coordinates
• Background image may hide (embeddings have no tissue image)
• Zoom level resets to fit the new view
• Color mapping and subsets remain active

Lasso in Different Projections

Lasso selections are projection-aware:

• Selections in spatial view select by tissue location
• Selections in UMAP/t-SNE select by transcriptional similarity
• Each selection stores its source projection

View State

Preserved State

These settings persist when navigating:

• Current feature/color mapping
• Active subsets
• Point size and opacity settings

Reset State

These reset when changing projections:

• Zoom level (fits to new view)
• Pan position (centers on data)

Performance Tips

Large Datasets

For datasets with millions of points:

1. Allow loading time - Initial render may take a moment
2. Zoom strategically - Zoomed views render faster
3. Use subsets - Reduce visible points for smoother interaction

Smooth Navigation

1. Pause between actions - Let rendering complete
2. Zoom before panning - Zoom into region, then pan within it
3. Use projection wisely - Switch only when needed

Troubleshooting

View is Stuck

• Try clicking the reset/home button
• Refresh the page if necessary
• Check if Selection mode is active (switch to Pan)

Zoom Not Working

• Ensure mouse is over the map area
• Check if zoom controls are disabled
• Try using scroll wheel vs. buttons

Projection Won't Change

• Wait for current view to finish loading
• Check if projection data is available
• Some datasets may not have all projections

Related Topics

• Map Viewer - Complete map viewer documentation
• Lasso Selection - Selection mode details
• Layer Settings - Point appearance