Layer Settings

Core Feature

This feature is available in all MATISSE Explorer deployments.

Layer Settings control the appearance of data points and background images in the map viewer. Access these settings through the Layers button (layer icon) in the map viewer toolbar.

Accessing Layer Settings

1. Click the Layers button (layer icon) in the map viewer toolbar
2. A popover panel opens with all layer controls
3. Changes apply immediately to the view

Projection Mode

At the top of the toolbar, select the coordinate system for displaying your data:

• For 2 or fewer projection modes: Segmented control buttons
• For 3 or more projection modes: Dropdown selector

Available projections depend on your project data (e.g., Spatial, UMAP, t-SNE, PCA).

Layers

Feature Layer

Controls the opacity of all data points on the map.

Control	Description
Opacity slider	0 (transparent) to 1 (opaque)
Eye toggle	Quick show/hide toggle

Default: 1 (fully visible)

Image Layer

TIP

Image layer settings only appear when the current projection mode includes a background image (e.g., Spatial view with tissue image).

Controls for the background tissue image:

Control	Range	Default	Description
Opacity	0 to 1	1	Image transparency
Brightness	-1 to 1	0	Lighten or darken the image
Contrast	-1 to 1	0	Adjust light/dark differences
Saturation	-1 to 1	0	Adjust color intensity

Additional controls for single-band (grayscale) images:

Control	Range	Default	Description
Max Intensity	1 to 65535	2048	Contrast stretch (lower = brighter)
Channel Color	Select	Grayscale	Pseudocolor for visualization

Automatic Detection

MATISSE Explorer automatically detects single-band (grayscale) vs multi-band images from the GeoTIFF file. Single-band (grayscale) images (common in fluorescence microscopy) will show the additional Max Intensity and Channel Color controls.

Each setting includes:

• A slider for adjustment
• Eye toggle for opacity (quick show/hide)
• Reset button to restore all image settings to defaults

Point Size

Controls how large data points appear on the map.

Control	Description
Auto toggle	Enable automatic point sizing
Size slider	Manual size from 1px to 15px

Defaults:

• Auto: Enabled (points scale with zoom level)
• Size: 3px (when Auto is disabled)

Auto Point Size

When enabled:

• Points automatically scale based on zoom level
• Maintains appropriate visibility across zoom ranges
• Size slider is disabled

When disabled:

• Points remain at fixed size regardless of zoom
• Use the slider to set exact pixel size (1-15px)

TIP

Manually adjusting the point size slider will automatically disable Auto mode, allowing you to fine-tune the size without needing to toggle it off first.

Tips for Effective Settings

Dense Data

For datasets with many overlapping points:

1. Lower feature layer opacity - See through overlapping points
2. Disable Auto, use smaller point size - Reduce overlap
3. Lower image layer opacity - Reduce visual noise

Sparse Data

For datasets with fewer points:

1. Full feature layer opacity - Clear visibility
2. Larger point size - Better visibility
3. Keep image visible - Provides spatial context

Presentation

For figures and screenshots:

1. Full opacity on feature layer - Clear, distinct colors
2. Appropriate point size - Visible but not overwhelming
3. Adjust image brightness/contrast - Professional appearance

Troubleshooting

Points Not Visible

• Check feature layer opacity is not 0
• Increase point size or disable Auto
• Verify data is loaded (check point count in toolbar)

Background Image Not Showing

• Check image layer opacity is not 0
• Verify projection mode has a raster layer (e.g., Spatial view)
• Click the eye toggle to show the layer

Points Too Small When Zoomed Out

• Enable Auto point size for automatic scaling
• Or disable Auto and increase point size manually

Image Too Dark or Washed Out

• Use the reset button to restore defaults
• Adjust brightness and contrast together
• Typical adjustment: brightness +0.1 to +0.3, contrast +0.1 to +0.2

Fluorescence Image Too Dark

• Lower the Max Intensity value (e.g., from 2048 to 1000)
• This stretches the contrast to make dim signals visible
• If still too dark, try values below 500

Related Topics

• Map Viewer - Map viewer overview
• Color Mapping - Point coloring based on features
• Navigation - Zoom and pan controls