Preferences

Core Feature

This feature is available in all MATISSE Explorer deployments.

Configure application settings including theme, colorscale preferences, and view version information.

Accessing Settings

Open Settings using either method:

• Click the Settings icon (gear) at the bottom of the Activity Bar
• Use keyboard shortcut: Ctrl + I

The Settings dialog displays with a search bar and organized sections.

TIP

All settings are stored locally in your browser and persist across sessions.

Settings Search

Use the search bar at the top of the Settings dialog to quickly find settings:

1. Type a keyword (e.g., "theme", "color")
2. Settings are filtered in real-time
3. Only matching items are displayed

Settings Sections

Appearance

Configure visual preferences for the application.

Theme

Choose your preferred visual theme:

Theme	Description
System	Matches your operating system setting
Light	Bright background, dark text
Dark	Dark background, light text

Theme changes apply immediately without requiring a page refresh.

Colorscale

Configure default colormaps used throughout the application for data visualization.

Continuous Colormap

Select the default colormap for continuous data (gene expression, numeric values).

Category	Colormaps
Sequential	Cool, Viridis, Inferno, Plasma, Magma, Cividis, Turbo, Blues, Greens, Reds, Purples
Diverging	Red-Blue, Red-Yellow-Green, Red-Yellow-Blue, Brown-Blue-Green, Pink-Yellow-Green, Spectral

Choosing a colormap:

• Sequential colormaps are best for expression data where higher values are more important
• Diverging colormaps are ideal for data with a meaningful center point, like fold changes

Categorical Colormap

Select the default colormap for categorical data (cell types, clusters).

Colormap	Description
Rainbow	Full spectrum of distinct colors
Sinebow	Smoother rainbow with perceptual balance
Turbo	Vibrant colors with high contrast

How Colormaps Are Applied

Global colormap settings affect:

• Map Viewer - Point coloring in spatial view
• Scatter Plot - Point coloring in embedding views
• Annotation Detail Panel - Category color previews
• Variable Set Detail Panel - Score visualizations

TIP

Individual views may override the global colormap if specific settings are available. The global setting serves as the default.

About

View application version information.

Version Display

Field	Description
Core Version	Version of the MATISSE core library
App Version	Application version with Git commit hash (if available)

Copying Version Info

Click the Copy button next to each version field to copy to clipboard. Include this information when reporting bugs or requesting support.

Settings Storage

Local Storage

• No account required
• Settings persist on your device
• Clearing browser data resets settings

Per-Browser

• Settings are specific to each browser
• Different devices have separate settings
• No automatic sync between browsers

Troubleshooting

Settings Not Saving

• Ensure browser allows local storage
• Check privacy/cookie settings
• Disable strict privacy modes temporarily

Theme Not Applying

• Try selecting a specific theme instead of System
• Check your OS dark mode settings
• Refresh the page if needed

Related Topics

• Interface Overview - Application layout
• Quick Start - Getting started guide
• Color Mapping - Detailed colormap usage