Frequently Asked Questions

Core Feature

This FAQ covers questions about features available in all MATISSE Explorer deployments.

Common questions and answers about using MATISSE Explorer.

General

What is MATISSE Explorer?

MATISSE Explorer is an interactive web-based platform for visualizing and analyzing spatial transcriptomics data. It allows researchers to explore tissue images overlaid with gene expression data, subset cell populations, and export results.

What browsers are supported?

MATISSE Explorer works best in modern browsers:

• Google Chrome (recommended)
• Mozilla Firefox
• Microsoft Edge
• Safari

For optimal performance, use the latest version of your preferred browser.

How large a dataset can MATISSE Explorer handle?

MATISSE Explorer is designed to handle large spatial transcriptomics datasets with hundreds of thousands to millions of data points. Performance depends on:

• Your device's hardware (RAM, GPU)
• Browser capabilities
• Network speed for data loading

Data and Loading

Why is my data taking so long to load?

Large datasets require time to load and render. Factors affecting load time:

• Dataset size (number of points and features)
• Network connection speed
• Server response time
• Initial rendering complexity

Allow the loading to complete before interacting heavily.

Why are some genes not found?

Genes may not be found due to:

• Different naming conventions (symbol vs. Ensembl ID)
• Typos in gene names
• The gene not being present in your dataset
• Case sensitivity issues

Check your dataset's gene naming format and try alternative names.

Can I load my own data?

MATISSE Explorer works with pre-configured projects. Contact your data administrator about loading custom datasets.

Visualization

Why do I only see a blank map?

Possible causes:

• Data is still loading (check for loading indicators)
• All points are excluded by subset (clear subsets)
• Projection has no data (switch projection modes)
• Browser rendering issue (try refreshing)

Why are colors not showing?

Ensure you have:

1. Selected a feature for color mapping
2. Waited for the feature data to load
3. Not excluded all data points with subset
4. Checked that the feature has varying values

How do I see the background tissue image?

The background image:

• Only appears in Spatial projection (not in UMAP/t-SNE)
• May need opacity adjustment (see Layer Settings)
• Requires the image data to be loaded
• Some datasets may not include background images

Why is the view so slow or laggy?

Performance tips:

1. Allow initial rendering to complete
2. Reduce point size for dense data
3. Apply subsets to reduce visible points
4. Avoid rapid zoom/pan operations
5. Close other browser tabs to free memory

Subsetting

Why does my subset show zero results?

Your subset may be too restrictive:

• Check if multiple AND conditions combine to exclude everything
• Verify value ranges are appropriate for your data
• Check categorical selections match available values
• Review lasso conditions are in the correct projection

Can I save my subsets?

Yes, use Saved Subsets:

1. Configure your subset
2. Save with a descriptive name
3. Load saved subsets from the Subset Panel

Saved subsets are stored in your browser and persist across sessions.

How do I subset by multiple cell types?

In the Subset:

1. Add a column condition for cell type
2. Select multiple categories (OR logic within the condition)

Or use multiple conditions with OR operator between them.

Signatures

How do I search for gene sets from MSigDB?

When creating or editing a Signature, click Browse MSigDB gene sets... to search over 18,500 curated gene sets. You can filter by species (Human/Mouse) and category (Hallmark, Reactome, GO). Selecting a gene set automatically adds all its genes to your Signature.

What's the difference between combination methods?

Method	Use When You Want
Max	Cells where ANY gene is highly expressed
Min	Cells where ALL genes are expressed
Sum	Total pathway activity
Average	Balanced expression across genes
UMI Count	Normalized for sequencing depth

Why doesn't my signature match any genes?

Check:

• Gene name spelling
• Gene naming format (symbols vs. IDs)
• Case sensitivity
• Whether genes are in your dataset's continuous features

Export

What format are exports in?

Exports are in CSV (Comma-Separated Values) format, compatible with:

• Microsoft Excel
• R (read.csv)
• Python (pandas.read_csv)
• Other data analysis tools

Can I export subset data only?

Yes, exports respect your current subset:

1. Apply the subset you want
2. Navigate to the feature to export
3. Export - only subset points are included

Why is my export file empty?

Check if:

• Any data is loaded
• Your subset isn't excluding all points
• The feature has data
• The export completed successfully

Lasso Selection

My lasso selection isn't working

Ensure:

1. You're in Selection mode (not Pan mode)
2. You're clicking and dragging on the map area
3. The data is loaded and visible
4. You draw a closed shape (the system closes it automatically)

How do I select cells in UMAP space?

1. Switch to UMAP projection mode
2. Enable Selection mode
3. Draw lasso around the cluster of interest
4. The selection applies to those transcriptionally similar cells

Settings

Are there keyboard shortcuts?

Yes. See Interface Overview - Keyboard Shortcuts for the full list. Key shortcuts include number keys (1-9) to switch extensions, Ctrl/Cmd+\ for Compact Mode, and L to open Layer Settings.

Where are my settings saved?

Settings are stored in your browser's local storage:

• Specific to each browser
• Persist until cleared
• Not synced between devices or browsers

How do I reset all settings?

Clear browser data for the site:

1. Open browser settings/preferences
2. Find site data or local storage options
3. Clear data for the MATISSE Explorer site
4. Refresh the page

Warning: This also clears saved subsets and signatures.

Troubleshooting

The application is unresponsive

Try these steps in order:

1. Wait for any loading to complete
2. Clear active subsets
3. Refresh the page
4. Clear browser cache and reload
5. Try a different browser

I found a bug. How do I report it?

When reporting issues, include:

• Browser name and version
• Operating system
• Steps to reproduce the issue
• Screenshots if possible
• Application version (from Settings)

Contact your administrator or support team with this information.

The view looks different than expected

Check:

• Current projection mode (Spatial vs. UMAP vs. t-SNE)
• Active subsets that may be hiding data
• Color mapping selection
• Zoom level and position
• Theme setting (Light vs. Dark)

InSilicoLab

InSilicoLab Feature

These questions relate to features exclusive to Portrai InSilicoLab.

How do I get notified when DEG analysis completes?

MATISSE Explorer includes a notification system. When a DEG analysis finishes, a success notification appears automatically via the bell icon in the Activity Bar. Click the notification to navigate to the results.

Can I create a Signature from DEG results?

Yes. In the DEG results Data Table, select genes using the row checkboxes, then click Create Signature. This creates a new Signature that appears in the Explorer's Signatures tab for immediate use.

What is the difference between Core and InSilicoLab features?

Core features are available in all MATISSE Explorer deployments and include visualization, subsetting, and data export. InSilicoLab-exclusive features are specific to the Portrai InSilicoLab platform and include advanced analysis tools like DEG analysis.

How do I access InSilicoLab features?

InSilicoLab features are available when using MATISSE Explorer through the Portrai InSilicoLab platform. Look for additional icons in the Activity Bar, such as the DEG (DNA) icon.

What is DEG analysis used for?

DEG (Differentially Expressed Genes) analysis identifies genes with significantly different expression levels between cell populations. Use it to:

• Find marker genes for cell types
• Compare tumor vs. normal tissue
• Identify spatially variable genes
• Understand treatment effects

How many groups do I need for DEG analysis?

You need at least 2 groups for DEG analysis. Each group should contain enough cells (typically 50-100+) for reliable statistical results.

What FDR threshold should I use?

Threshold	When to Use
No threshold	Initial exploration of all results
FDR < 0.1	Exploratory analysis, hypothesis generation
FDR < 0.05	Standard significance level for publications
FDR < 0.01	High confidence results, validation candidates

Can I change the logFC threshold for direction filtering?

Yes. When selecting a direction filter (Upregulated, Downregulated, or Bidirectional), an inline input field appears where you can adjust the logFC threshold. The default is 1 (2-fold change). Lower values are more permissive, higher values are more strict.

Why are there no significant genes in my DEG results?

Possible causes:

• Groups are too similar - try comparing more distinct populations
• Too few cells per group - increase group sizes
• High biological variability - consider stricter group definitions
• FDR threshold too strict - try a more lenient threshold first

How do I handle overlapping cells between groups?

Use the overlap handling options:

• Allow overlaps - Keep cells in all groups (warning only)
• Exclude from all - Remove overlapping cells completely
• Keep in first group - Priority-based assignment
• Keep in largest group - Maximize statistical power

See DEG Analysis for details.

Getting Help

Where can I find more documentation?

• Browse the documentation sections in the sidebar
• Start with Quick Start Guide
• Check Tutorials for guided workflows
• Review the Glossary for term definitions

Who should I contact for support?

Contact your data administrator or the support team responsible for your MATISSE Explorer installation.