Tutorial: Basic Exploration Workflow

Core Feature

This tutorial covers features available in all MATISSE Explorer deployments.

This tutorial walks you through a typical workflow for exploring spatial transcriptomics data in MATISSE Explorer. You'll learn how to navigate your data, visualize patterns, and extract insights.

Scenario

You've loaded a spatial transcriptomics dataset and want to:

1. Understand the overall tissue structure
2. Identify different cell populations
3. Examine gene expression patterns
4. Export findings for further analysis

Prerequisites

• A project loaded in MATISSE Explorer
• Basic familiarity with the interface (see Interface Overview)

Step 1: Initial Overview

Start by getting a broad view of your data.

View the Full Tissue

1. Open the Explorer extension (if not already active)
2. Ensure you're in Spatial projection mode
3. Click the Reset View button to see the entire tissue
4. Note the total number of points displayed

Observe the Distribution

• Look at how data points are distributed across the tissue
• Notice any obvious regions or clusters
• Check if the background tissue image provides context

Step 2: Color by Cell Type

Apply categorical coloring to see cell populations.

Select Cell Type Feature

1. In the Sidebar, click the Categorical tab
2. Find the cell type feature (e.g., "cell_type", "cluster")
3. Click to apply coloring
4. Observe the legend showing different cell types

Explore the Distribution

• Identify where different cell types are located
• Notice any spatial organization or clustering
• Hover over the legend to highlight specific types

Step 3: Navigate and Zoom

Explore specific regions in detail.

Zoom to a Region of Interest

1. Use scroll wheel to zoom into an interesting area
2. Click and drag to pan around
3. Notice how cell type composition varies by region

Compare Regions

1. Zoom out to full view
2. Zoom into a different region
3. Compare cell type compositions between regions

Step 4: Examine Gene Expression

Switch to continuous coloring for gene expression.

Select a Gene

1. Click the Continuous tab in the feature list
2. Search for a gene of interest (e.g., CD3E, MS4A1)
3. Click to apply expression coloring
4. Observe the expression gradient across the tissue

Interpret the Pattern

• High expression areas appear in warm/intense colors
• Low expression areas appear in cool/dim colors
• Compare expression pattern to cell type distribution

Step 5: Apply a Subset

Focus on a specific population.

Subset by Cell Type

1. Open the Subset Panel
2. Add a condition for cell type
3. Select one cell type (e.g., "T cells")
4. Apply the subset
5. Only T cells remain visible

Examine Subset Population

1. Note the reduced point count
2. Color by gene expression
3. See expression patterns within the T cell population

Step 6: Use Lasso Selection

Define a custom region.

Draw a Selection

1. Clear any existing subsets
2. Click the Selection button (Lasso icon)
3. Draw a closed shape around a region of interest
4. View the count of selected points

Add Selection to Subset

1. Click the Items dropdown
2. Select Add selection to subset
3. The region becomes a subset condition
4. Only points in the selected region remain visible

Step 7: Switch Projections

View data in embedding space.

View UMAP

1. Find the projection selector
2. Switch to UMAP
3. The view transforms to show UMAP coordinates
4. Color by cell type to see clusters

Compare to Spatial

1. Note how cell types cluster in UMAP
2. Switch back to Spatial view
3. Understand the relationship between transcriptional similarity and spatial location

Step 8: Export Results

Save your findings.

Export Feature Data

1. Apply the subset you want to export
2. Navigate to the feature to export
3. Click Export or Download
4. Save the CSV file

Document Your Findings

• Note the subset settings used
• Record the export timestamp
• Save screenshots for reference

Summary

In this tutorial, you learned to:

Step	Action	Purpose
1	Overview	Understand overall data structure
2	Cell type coloring	Identify populations
3	Navigation	Explore specific regions
4	Gene expression	Examine expression patterns
5	Subsetting	Focus on subsets
6	Lasso selection	Define custom regions
7	Projections	Compare spatial and transcriptional views
8	Export	Save results

Next Steps

• Analysis Workflow - Advanced subsetting and analysis
• Group Comparison Workflow - Compare cell populations
• Subset - Build complex queries