What is MATISSE Explorer?

Core Feature

This feature is available in all MATISSE Explorer deployments.

MATISSE (Multi-modal Analysis Toolkit for Interactive Spatial Transcriptomics & Systems Exploration) Explorer is an interactive visualization platform designed specifically for spatial transcriptomics data analysis. It provides researchers with powerful tools to explore, filter, and analyze complex biological datasets through an intuitive web-based interface.

Why Spatial Transcriptomics Analysis Matters

Spatial transcriptomics is a revolutionary technology that combines gene expression data with spatial location information within tissue samples. This allows researchers to:

• Understand tissue architecture - See how different cell types are organized within tissues
• Discover spatial patterns - Identify gene expression gradients and localized clusters
• Study cell-cell interactions - Analyze how neighboring cells influence each other
• Map disease states - Visualize how pathological changes are distributed across tissue

However, spatial transcriptomics generates massive, high-dimensional datasets that are challenging to explore using traditional tools. MATISSE Explorer addresses this challenge by providing:

• High-performance rendering capable of displaying millions of data points
• Intuitive filtering to isolate specific cell populations
• Multiple visualization modes for different analytical perspectives
• Interactive tools for defining and comparing regions of interest

Key Use Cases

Cell Type Exploration

Visualize the spatial distribution of different cell types across your tissue sample. Use categorical annotations to color-code cells by type and understand their organization patterns.

Gene Expression Analysis

Examine how specific genes or gene sets are expressed across tissue regions. Apply continuous color mapping to visualize expression gradients and identify hotspots.

Region Comparison

Use lasso selection to define custom regions of interest. Compare gene expression between regions or export selected populations for downstream analysis.

Multi-dimensional Analysis

Switch between spatial coordinates and dimensionality reduction views (UMAP, t-SNE) to understand both physical and transcriptional relationships in your data.

Data Filtering and Export

Build complex filter queries to isolate specific cell populations based on multiple criteria. Export filtered data for further analysis in other tools.

Supported Data

MATISSE Explorer works with pre-processed spatial transcriptomics data. The platform supports:

Image Formats

• GeoTIFF - Cloud Optimized GeoTIFF for efficient streaming
• Static Images - PNG, JPEG for simple backgrounds
• Tile Pyramids - Multi-resolution tiles for large images

Data Types

• Observations (cells/spots) - Individual data points with spatial coordinates
• Annotations - Categorical labels, continuous values, and embedding coordinates
• Gene Expression - Expression values for individual genes or gene sets

Next Steps

• Interface Overview - Learn about the application layout
• Quick Start Guide - Start exploring your data