MATISSE ExplorerMulti-modal Analysis Toolkit for Interactive Spatial Transcriptomics & Systems Exploration

Explore and analyze your spatial transcriptomics data with powerful interactive tools

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Spatial Visualization

View tissue images with data points, zoom and pan seamlessly, switch between spatial and embedding projections

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Color-code your data by any annotation - cell types, gene expression, or custom variable sets

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Build complex filter queries with AND/OR logic, lasso selections, and reusable presets

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Explore relationships with configurable scatter plots and direct lasso selection on plots

Section	Description
Explorer	Map viewer, annotations, variable sets, navigation
Filtering	Filtering, lasso selection, presets
Visualization	Color mapping, layer settings, image adjustments, scatter plots
Data Export	Exporting data to CSV format
Settings	Theme and preferences
Analysis	DEG analysis and platform-exclusive features
Tutorials	Step-by-step workflow guides
Reference	Glossary, FAQ