Glossary

Core Feature

This reference covers terminology used across all MATISSE Explorer deployments.

Definitions of key terms used in MATISSE Explorer.

A

Activity Bar

The vertical bar on the left side of the interface containing icons for switching between extensions (Explorer, Plot) and accessing settings.

Filter

A filtering system that allows combining multiple conditions with AND/OR logic, including column conditions, lasso conditions, and variable set conditions.

Annotation

A data column that describes properties of each data point. Can be categorical, continuous, or embedding type.

C

Categorical Annotation

An annotation containing discrete labels or categories (e.g., cell types, clusters). Each data point belongs to exactly one category.

Colormap

A color scheme used to represent continuous values. Examples include Cool, Rainbow, Viridis.

Combination Method

The mathematical operation used to compute a score from multiple variables in a Variable Set. Options: Max, Min, Sum, Average, UMI Count.

Condition

A single filter rule specifying criteria for including or excluding data points.

Continuous Annotation

An annotation containing numeric values that vary continuously across data points (e.g., gene expression levels).

D

Data Point

An individual observation in the dataset, typically representing a cell or spatial spot.

DEG (Differentially Expressed Genes)

InSilicoLab

Genes that show statistically significant differences in expression levels between two or more groups of cells. DEG analysis is used to identify marker genes and understand biological differences between populations.

DEG Analysis

InSilicoLab

A statistical analysis method that compares gene expression between defined cell groups to identify significantly up- or down-regulated genes. Available in InSilicoLab.

E

Embedding

A low-dimensional representation of high-dimensional data, typically produced by dimensionality reduction algorithms like UMAP or t-SNE.

Embedding Annotation

An annotation containing X and Y coordinates from a dimensionality reduction, used for alternative projections.

Extension

A modular component of MATISSE Explorer that provides specific functionality. Current extensions: Explorer, Plot.

Explorer

The primary extension for visualizing and navigating spatial data, managing annotations, and applying filters.

F

Filter

A set of conditions that determine which data points are visible. Points not matching the filter criteria are hidden.

Filter Preset

A saved filter configuration that can be loaded and reused.

FDR (False Discovery Rate)

InSilicoLab

A statistical method for correcting p-values when performing multiple comparisons. In DEG analysis, FDR-adjusted p-values (q-values) indicate the expected proportion of false positives among significant results.

G

GeoTIFF

A georeferenced image format used for background tissue images. Cloud Optimized GeoTIFF enables efficient streaming.

Group (Filter)

A collection of filter conditions combined with a single logical operator (AND or OR).

I

InSilicoLab

A cloud-based spatial transcriptomics analysis platform by Portrai. InSilicoLab provides MATISSE Explorer with additional features including DEG analysis and server-side data processing capabilities.

L

Lasso Selection

An interactive tool for selecting data points by drawing a closed polygon around them.

Lasso Condition

A filter condition based on a saved lasso selection, allowing reuse of spatial or embedding-based selections.

Legend

A visual reference showing the mapping between colors and values or categories in the current view.

Log Fold Change (logFC)

InSilicoLab

A measure of expression difference between two groups, calculated as log2(GroupB/GroupA). Positive values indicate upregulation in Group B; negative values indicate downregulation. A logFC of 1 represents a 2-fold increase.

M

MATISSE

Multi-modal Analysis Toolkit for Interactive Spatial Transcriptomics & Systems Exploration. The name of the platform.

Map Viewer

The main visualization component in the Explorer extension, displaying data points overlaid on a background image.

O

Opacity

The transparency level of visual elements. Lower opacity allows seeing through overlapping elements.

P

Pan Mode

The default interaction mode for navigating the map by clicking and dragging.

Plot Extension

An extension providing scatter plot visualizations for exploring relationships between annotations.

Point

See Data Point.

Preset

See Filter Preset.

Projection Mode

The coordinate system used to display data points. Options typically include Spatial, UMAP, and t-SNE.

S

Scale Type

The mathematical transformation applied to values for visualization. Options: Linear, Log, Sqrt, SymLog, Quantile.

Scatter Plot

A two-dimensional visualization showing data points positioned by X and Y values from selected annotations.

Selection Mode

An interaction mode that enables drawing lasso selections to highlight or filter data points.

Sidebar

The panel between the Activity Bar and Workspace, containing controls and settings for the active extension.

Spatial Coordinates

The original physical coordinates of data points within the tissue sample.

T

t-SNE

t-distributed Stochastic Neighbor Embedding. A dimensionality reduction technique that preserves local structure, often used for visualizing clusters.

Tile

A portion of a large image, used in tile pyramid systems for efficient loading at different zoom levels.

Tooltip

A small popup displaying information about a data point when hovering over it.

U

UMAP

Uniform Manifold Approximation and Projection. A dimensionality reduction technique that preserves both local and global structure.

UMI Count

Unique Molecular Identifier count. A method for quantifying gene expression that accounts for sequencing depth: ln(10000 × sum/totalUMI + 1).

V

Variable Set

A user-defined collection of variables (typically genes) that can be combined into a single score for visualization and filtering.

W

Workspace

The main content area of the interface, displaying either the map viewer (Explorer) or plots (Plot extension).