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. In Compact Mode, the Activity Bar also displays panel buttons for quick access to sidebar content.

App Color

The customizable accent color used for buttons, highlights, and interactive elements throughout the application. Configurable in Settings under Appearance. Default is Portrai Blue.

Subset

A subsetting system that allows combining multiple conditions with AND/OR logic, including column conditions, lasso conditions, and signature conditions.

Feature

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

C

Categorical Feature

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

Category Color Picker

A tool for customizing individual category colors in categorical visualizations. Provides three selection methods: a 20-color preset palette, direct HEX code input, and a native system color picker. Custom colors are stored locally and persist across sessions.

Colormap

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

Column Sorting

A global feature that allows sorting the Feature list alphabetically. Options include Default (original dataset order), Name A-Z (ascending), and Name Z-A (descending). The sort preference persists across sessions.

Combination Method

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

Compact Mode

A layout mode that collapses the Sidebar to maximize the Workspace area. When active, panel buttons appear in the Activity Bar, allowing access to sidebar content via hover preview or click-to-pin popovers. Activated by dragging the Sidebar width below approximately 100 pixels.

Condition

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

Continuous Feature

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

D

Details Panel

A panel in the Sidebar that displays information about the currently selected feature or Signature. Available in both Explorer and Plot extensions. Shows category counts, value ranges, and Signature variable details.

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 Feature

A feature 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 features, and applying subsets.

F

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 (Subset)

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

K

Keyboard Shortcut

A key combination that performs an action in MATISSE Explorer. Examples include number keys (1-9) to switch extensions, Ctrl/Cmd+\ to toggle Compact Mode, and L to open Layer Settings.

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 subset 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.

LogFC Threshold

A user-configurable threshold for the log fold change value used in DEG direction filtering. The default value is 1 (2-fold change). Can be adjusted in the DEG analysis direction filter controls.

M

MSigDB

Molecular Signatures Database. A curated collection of gene sets organized by categories (Hallmark, Reactome, Gene Ontology) that can be searched and used when creating Signatures.

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.

Notification

An in-app alert displayed via the bell icon in the Activity Bar. Notifications inform users of events such as completed analyses or session warnings. Supports info, success, warning, and error types.

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 features.

Point

See Data Point.

Preset

See Saved Subset.

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, Log2, Log1p, SymLog, Sqrt, Power.

Scatter Plot

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

Saved Subset

A saved subset configuration that can be loaded and reused.

Selection Mode

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

Signature

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

Subset

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

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).

W

Workspace

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