Glossary

This page collects the terms and concepts you will meet throughout the xOpat documentation. If something in another chapter is unclear, look it up here first.

Imaging concepts

WSI (Whole-Slide Image)

A digitized microscopy slide. WSIs are high-resolution images, ranging from hundreds of megabytes to several gigabytes. They are stored in a pyramidal structure: the same image at progressively lower resolutions, so a viewer can load only the detail it currently needs.


Tile

A small rectangular piece of one pyramid level. Instead of downloading a whole multi-gigabyte slide, the viewer requests only the tiles visible at the current zoom and position, which makes real-time viewing possible.

Image Server (WSI Server / Service)

A service that reads WSI files and serves their tiles over HTTP. xOpat has no hardwired backend — you connect it to an image server of your choice. The RationAI WSI-Service is the reference server used throughout these docs, but any server xOpat can speak to works. All OpenSeadragon-supported (and FlexDrawer) protocols, other APIs through modules/plugins, or add support for your custom server with a single file.

Image Protocol / Slide Protocol

The recipe xOpat uses to turn a slide identifier into a tile-source URL for a specific image server. Protocols are registered in the static configuration (slide_protocols) and can also be added at runtime by plugins via window.SLIDE_PROTOCOLS.register(...). The default_background_protocol and default_visualization_protocol keys pick which protocol is used by default.

Tile Source

xOpat's (OpenSeadragon) object that knows how to fetch tiles for one image from one image server. A protocol produces a tile source for a given slide.

The viewer

xOpat

The eXplainable Open Pathology Analysis Tool — a browser-based, server-agnostic WSI viewer. It behaves like an enhanced OpenSeadragon with powerful visualization, annotation, and extensibility on top.

OpenSeadragon (OSD)

The underlying open-source deep-zoom image viewer xOpat builds on. Each viewport in xOpat is an OpenSeadragon instance.

Viewer / Viewport

A single rendering surface (one OpenSeadragon instance) showing one slide context. xOpat supports multiple simultaneous viewports in a grid, each with its own background and visualization selection.

Background

The base raster image shown in a viewport — typically the WSI itself. A viewer session references background slides through the background configuration.

Visualization

A configurable stack of rendered layers drawn over the background, similar to Photoshop layers. Each layer is produced by a shader and can be toggled, reordered, and parameterized. Visualizations are how xOpat overlays AI outputs, heatmaps, and other derived data on a slide.

Shader (Visualization Layer)

The rendering recipe for one visualization layer (e.g. heatmap, colormap, edge, identity). Shaders are provided by the WebGL rendering modules and referenced by type in the visualization configuration.

Data Reference

An index into the session's data array used by backgrounds and visualization layers to declare which slide(s) they render, decoupling the data list from how each piece of data is displayed.

Configuration & sessions

Static configuration (env.json)

System-manager-level configuration that sets up the viewer itself: gateway, active client, server protocols, default plugins/modules. It can be generated with grunt env. Unsafe options are configurable only here. See Viewer Configuration.

Dynamic configuration (Session)

The configuration handed to the viewer at startup that defines a session — the data to view, the visualizations, and per-session plugin configuration. Provided via URL parameters, the #visualization=... hash, or a POST visualization field.

Cached configuration

Per-user state cached while using the viewer. Higher configuration levels override lower ones (cached → dynamic → static).

Plugin

A unit delivering user-facing features, tools, or integrations with their own UI (annotations, tutorials, OIDC auth, etc.). Plugins live in plugins/; the Plugins → Catalogue section lists the ones that ship with the viewer.

Module

A shared library or hidden logical extension (annotation mapping, WebGL rendering, tile-source adapters) without a primary UI of its own. Modules live in modules/; the Modules → Catalogue section lists the ones that ship with the viewer.

Server

The optional backend that parses modules/plugins and reads POST data. xOpat ships PHP and Node.js servers, and can also run server-less as a statically compiled build. The choice is covered in the Deployment section.

secureMode

A static-configuration flag that gates dangerous-by-default behaviour (remote tile sources, scripting, etc.). When enabled, risky features must be explicitly opted into.