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Module Catalogue

xOpat ships with the following modules. Pages are generated from each component's include.json; availability in a concrete deployment depends on the server configuration.

auth

ModuleIDVersionDescription
HTTP Basic Authenticationbasic-auth1.0.0Prompts for a username and password and attaches them as an HTTP Basic credential.experimental
SAML Authenticationsaml-auth1.0.0SAML 2.0 Single Sign-On. Validates the IdP assertion on the server and provisions a short-lived token into the viewer session.

Data

ModuleIDVersionDescription
Vector layers (demo)demo-vector-layers1.0.0Opens Mapbox Vector Tiles as a slide layer aligned to the slide's own pixel grid, for the visualization-flexibility showcase.disabled by default experimental
EMPAIA Workbench Clientempaia-workbench0.1.0Runs xOpat as an EMPAIA Workbench v3 vendor app UI: reads the scope, token and backend URL from the workbench client, opens the examination's slides, syncs annotations with the workbench data API, and drives app jobs.
TIFF / GeoTIFF supportgeotiff0.2.0Opens TIFF, OME-TIFF and QPTIFF slides, including high-bit-depth and floating-point samples, and picks the shader that fits the slide's channel layout.deprecated
TIFF / WSI support (web-tiff)webtiff1.0.0Opens TIFF, BigTIFF, OME-TIFF, QPTIFF and TIFF-based whole-slide formats with a libtiff WebAssembly decoder, including high-bit-depth and floating-point samples, and picks the shader that fits the slide's channel layout.experimental

Uncategorized

ModuleIDVersionDescription
Annotation Measurementsannotation-measurements0.2.0Measure annotated regions: area and distances in physical units, intensity statistics, % positive and connected-component counts, with a canvas-first panel for comparing regions against each other, a class, or a derived tissue mask.
Annotations Moduleannotations0.1.0A module that brings annotations functionality.
Chat Based Testerchat-based-tester1.0.0Developer chat harness for viewer testing using vercel-ai-chat-sdkexperimental
RationAI Enhanced WSI Service by Empaiaempaia-wsi-tile-source0.1.0deprecated
Graphics canvas FabricJS over OSDfabricjs0.1.0
Human-readable ID generatorhuman-readable-ids0.1.0
ICC Profiles On Clienticc-profiles0.1.0Mounts ICC Profile loading to OpenSeadragon. It is implemented using WASM with thread workers.
IO GitHub Sinkio-github-sink0.1.0GitHub-backed bundle sink for the IO pipeline. Hydrates from and writes back to a configured repository path; admin-routable via ENV.client.io.bindings. The GitHub PAT is held server-side under server.secure.proxies..headers — never on the client.
IO MLflow Sinkio-mlflow-sink0.1.0Routes xOpat data into MLflow experiments and runs through the IO pipeline. Admin-routable via ENV.client.io.bindings; the record layout is chosen from named templates or a custom mapper. The MLflow credential is held server-side by a proxy alias and never reaches the client.experimental
JWT Token Decoderjwt-decode4.0.0
Markdownmarkdown1.0.0Renders markdown text safely and turns #xopat-… links into actions any subsystem can register.
Page builder for Advanced Menumenu-pages0.1.0
MLflow Clientmlflow0.2.0Low-level MLflow REST client (experiments, runs, metrics, artifacts). A plain library — it performs no IO on its own. To route xOpat data into MLflow, use the io-mlflow-sink module.experimental
OIDC Client for JavaScriptoidc-client-ts2.5.0Library to provide OpenID Connect (OIDC) and OAuth2 protocol support for client-side, browser-based JavaScript client applications. Also included is support for user session and access token management.
Server-side OIDC (confidential)oidc-server-ts1.0.0Server-side OIDC token provider: keeps the client_secret + refresh_token on the server, runs authorize/callback/refresh server-side, and injects the current access/id token into XOpatUser so HttpClient works transparently. Use for IdPs that require a confidential client.
Pathology Foundation Modelspathology-foundation0.2.0Broker that runs named pathology jobs on the active viewport. Ships a built-in, dependency-free tissue detector (works out of the box, nothing leaves the viewer) and lets drivers register per feature (tissue-mask / segment / analyze). Exposes the pathology scripting namespace for LLM/agent use.
RationAI Enhanced WSI Service by Empaiarationai-wsi-tile-source0.1.0
Recorderrecorder1.0.0Captures keyframe and navigation snapshots per viewer as named recordings and plays them back as a timeline.
Html Sanitizationsanitize-html2.11.0
Speech to Textspeech-to-text1.0.0Microphone capture and speech transcription with pluggable drivers (remote self-hosted Whisper by default, in-browser WASM fallback).
VEGA: The visualization grammarvega
VEGA: The visualization grammar (with secure interpreter)vega-secure
AI Chatvercel-ai-chat-sdk1.0.0Integration hub for AI chat models