XOpat — OpenSeadragon-based histology data visualizer

xOpat is a JavaScript application. Two reference backends ship in the repo and either may serve it:

• server/node/ — canonical Node.js backend (see server/node/README.md). Started with npm run s-node (production) or npm run dev (server/utils/node/dev-mode.js).
• server/php/ — legacy PHP backend (entrypoint server/php/index.php → server/php/init.php).

Both backends inject the same runtime configuration into the browser and provide the proxy/auth/storage endpoints the client expects. A high-level integration story lives in ../INTEGRATION.md; operational/deployment docs at https://xopat.org.

Configuration

The viewer always boots from a single object (XOpatRuntimeConfig, see src/types/app.d.ts) carrying params, data, background, visualizations, plugins. The client resolves where that object comes from in this order — first hit wins (src/parse-input.js:94–209):

1. POST body, field visualization (legacy alias visualisation also accepted). Canonical delivery for non-trivial sessions; the field carries either a JSON object or a JSON-encoded string. The server advertises POST support via XOpatServerConfig.supportsPost (src/types/config.d.ts:113).
2. URL hash #<urlencoded-json> — parsed locally. If supportsPost is true the viewer transparently rewrites the navigation into a self-POST (hidden form at parse-input.js:110–123) so refreshes/shares stay POST-backed and the address bar is clean.
3. ?visualization=<urlencoded-json> query parameter — same parser as the hash path.
4. ?slides=id1,id2&masks=m1,m2 shorthand — synthesizes one background per slide plus a heatmap-shader visualization per mask (parse-input.js:131–174). Convenient for quick links and CI tests.
5. Storage fallback — localStorage["xoSessionCache"] (or sessionStorage["xoSessionCache"]) restores the last successful session if it is < 30 minutes old. The restored config is marked __fromLocalStorage: true so plugins can detect it. Every successful boot writes the current session back to both storages, so an auth-redirect round-trip never loses state.

A simple form that just POSTs a session JSON into the visualization field is available at /dev_setup on both backends (server/node/index.js:438–473, 610–611, server/php/dev_setup.php, template server/templates/dev-setup.html). Use it during development; in production the embedding application supplies POST data directly.

Plugins may layer additional opening behavior on top of this pipeline — check the relevant plugin README.

Example session

{
  "params": {
    "sessionName": "Demo case 0042",
    "locale": "en"
  },
  "data": [
    {
      "dataID": "path/to/tissue/scan.tif",
      "microns": 0.001,
      "protocol": "dzi",
      "options": { "format": "jpeg" }
    },
    "path/to/annotation.tif",
    "path/to/probability.tif"
  ],
  "background": [
    { "dataReference": 0 }
  ],
  "visualizations": [
    {
      "name": "A visualization setup 1",
      "shaders": {
        "shader_id_1": {
          "name": "Advanced visualization layer",
          "type": "edge",
          "fixed": false,
          "visible": 1,
          "dataReferences": [2, 0],
          "params": {}
        },
        "another_shader_id": {
          "name": "Probability layer",
          "type": "edge",
          "visible": 1,
          "dataReferences": [1],
          "params": { "color": "#fa0058", "use_gamma": 1.0 }
        }
      }
    }
  ],
  "plugins": {
    "recorder": {}
  }
}

data — DataSpecification[] (required)

Each entry is either a bare DataID (string/object the image server understands — most often a UUID4 or file path; objects are used by sources like DICOM) or a DataOverride (src/types/app.d.ts:31–39):

• dataID (required) — the underlying DataID.
• options — generic map forwarded to the TileSource (SlideSourceOptions, src/types/app.d.ts:46–49). Standard keys: format.
• microns / micronsX / micronsY — pixel size in micrometers.
• protocol — name of a registered slide protocol (see Slide protocols below). In non-secure mode a backtick-template string is accepted for back-compat, but is rejected with a warning in secure mode.
• imageSmoothingEnabled — when false, tiles for this data source are sampled with gl.NEAREST (blocky pixels at high zoom — useful for label maps or integer-coded segmentation layers). When true or unset (default), tiles use gl.LINEAR. Honored by drawers that implement setTiledImageSmoothingEnabled (currently FlexDrawer); silently ignored otherwise.
• tileSource — deprecated escape hatch for code-only consumers; not serializable.

params — viewer setup (optional)

Aligned with XOpatSetup in src/types/config.d.ts:53–87. initXOpat silently drops unknown keys with a console warning (src/app.ts:108–122), so typos vanish quietly — verify names against the type.

Key	Type	Default	Notes
sessionName	string	—	Unique session id; overridable by background[i].sessionName.
locale	string	"en"	i18next locale.
theme	"auto" \| "light" \| "dark"	"auto"	DaisyUI data-theme; "auto" follows the OS preference. ("dark_dimmed" / "dimmed" were never wired up in the v3 UI.)
customBlending	bool	false	Allow user-programmed blending.
debugMode	bool	false	Verbose runtime instrumentation.
webglDebugMode	bool	false	Debug post-processing.
webGlPreferredVersion	string	—	Select WebGL backend version.
valueInspectorEnabled	bool	false	Hover value inspector.
visualizationInspectorEnabled	bool	false	Pixel/lens inspector overlay.
visualizationInspectorMode	string	—	Inspector mode (paired with UTILITIES.setVisualizationInspectorMode).
visualizationInspectorRadiusPx	number	—	Inspector radius.
visualizationInspectorLensZoom	number	—	Lens zoom factor.
activeBackgroundIndex	number | number[]	0	Initial bg index; array for multi-view.
viewport	ViewportSetup \| ViewportSetup[]	—	{ point, zoomLevel, rotation? }; single value applies to all viewers or one per viewer in multi-view.
preventNavigationShortcuts	bool	false	Disable xOpat navigation bindings (OSD defaults still apply).
scrollRequiresCtrl	bool	false	Require Ctrl/Cmd + wheel to zoom; plain wheel scrolls the host page. Use for notebook / scrollable-host embeddings. A throttled toast nudges first-time users toward the modifier.
scaleBar	bool	true	Deprecated, use ui.scaleBar. Requires microns to render.
toolBar	bool	—	Deprecated, use ui.toolBar.
statusBar	bool	—	Deprecated, use ui.statusBar.
ui	XOpatUiSetup	—	Initial visibility of UI components — see table below.
disablePluginsUi	bool	false	Hide plugin UI without unloading the plugins.
disablePluginsAutoload	bool	false	Skip the _plugins cookie restore for this session. permaLoad plugins and plugins listed in config.plugins still load. Use to ignore the user's prior manual picks while respecting deployment defaults and session-declared plugins.
grayscale	bool	false	Force grayscale transfer.
tileCache	bool	true	Enable tile caching.
maxImageCacheCount	number	1200	Tile cache size.
preferredFormat	string	—	Hint to the protocol; must be honored by the TileSource.
background	string	—	Hex #RGB/#RGBA clear color (e.g. fluorescence). Transparent if unset.
permaLoadPlugins	bool	true	Remember loaded plugins across sessions.
bypassCookies	bool	false	Skip cookie-backed user state.
bypassCache	bool	false	Never reuse cached values.
bypassCacheLoadTime	bool	false	Ignore cache at initial load only — avoids pulling cached content from a foreign session.
historySize	number	—	Cap on the history stack (src/classes/history.ts).
isStaticPreview	bool	false	Disable interactive controls for thumbnail/preview embeds.
maxMobileWidthPx	number	—	Responsive breakpoint.

params.ui — UI initial visibility

Each flag is the initial visible state at boot. false boots the component collapsed, but the user can still bring it back via the settings menu, the hide-UI button, or the relevant opener. Defaults to true for every key. Reads go through APPLICATION_CONTEXT.getUiOption(key) which also honors the legacy flat aliases (scaleBar / toolBar / statusBar) and the AppCache of user-toggled settings — see XOpatUiSetup in src/types/config.d.ts.

Shorthand: set params.ui: false (or setup.ui: false for a deployment-wide default) to hide every global UI component in one shot — handy for notebook embeddings. params.ui: true is equivalent to leaving the field unset.

Key	Affects
scaleBar	Per-viewer OSD scalebar overlay. Replaces legacy flat scaleBar.
toolBar	Top viewer toolbar. Replaces legacy flat toolBar.
statusBar	Bottom status bar (#viewer-status-bar). Replaces legacy flat statusBar.
mainMenu	Global menu (FullscreenMenus). false boots collapsed; menu-open buttons still work.
navigator	Per-viewer OSD navigator panel.
appBar	Top AppBar chrome — false is equivalent to the hide-UI button being pre-toggled.
globalMenu	Global right-side dock (window.LAYOUT) that hosts plugin tabs (chats, slide-switcher, questionnaire, …). false boots the dock closed; user opens/plugins focus still work.

background — BackgroundItem[]

Each item is an image group rendered as one OSD layer (src/types/app.d.ts:76–90):

• dataReference (required) — index into data, or an inline DataID / DataOverride. One reference per background entry.
• shaders (optional) — shader configuration array, same shape as visualization shaders (dataReferences becomes optional). When unset, the renderer synthesizes an implicit identity shader keyed under the background's id. As soon as any entry is set, the implicit identity is replaced. canonical-scene.ts materializes the implicit entry as [{ type: "identity", … }] when a tool edits it, so the change persists across reopens.
• id — unique id; derived from the data path if unset.
• name — tissue name shown in the UI.
• sessionName — overrides params.sessionName for this background.
• visualizationIndex — index into visualizations selected when this background is mounted. Authoritative per-viewer viz binding — the slot's viz follows the bg entry through slot reordering / insertion / deletion. Pass null for "no overlay". Legacy goalIndex is still accepted on read (folded with a one-time warning).
• options — forwarded to the TileSource.

Legacy fields lossless, protocol, microns, micronsX, micronsY are still accepted at the background level for back-compat, but new code should put them on the DataOverride instead.

visualizations — VisualizationItem[]

WebGL composition goals over the data group (src/types/app.d.ts:109–116):

• shaders (required) — map of shader id → layer spec:
  • type (required) — color, edge, dual-color, identity, heatmap, none, or any custom-registered shader.
  • dataReferences (required) — index array into data.
  • visible — 1/0 or boolean.
  • name — UI label.
  • fixed — if false, user can change the shader type; default true.
  • params — shader-specific defaults; invalid entries fall back silently.
• name — goal label.
• goalIndex — preferred index when this item is selected.

Legacy lossless and protocol are accepted at the visualization level for back-compat — prefer DataOverride.

plugins

Plugin-id → plugin-config map; consult each plugin's README.

Advanced features

**Internal parameters.** The runtime augments visualization items at runtime with fields that show up in serialized sessions: - `order` — shader-id array on a visualization goal; sets render order. All referenced data with `visible=1` must be present and valid. - `cache` — per-shader, shader-type-dependent value bag (equivalent to default-value overrides). Type-sensitive: writing a wrong-type value will break rendering. **Slide protocols.** A protocol is a named entry in `ENV.client.slide_protocols` (see `src/types/config.d.ts:5–28`, registry implementation at `src/classes/slide-protocols.ts`). Each entry is either: - a URL template string with `data` in scope (non-secure mode only — rejected in secure mode), or - an object `{ url, proxy?, baseURL?, auth?, … }` whose extra fields are forwarded verbatim to `new HttpClient(...)`, so every metadata + tile request the resulting TileSource issues inherits proxy routing, CSRF tokens, and JWT/auth headers uniformly. `DataOverride.protocol` (and legacy `BackgroundItem.protocol` / `VisualizationItem.protocol`) reference an entry **by name** (`"dzi"`, `"dicomweb"`, …). Defaults come from `default_background_protocol` / `default_visualization_protocol`; the legacy `image_group_*` / `data_group_*` env keys are auto-migrated into synthesized `__legacy_bg` / `__legacy_viz` entries. Plugins register protocols at runtime via `window.SLIDE_PROTOCOLS.register({ id, createTileSource })`. Use this registry instead of hand-rolling URLs in `background.protocol`/`visualizations.protocol` — those evaluations are blocked in secure mode and lose proxy/auth integration.

Structure

Each folder ships a README with more detail. The most up-to-date ones are this file, ../plugins/README.md, and ../modules/README.md.

../ (repo root)

• index.html and the server/ tree (Node + PHP entrypoints).
• package.json — s-node, s-node-test, dev, docker-node, docker-php.

./ (src/)

• app.ts — initXOpat(...) entrypoint; builds APPLICATION_CONTEXT, VIEWER_MANAGER, SESSION, IO_PIPELINE.
• loader.ts — module/plugin loader and the global helpers plugin(id), singletonModule(id), viewerSingletonModule(className, viewerLike).
• parse-input.js — the precedence chain described in Configuration above.
• store.ts — pluggable storage middleware (KV drivers used by the IO pipeline).
• tile-source.ts — common TileSource scaffolding.
• classes/
  • app/ — viewer-open pipeline and canonical-scene round-trip (viewer-open-pipeline.ts, canonical-scene.ts, application-lifecycle-controller.ts, viewer-inspector-controller.ts).
  • io/ — IO pipeline implementation (see IO_PIPELINE.md).
  • session/ — live-collaboration controller (see SESSION.md).
  • scripting/ + scripting-manager.ts — sandboxed scripting API.
  • slide-protocols.ts — SLIDE_PROTOCOLS registry.
  • http-client.ts — HttpClient (see HTTP_CLIENT.md).
  • history.ts, user.ts.
• external/ — always-loaded third-party libraries and OSD extensions (DZI ext tile source, scalebar, autocomplete, …).
• libs/ — vendored libraries: jQuery, i18next, OpenSeadragon (openseadragon.js), Tailwind CSS, Monaco, FontAwesome, Phosphor Icons (phoshor-icons/), plus flex-renderer/ (WebGL renderer). Do not edit libs/ — upstream-only. Exception: phoshor-icons/fa-overrides.css is xOpat-owned and should be edited to extend the Font Awesome → Phosphor mapping as we migrate.
• assets/ — style.css, icons, and other static assets.
• types/ — ambient TypeScript declarations (app.d.ts, config.d.ts, globals.d.ts, slide-protocols.d.ts, io.d.ts).

OpenSeadragon (v6+) is bundled under src/libs/openseadragon.js and configured via openSeadragonPrefix / openSeadragon in src/config.json. To run a debug build, point those values at an unminified copy.

../plugins/, ../modules/

User-facing features and shared libraries respectively; both are dynamically loadable via the loader. See their READMEs.

Available API

Make sure you've read ../INTEGRATION.md first.

Globals

Established by src/app.ts and src/loader.ts. These are the supported, ambiently-typed entrypoints:

Global	Where it's set	Purpose
window.APPLICATION_CONTEXT	src/app.ts:159	Session, config accessors, open pipeline.
window.VIEWER_MANAGER	src/app.ts:224	Manager for all OSD viewer instances (single- and multi-view).
window.USER_INTERFACE	UI layer	Core generic UI operations (notifications, menus).
window.UTILITIES	UI / inspector controllers	System utilities (inspector toggles, serializers).
window.HttpClient	src/classes/http-client.ts:349	Auth-aware HTTP client (proxy, JWT, CSRF).
window.SESSION	src/app.ts:230	Live-collaboration SessionSyncController.
window.IO_PIPELINE	bootstrapIOPipeline() in src/app.ts:149	Save/load pipeline; also reachable as APPLICATION_CONTEXT.io.
window.SLIDE_PROTOCOLS	src/classes/slide-protocols.ts	Slide-protocol registry.
window.xmodules	src/loader.ts	Object store of module exports. Use the helpers below — don't reach in directly.
plugin(id)	src/loader.ts:298	Returns the plugin instance.
singletonModule(id)	src/loader.ts:313	Returns (and lazily instantiates) the module singleton.
viewerSingletonModule(className, viewerLike)	src/loader.ts:330	Returns a per-viewer XOpatViewerSingleton.

window.VIEWER is not a stable handle — it tracks whichever viewer most recently took focus, which is the wrong instance whenever multi-view is active. Resolve the right viewer with VIEWER_MANAGER.get(...), with viewerSingletonModule(...), or from e.eventSource on broadcast events. Likewise, do not store long-lived TiledImage references unless you own them, and prefer VIEWER_MANAGER events over reaching for the focused viewer. When you only need to retarget one viewer, use updateViewerSelection(...) instead of rebuilding the whole session. See MULTI_VIEWPORTS.md.

Viewer Open API

xOpat treats viewer opening as an explicit transaction rather than a loose mix of config mutation and OpenSeadragon world edits. The runtime opening pipeline is class-based and lives under src/classes/app/ — viewer rebinding, visualization runtime checks, synthetic-open handling, inspector integration, and session lifecycle all stay there, and src/app.ts is intentionally reduced to bootstrap/composition. The public entrypoints exposed to plugins/modules remain global through window.APPLICATION_CONTEXT.

• APPLICATION_CONTEXT.openViewerWith(data?, background?, visualizations?, bgSpec?, vizSpec?, opts?)
  • Main transaction entrypoint.
  • Can replace or merge session data / background.
  • Can create additional viewers when multiple backgrounds are targeted.
  • vizSpec arrays may contain explicit undefined entries to mean "no visualization for this viewer"; omitted vizSpec still means "keep the current selection".
  • Rebinds navigator title, scalebar reference, measurements, visualization menu, history, and synthetic open events.
• APPLICATION_CONTEXT.updateViewerSelection(viewerIndex, { backgroundIndex?, visualizationIndex? }, opts?)
  • Use when one existing viewer should switch background and/or visualization without rebuilding unrelated viewers.
  • Passing visualizationIndex: null clears the active visualization for that viewer.
  • Delegates to the same open pipeline, keeping history/session synchronization consistent.
• APPLICATION_CONTEXT.replaceVisualizations(visualizations, newData?, activeVizIndex?)
  • Replaces the session visualization list while preserving the rest of the session.
  • Preferred over the older updateVisualization(...) name.

Options are ambiently typed as ViewerOpenOptions and per-viewer patches as ViewerSelectionPatch, so plugins/modules use them without importing from core.

Canonical Scene

src/classes/app/canonical-scene.ts is the single round-trip pair for full session state. Use it whenever you need to capture what is currently rendered and replay it later — playground Apply, session sync's heavy-apply path, scripting export/import, and draft persistence all go through it.

• serializeScene() — captures cfg (data, background, visualizations, active indices) and merges per-shader runtime cache/state from every viewer's renderer back into the structural shader entries. Returns a CanonicalScene JSON object.
• serializeSceneFromViewer(viewer, init, live?) — single-viewer slice, used by the playground page (passes its namespace-stripped live so renderer ids match the structural ids).
• deserializeScene(scene, opts) — calls APPLICATION_CONTEXT.openViewerWith(...) with the canonical cfg shape and forwards historyMode / historyLabel. The pipeline rebuilds renderers from the inlined cache — no second per-layer apply pass needed.
• backgroundShaderRendererIds(bg) / visualizationShaderRendererIds(viz) — single source of truth for renderer-id derivation. Bg shader ids follow bgRef.id for index 0 and ${bgRef.id}-N for subsequent entries (mirrors assemble-render-output.ts:149-150); viz shader ids are the structural map keys.

Devtools handle: window.__SCENE = { serialize, serializeFromViewer, deserialize, … }. Inspect the round-trip from the console — e.g. await __SCENE.deserialize(__SCENE.serialize(), { historyMode: "skip" }) should be a visual no-op.

Implicit identity rule. When cfg.background[i].shaders is unset, the renderer synthesizes an identity shader at bg.id. If a tool edits that implicit shader, the canonical-scene serializer materializes it as [{ type: "identity", cache: {…} }] so the change persists across reopens.

Session Restore and Lifecycle

Session bootstrap and restore live in ApplicationLifecycleController.

• Startup restores the last successful session from browser storage when no explicit POST/hash/query session is provided (see Configuration above).
• beginApplicationLifecycle(...) loads required plugins, initializes layers, raises before-app-init, and then opens the requested viewer state.
• Inspector registration is centralized in ViewerInspectorController (no longer mixed into app.ts).

IO Pipeline

window.IO_PIPELINE (also APPLICATION_CONTEXT.io) decouples what modules want to save/load from where it goes. Modules declare capabilities in their include.json (io.capabilities); admin config (ENV.client.io.bindings) binds those to concrete sinks. Plugin authors typically:

• Register bundle-level hooks via this.initIO({ bundleScope, exportBundle, importBundle }).
• Define per-element CRUD resources via this.defineResource({ name, validate, serialize, deserialize }).

The pipeline queues sink dispatch per-resource, supports coalescing, and persists its outbox to IndexedDB. Bundle sinks include file-download, file-upload, post-data, http-rest. See IO_PIPELINE.md for the full design.

Session / Collaboration

window.SESSION is a SessionSyncController singleton enabling real-time peer-to-peer collaboration. Plugins/modules participate by calling window.SESSION?.registerProvider({ id, scope, snapshot, applySnapshot, subscribe, applyDelta }). The sessionCompatible flag in include.json declares participation: "provider" = actively syncs, true = safe but non-syncing, false = incompatible (undeclared plugins trigger a warnings modal). Hosts provision guest URLs via UTILITIES.serializeApp(...) so guests load the host's exact plugin set. Read meta.role in post-event handlers to avoid duplicate side effects on guests. See SESSION.md.

HttpClient

Never use native fetch or XMLHttpRequest for upstream calls — HttpClient (src/classes/http-client.ts) integrates with xOpatUser and injects JWT, CSRF, and proxy paths automatically. See HTTP_CLIENT.md.

const client = new HttpClient({
  proxy: "cerit",           // alias defined in server proxies
  baseURL: "/api/v1",
  auth: { contextId: "core", types: ["jwt"], required: true },
  timeoutMs: 30000,         // optional, default 30s
  maxRetries: 3,            // optional, default 3
});

const response = await client.request("data", {
  method: "POST",
  body: { object: "goes here" },
  expect: "json",           // "json" | "text" | "auto"
  // query: { foo: "bar" },
});

Inspector Utilities

Ambiently typed, part of the supported runtime surface:

• UTILITIES.toggleVisualizationInspector(enabled?)
• UTILITIES.setVisualizationInspectorRadius(radiusPx)
• UTILITIES.adjustVisualizationInspectorRadius(deltaPx)
• UTILITIES.setVisualizationInspectorMode(mode)
• UTILITIES.toggleValueInspector(enabled?)

Scripting

src/classes/scripting-manager.ts + src/classes/scripting/ is a Worker-based sandbox exposing scripting namespaces (XOpatApplicationScriptApi, XOpatViewerScriptApi, XOpatVisualizationScriptApi) to user/plugin scripts. Use it for advanced automation and LLM integration; not required for typical plugin development.

UI

Use the new UI components — see ../ui/README.md and ../ui/classes/README.md. Extend BaseComponent and rely on Van.js reactivity instead of manual jQuery DOM work. The CORE UI singletons (AppBar, FloatingManager, FullscreenMenus, GlobalTooltip, …) are listed in ../ui/services/README.md.

Reuse the existing components before pulling new dependencies. If you need a DaisyUI element that isn't already wrapped, add it under ui/classes/elements so other plugins can reuse it.

Localization

Driven by i18next. Use $.t('translation_key') at runtime; $.i18n holds the instance. Server-side i18n is available with limited capabilities. In spawned child windows, $.t(...) works but jquery-i18next is not bundled.

For plugin localization specifics, see the plugins README.

Embedding the viewer in a custom server

The two reference backends are the documentation:

• PHP — server/php/init.php shows the canonical wiring. The helpers in server/php/inc/core.php (require_libs, require_openseadragon, require_external, require_core) and server/php/inc/plugins.php (require_modules, require_plugins) are still the building blocks for embedding xOpat into a PHP host. The browser-side entry is initXOpat(PLUGINS, MODULES, ENV, POST_DATA, PLUGINS_FOLDER, MODULES_FOLDER, VERSION, I18NCONFIG?) (src/app.ts:44).
• Node — server/node/index.js and server/node/README.md cover the modern integration story: session-cookie CSRF, RPC for plugins/modules, dev-mode hot reload via server/utils/node/dev-mode.js.

Further reading

• Lifecycle events: EVENTS.md
• HTTP / proxies / token verifiers: HTTP_CLIENT.md
• IO pipeline (save/load): IO_PIPELINE.md
• Live collaboration: SESSION.md
• Multi-viewport rules: MULTI_VIEWPORTS.md
• NPM-packaged modules/plugins: NPM_MODULES_PLUGINS.md
• Plugin development: ../plugins/README.md
• Module development: ../modules/README.md
• UI design system: ../ui/README.md, ../ui/classes/README.md, ../ui/services/README.md