@jax-data-science/sci-image-visualizer 0.10.0 → 0.12.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs}

@@ -1,11 +1,13 @@
 import { LruCache } from 'napari-js';
 import * as ort from 'onnxruntime-web';
-import { g as getOrtWasmBase, f as fetchModel, r as runEncoder, a as runDecoder } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-BKQhpbHv.mjs';
+import { g as getOrtWasmBase, f as fetchModel, r as runEncoder, a as runDecoder } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-a68Hw5rw.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
 import 'rxjs/operators';
 import 'napari-js/geometry';
+import 'fast-png';
+import 'fzstd';
 import '@angular/core/rxjs-interop';
 import '@angular/common';
 import '@angular/forms';
@@ -235,4 +237,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs","sources":["../../src/lib/toolbar/segmentation/pending-calls.ts","../../src/lib/toolbar/segmentation/onnx-sam-session.ts"],"sourcesContent":["/** A reply from the SAM worker: progress for, or the result of, call `id`. */\nexport interface WorkerReply {\n  id: number;\n  type: string;\n  /** Present on `type: 'progress'` replies. */\n  fraction?: number;\n  /** Present on `type: 'error'` replies. */\n  error?: string;\n  [key: string]: unknown;\n}\n\ninterface Pending {\n  resolve: (reply: WorkerReply) => void;\n  reject: (err: Error) => void;\n  onProgress?: (fraction: number) => void;\n}\n\n/**\n * Request/response bookkeeping for a worker RPC: each call gets an id and a\n * promise that its reply settles. Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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package/fesm2022/jax-data-science-sci-image-visualizer.mjs

@@ -1,4 +1,4 @@
-export { A as ALL_GENES, b as ALL_TOOLBAR_TOOLS, C as CANVAS_TOOL_IDS, c as CELL_SEGMENTER, d as CHANNEL_HISTOGRAM_API, e as CellposeSegmenterService, h as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, i as DEFAULT_FALLBACK_PALETTE, j as DEFAULT_MUTED_OPACITY, k as DEFAULT_SAM_MODEL_ID, l as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, m as INSTANCE_SEGMENTER, n as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, o as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, p as NAPARI_DEFAULT_DECIMATE, q as NO_CATEGORY, s as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, t as PLOT_MODE_SESSION, u as PLOT_TYPE_CONTRIBUTIONS, v as PLOT_TYPE_DESCRIPTORS, w as PREFERENCES_PORT, x as PlotType, y as Polygon, z as ProcessingImage, R as REGION_EDITOR_API, B as REGION_IO_PORT, E as REGION_SOURCE_MIN_CHARS, F as Rectangle, G as Region, J as RegionEditorComponent, K as RoutingVisualizerService, S as SAM_MODELS, O as SEMANTIC_SEGMENTER, Q as SPATIAL_DATA_PORT, T as SPATIAL_WIRE_VERSION, U as ShapeSelection, V as SpatialChartsComponent, W as SpatialControlsComponent, X as SpatialDataHttpService, Y as SpatialSelectionStore, Z as SupersededError, _ as TILE_ACCESS_PORT, $ as TOOLBAR_TOOLS, a0 as VISUALIZER, a1 as VIZ_ALERT_TOAST_KEY, a2 as VIZ_CONFIG, a3 as VIZ_TOAST_KEY, a4 as ViewerFeature, a5 as VisualizationModule, a6 as VisualizerComponent, a7 as assertManifestVersion, a8 as benefitsFromGrouping, a9 as buildOmicsTraces, aa as capabilitiesOf, ab as clearSamModelCache, ac as contrastWindow, ad as contributedPlotTypeOption, ae as countMask, af as cropImage, ag as datasetFromManifest, ah as decodeColumn, ai as decodeCoords, aj as decodeFeatureVector, ak as decodePolygons, al as decodeRadius, am as defaultPresetSet, an as dialogToolContributions, ao as emptySelection, ap as encodeCategorical, aq as encodeContinuous, ar as findColumnMeta, as as getDefaultSamModelId, g as getOrtWasmBase, at as getPlotTypeDescriptor, au as getSamModel, av as hydrateBounds, aw as isBuiltinPlotType, ax as isCanvasToolId, ay as isCategoricalColumn, az as isContinuousColumn, aA as isDialogToolContribution, aB as isEmptyPresetSet, aC as isLittleEndian, aD as isNapari3d, aE as isNapariIsosurface, aF as isNapariScatter, aG as isNapariScatter3d, aH as isNapariSurface, aI as isNapariVolume, aJ as isSamModelReady, aK as isSpatialOmics, aL as isSpatialOmics3d, aM as isThreeDimensional, aN as lutFor, aO as markerDiameters, aP as maskToIndices, aQ as mutedFromSelection, aR as omicsLayout, aS as openGeoJsonRegionSource, aT as openHttpRegionSource, aU as parsePresetSet, aV as pointInRing, aW as provideVisualization, aX as rendererOwnsWheel, aY as resolveCategoryColors, aZ as selectByCategory, a_ as selectInRegions, a$ as setDefaultSamModel, b0 as setOrtWasmBase, b1 as setSamModelUrls, b2 as sortToolContributions, b3 as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-BKQhpbHv.mjs';
+export { A as ALL_GENES, b as ALL_TOOLBAR_TOOLS, c as ANNOTATION_IMAGE_MAX_DIM, C as CANVAS_TOOL_IDS, d as CELL_SEGMENTER, e as CHANNEL_HISTOGRAM_API, h as CellposeSegmenterService, i as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, j as DEFAULT_FALLBACK_PALETTE, k as DEFAULT_MUTED_OPACITY, l as DEFAULT_SAM_MODEL_ID, m as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, n as INSTANCE_SEGMENTER, o as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, p as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, q as NAPARI_DEFAULT_DECIMATE, s as NO_CATEGORY, t as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, u as PLOT_MODE_SESSION, v as PLOT_TYPE_CONTRIBUTIONS, w as PLOT_TYPE_DESCRIPTORS, x as PREFERENCES_PORT, y as PlotType, z as Polygon, B as ProcessingImage, R as REGION_EDITOR_API, E as REGION_IO_PORT, F as REGION_SOURCE_MIN_CHARS, G as Rectangle, J as Region, K as RegionEditorComponent, O as RoutingVisualizerService, S as SAM_MODELS, Q as SEMANTIC_SEGMENTER, T as SPATIAL_DATA_PORT, U as SPATIAL_WIRE_VERSION, V as ShapeSelection, W as SpatialChartsComponent, X as SpatialControlsComponent, Y as SpatialDataHttpService, Z as SpatialSelectionStore, _ as SupersededError, $ as TILE_ACCESS_PORT, a0 as TOOLBAR_TOOLS, a1 as VISUALIZER, a2 as VIZ_ALERT_TOAST_KEY, a3 as VIZ_CONFIG, a4 as VIZ_TOAST_KEY, a5 as ViewerFeature, a6 as VisualizationModule, a7 as VisualizerComponent, a8 as assertManifestVersion, a9 as benefitsFromGrouping, aa as buildOmicsTraces, ab as capabilitiesOf, ac as clearSamModelCache, ad as contrastWindow, ae as contributedPlotTypeOption, af as countMask, ag as cropImage, ah as datasetFromManifest, ai as decodeColumn, aj as decodeCoords, ak as decodeFeatureVector, al as decodePolygons, am as decodeRadius, an as defaultPresetSet, ao as dialogToolContributions, ap as emptySelection, aq as encodeCategorical, ar as encodeContinuous, as as expandZips, at as findColumnMeta, au as getDefaultSamModelId, g as getOrtWasmBase, av as getPlotTypeDescriptor, aw as getSamModel, ax as hasZarrMetadata, ay as hydrateBounds, az as importFile, aA as isBuiltinPlotType, aB as isCanvasToolId, aC as isCategoricalColumn, aD as isContinuousColumn, aE as isDialogToolContribution, aF as isEmptyPresetSet, aG as isLabelVolumeName, aH as isLittleEndian, aI as isNapari3d, aJ as isNapariIsosurface, aK as isNapariScatter, aL as isNapariScatter3d, aM as isNapariSurface, aN as isNapariVolume, aO as isSamModelReady, aP as isSpatialOmics, aQ as isSpatialOmics3d, aR as isThreeDimensional, aS as isZipName, aT as labelClasses, aU as labelSliceGeoJson, aV as lutFor, aW as markerDiameters, aX as maskToIndices, aY as mutedFromSelection, aZ as omicsLayout, a_ as openAnnotations, a$ as openGeoJsonRegionSource, b0 as openHttpRegionSource, b1 as parsePresetSet, b2 as planRegionImport, b3 as pointInRing, b4 as provideVisualization, b5 as readAnnotationSlices, b6 as readLabelVolume, b7 as readOmeZarrLabels, b8 as readZip, b9 as rendererOwnsWheel, ba as resolveCategoryColors, bb as selectByCategory, bc as selectInRegions, bd as setDefaultSamModel, be as setOrtWasmBase, bf as setSamModelUrls, bg as sortToolContributions, bh as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-a68Hw5rw.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';
@@ -6,6 +6,8 @@ import 'rxjs';
 import 'rxjs/operators';
 import 'onnxruntime-web';
 import 'napari-js/geometry';
+import 'fast-png';
+import 'fzstd';
 import '@angular/core/rxjs-interop';
 import '@angular/common';
 import '@angular/forms';

package/fesm2022/jax-data-science-sci-image-visualizer.mjs.map

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer.mjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}
+{"version":3,"file":"jax-data-science-sci-image-visualizer.mjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/index.d.ts

@@ -50,6 +50,18 @@ export { openGeoJsonRegionSource } from './lib/region-source/worker-region-sourc
 export { openHttpRegionSource } from './lib/region-source/http-region-source';
 export type { HttpRegionSourceOptions, WireTileFeature } from './lib/region-source/http-region-source';
 export { REGION_SOURCE_MIN_CHARS } from './lib/region-source/region-source';
+export { isLabelVolumeName, readLabelVolume } from './lib/region-import/label-volume';
+export type { LabelVolume } from './lib/region-import/label-volume';
+export { labelClasses, labelSliceGeoJson } from './lib/region-import/label-classes';
+export type { LabelClasses } from './lib/region-import/label-classes';
+export { importFile, planRegionImport } from './lib/region-import/region-import';
+export type { RegionImportFile, RegionImportPlan } from './lib/region-import/region-import';
+export { ANNOTATION_IMAGE_MAX_DIM, openAnnotations, readAnnotationSlices, } from './lib/region-import/open-annotations';
+export type { AnnotationDecoders, AnnotationSlices, OpenedAnnotations, } from './lib/region-import/open-annotations';
+export { hasZarrMetadata, readOmeZarrLabels } from './lib/region-import/ome-zarr-labels';
+export type { LabelStack, OmeZarrLabels } from './lib/region-import/ome-zarr-labels';
+export { expandZips, isZipName, readZip } from './lib/region-import/zip';
+export type { ZipEntry } from './lib/region-import/zip';
 export type { RegionSource, RegionSourceView, SourceFeature } from './lib/region-source/region-source';
 export type { RegionIndexPage, RegionIndexQuery, RegionIndexRow, RegionSourceInfo, RegionTile, RegionTileKey, TileFeature, } from './lib/region-source/region-tiles';
 export { VisualizationModule } from './lib/visualization.module';

package/lib/contracts/image.contract.d.ts

@@ -7,6 +7,7 @@
  * `ImageInfo`/`ImageMetadata` classes are pure data holders that satisfy them
  * structurally, so the host keeps passing its own instances unchanged.
  */
+import type { RegionSource } from '../region-source/region-source';
 /** Per-channel metadata from the server descriptor (issue #76). */
 export interface IChannelInfo {
     name: string;
@@ -65,6 +66,12 @@ export interface IImageInfo {
      *  its regions are drawn from the server's level-of-detail tiles instead of being loaded
      *  from `roiJsonStr`. On a stack, slice z shows the source's plane z. */
     regionSourceUrl?: string;
+    /** The image's own regions, one region source per slice, opened the first time its slice is
+     *  shown: what an image built from annotations alone carries (see `openAnnotations`: a label
+     *  volume traced slice by slice, a folder of per-slice GeoJSON). Attached when the image lands,
+     *  replacing its regions, as an imported label volume or folder is; takes precedence over
+     *  `roiJsonStrs`, `roiJsonStr` and `regionSourceUrl`. Keyed by slice index. */
+    regionSlices?: ReadonlyMap<number, () => Promise<RegionSource>>;
     /** Per-slice, per-channel plane URLs for a SERVERLESS multichannel image
      *  (`tiled: false` + `imageMeta[0].channelCount > 1`). `channelUrls[z][c]`
      *  is a complete single-band image of channel c at slice z. The OSD simple

package/lib/contracts/ports/region-io.port.d.ts

@@ -25,6 +25,30 @@ export interface RegionIoPort {
         z: number;
         geoJsonStr: string;
     }[]): Observable<void>;
+    /**
+     * "Import regions from server": let the user pick region files or a region set in the host's
+     * storage (the current project's bucket, say) and hand them over. Emits null when the user
+     * cancels. Without it, the Region Editor shows no server import.
+     */
+    pickServerRegions?(): Observable<ServerRegionPick | null>;
 }
+/**
+ * Regions picked on the host's server (see {@link RegionIoPort.pickServerRegions}): files it
+ * downloaded, imported as the Region Editor imports chosen files (one GeoJSON; a label volume
+ * `.nii` / `.nii.gz` / `.nrrd` with its ontology JSON; a folder's per-slice GeoJSON files with its
+ * `regionset.json`), or a region set its server serves by level of detail (jit-service's
+ * `/regions/{id}/`), read through the host's `HttpClient` without downloading it.
+ */
+export type ServerRegionPick = {
+    kind: 'files';
+    files: Array<{
+        name: string;
+        data: Blob | ArrayBuffer | Uint8Array | string;
+    }>;
+} | {
+    kind: 'source';
+    url: string;
+    name?: string;
+};
 /** DI token for the host's {@link RegionIoPort}. Required by the region editor. */
 export declare const REGION_IO_PORT: InjectionToken<RegionIoPort>;

package/lib/contracts/region-editor-api.contract.d.ts

@@ -3,7 +3,7 @@ import { Observable } from 'rxjs';
 import { Region } from '../models/region';
 import { ClassPreset, PresetSet } from '../models/class-preset';
 import { IImageMetadata } from './image.contract';
-import type { RegionSourceView } from '../region-source/region-source';
+import type { RegionSource, RegionSourceView } from '../region-source/region-source';
 import type { RegionIndexPage, RegionIndexQuery } from '../region-source/region-tiles';
 import type { RegionStyle } from '../region-overlay/region-style';
 /**
@@ -87,6 +87,24 @@ export interface IRegionEditorApi {
      * and should be imported as regions; rejects when it is not a GeoJSON FeatureCollection.
      */
     importRegionSource?(geoJsonStr: string): Promise<boolean>;
+    /**
+     * A ticket for an import about to read or decode its files: an import method given a stale one
+     * (another import took a ticket since, or another image was plotted) changes nothing.
+     */
+    regionImportTicket?(): number;
+    /**
+     * Replace the regions and region sources with one source per slice (an imported label volume,
+     * or a folder of per-slice region files): openers by slice index, each opened the first time its
+     * slice is shown. A single image takes slice 0's. Returns how many slices have one, or null
+     * (changing nothing) when `ticket` is stale. A save writes every imported slice.
+     */
+    importSliceRegionSources?(openers: ReadonlyMap<number, () => Promise<RegionSource>>, ticket?: number): number | null;
+    /**
+     * Replace them with one imported source (a region set a server serves): over every slice of a
+     * stack when z-indexed, else on the slice shown. Resolves false, changing nothing, when the
+     * import went stale while the source opened.
+     */
+    importRegionSourceOpener?(open: () => Promise<RegionSource>, ticket?: number): Promise<boolean>;
     /**
      * Drop the slice's region source, for regions imported in its place (a small file replacing a
      * large one). The other slices keep theirs.

package/lib/implementations/napari-js/napari-spatial-3d-scene.d.ts

@@ -2,6 +2,8 @@ import { IHistogram } from '../../contracts/channel-histogram-api.contract';
 import { SpatialDataset, SpatialObservations } from '../../contracts/spatial-dataset.contract';
 import { SpatialViewState } from '../../contracts/display-types';
 import { SpatialSelectionMask } from '../../spatial/spatial-selection';
+import type { IImageInfo } from '../../contracts/image.contract';
+import { RegionMesh3D } from './napari-volume-region-meshes';
 import { Spatial3dScalars } from './napari-spatial-encoding';
 import { SpatialSceneBase, SpatialSession } from './napari-spatial-scene';
 import type { NapariScene, SceneContext } from './napari-scene';
@@ -17,6 +19,7 @@ import type { NapariScene, SceneContext } from './napari-scene';
  * shape while keeping the selection. The first 3D layer added frames the camera (`fit3d: 'once'`).
  */
 export declare class Spatial3dScene extends SpatialSceneBase implements NapariScene {
+    private readonly info?;
     /** The 3D point cloud. One layer: selection is a per-point alpha on it, not a second. */
     private points;
     private layerKey;
@@ -58,10 +61,46 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
      *  one; a rebuild that leaves the key alone lets it finish. */
     private readonly densityLoads;
     private readonly geneMapLoads;
+    /**
+     * The region reconstructions (an atlas's structures, imported onto the reference volume's image
+     * stack), drawn by the same {@link VolumeRegionMeshes} as the Volume view's, so a structure is the
+     * same surface in both. Placed in the reference volume's box, once it is there and the image the
+     * regions were drawn on is that volume's stack (see {@link placeRegionMeshes}).
+     */
+    private readonly regionMeshes;
+    /** Whether the reference volume lets every region surface through (see setRegionsThroughVolume). */
+    private regionsThrough;
     /** The store's invert setting, which the density volumes follow (no other subscription of
      *  this scene carries it). */
     private invertSub;
-    constructor(ctx: SceneContext, session: SpatialSession);
+    /**
+     * @param info the image plotted with the cloud: the reference volume's stack (the 2D view's
+     *        image, see showVolumeAsImage) when the dataset has a volume, which the regions are on
+     */
+    constructor(ctx: SceneContext, session: SpatialSession, info?: IImageInfo | undefined);
+    /** Show these region reconstructions with the cloud (replacing the ones shown). */
+    setRegionMeshes(meshes: readonly RegionMesh3D[]): void;
+    setRegionHighlight(keys: readonly string[]): void;
+    setRegionHidden(keys: readonly string[]): void;
+    /** As the Volume view: the reference volume hides the surfaces behind what it shows, or none. */
+    setRegionsThroughVolume(through: boolean): void;
+    /**
+     * Place the region surfaces in the reference volume's box, as the Volume view places them in its
+     * own: image pixel (x, y) is voxel (x, y), slice k is voxel plane k, and the box is the volume's
+     * voxels times its voxel size, centred on the origin as napari centres the volume (and the cloud
+     * is offset to sit in it). Only when the plotted image IS that volume's stack: regions drawn on
+     * another image (a tissue image) have no place in it, and are not shown - nor are surfaces
+     * placed in a volume this one replaced.
+     */
+    private placeRegionMeshes;
+    /**
+     * Image px per voxel of the volume the surfaces sit in: 1, the reference volume being the stack's
+     * own voxels, as the Volume view's is at full resolution, so both reconstruct a class alike (and
+     * share its cached surface). Null while there is no volume stack to place them in.
+     */
+    voxelStep(): number | null;
+    /** Whether the plotted image is the reference volume's stack: its size and slice count. */
+    private isVolumeStack;
     mount(): Promise<void>;
     /** The observations' own z is on screen: there is no plane to step. */
     setZ(): void;

package/lib/implementations/napari-js/napari-volume-region-meshes.d.ts

@@ -54,6 +54,11 @@ export declare class VolumeRegionMeshes {
     /** The meshes shown. */
     get shown(): RegionMesh3D[];
     clear(): void;
+    /**
+     * The volume the surfaces sat in is gone (or no longer theirs): take every surface down, keeping
+     * the meshes wanted, so they come back when a frame is set again.
+     */
+    clearFrame(): void;
     private sync;
     private add;
     private opacityOf;

package/lib/implementations/osd/openseadragon-viewer-options.d.ts

@@ -23,6 +23,8 @@ export interface ViewerOptionsInput {
     sliceCount: number;
     /** How many slices the slice cache keeps resident (see SliceCache.maxSlices). */
     maxSlices: number;
+    /** Tiled images per slice: the channel count when channels are drawn per channel, else 1. */
+    channelImages?: number;
 }
 /**
  * The options object handed to the OpenSeadragon factory. Pure: every value

package/lib/implementations/osd/openseadragon-visualizer.service.d.ts

@@ -53,6 +53,8 @@ export declare class OpenSeadragonVisualizerService extends BaseStoreVisualizer
     private viewer;
     private overlay;
     private scaleBar;
+    /** "Image reloading…" while the view fetches its tiles. */
+    private tileLoading;
     private descriptor;
     /** Base64 RawFileInfo + current z-slice, kept so setZIndex can rebuild the
      *  tile source and swap slices live (stack navigation). */

package/lib/implementations/osd/osd-tile-loading.d.ts

@@ -0,0 +1,43 @@
+/** What it needs of the viewer. */
+interface LoadingViewer {
+    element: HTMLElement;
+    world: {
+        getItemCount(): number;
+        getItemAt(i: number): unknown;
+        addHandler(event: 'add-item' | 'remove-item', handler: (e: {
+            item: unknown;
+        }) => void): unknown;
+        removeHandler(event: 'add-item' | 'remove-item', handler: (e: {
+            item: unknown;
+        }) => void): unknown;
+    };
+}
+/**
+ * "Image reloading…" over the OpenSeadragon view while it fetches the tiles of what it shows, as
+ * napari's views show it for their image, cells and transcripts (the same badge). Driven by each
+ * world item's own `fully-loaded-change` (an image, a stack slice, a channel), so it covers every
+ * tile source alike, and shown only after a short delay, so tiles served from cache never flash it.
+ *
+ * Only items on screen count (opacity above 0): a hidden channel loads nothing by design (it is
+ * not preloaded), so it never becomes fully loaded, and a slice cached or loading in the
+ * background is not what the view shows. An item is weighed again when its opacity changes.
+ */
+export declare class OsdTileLoading {
+    private readonly viewer;
+    private readonly state;
+    /** Each item still loading, with the function that un-counts it. */
+    private readonly loading;
+    private readonly watched;
+    private readonly onAdd;
+    private readonly onRemove;
+    constructor(viewer: LoadingViewer);
+    /** The badge's text (shown, or about to be). */
+    get text(): string;
+    destroy(): void;
+    private watch;
+    private unwatch;
+    /** Whether the item is on screen and still fetching its tiles. */
+    private isLoading;
+    private set;
+}
+export {};

package/lib/implementations/osd/osd-viewer-like.d.ts

@@ -48,6 +48,18 @@ export interface OsdViewerLike {
     /** OSD's own pan/zoom (drag + wheel); region tools switch it off. */
     setMouseNavEnabled(enabled: boolean): unknown;
     isMouseNavEnabled(): boolean;
+    /** OSD's tile request queue: the jobs not started yet (see OsdQueuedTileJob). */
+    imageLoader?: {
+        jobQueue?: unknown[];
+    };
+}
+/** A tile request waiting in OSD's queue: `abort` (before it starts) only marks the tile as
+ *  not loading, so it is requested again when it is needed. */
+export interface OsdQueuedTileJob {
+    tile?: {
+        tiledImage?: unknown;
+    };
+    abort?: () => void;
 }
 /** A point in any OSD space (viewer-element px, viewport units or image px —
  *  the method it comes from says which). */
@@ -70,6 +82,8 @@ export interface OsdTiledImageLike {
     imageToViewportRectangle(r: OpenSeadragon.Rect): OpenSeadragon.Rect;
     viewportToImageRectangle(r: OsdRectLike): OsdRectLike;
     setOpacity(opacity: number): void;
+    /** Load tiles even while hidden (opacity 0); without it a hidden item loads nothing. */
+    setPreload?(preload: boolean): void;
     /** False while any of the image's tiles are still loading. */
     getFullyLoaded(): boolean;
     /** Re-run the tile pipeline (restore + re-process) for this image's tiles;

package/lib/implementations/osd/slice-cache.d.ts

@@ -106,14 +106,22 @@ export declare class SliceCache {
     /**
      * Add slice z's channel group: one additively-composited ('lighter' = Fiji
      * "Composite") TiledImage per channel, hidden (opacity 0) until revealed.
-     * Each is preloaded so the background loader can pre-fill every slice.
+     * The visible channels' are preloaded, so the background loader can pre-fill
+     * every slice; a hidden channel's loads nothing until it is shown (a 22-channel
+     * plate fetched and decoded every channel's tiles, overflowing the tile cache:
+     * tiles evicted mid-conversion failed to decode).
      * Cached so a revisit is an instant opacity toggle — no re-fetch, no
      * white-flicker. Mirrors addSlice for the composite path.
      */
     addChannelSlice(z: number): void;
     /** Reveal slice z's channel group (each visible channel → opacity 1) and
-     *  hide every other cached slice's group. Instant; no fetch/decode. */
+     *  hide every other cached slice's group. Instant; no fetch/decode. Only the
+     *  visible channels keep loading (preload): a hidden channel's tiles are not
+     *  fetched or decoded until it is shown. */
     revealChannelSlice(z: number): void;
+    /** Drop the tile requests still waiting in OSD's queue for `items` (channels just hidden), so
+     *  the visible channels' tiles are not stuck behind them. A request already sent completes. */
+    private dropQueuedTiles;
     /** Show the given composite slice (opacity 1) and hide all other cached slices. */
     private showOnlySlice;
     /** Re-tint after a display change: invalidate ONLY the visible slice's
@@ -154,7 +162,9 @@ export declare class SliceCache {
     private sliceCacheHas;
     /** The cached TiledImage(s) for slice z (0–1 for composite, N for multichannel). */
     private sliceGroup;
-    /** Whether slice z's tiles are still streaming (any cached image not fully loaded). */
+    /** Whether slice z's tiles are still streaming (any cached image not fully loaded). A hidden
+     *  channel loads nothing, so it never becomes fully loaded: only the visible channels count, or
+     *  the background loader would wait on it forever. */
     private sliceTilesLoading;
     /** Remove slice z's cached image(s) from the world and the active cache. */
     private removeCachedSlice;

package/lib/region-editor/region-editor.component.d.ts

@@ -26,6 +26,8 @@ export declare class RegionEditorComponent implements OnInit, OnDestroy {
      */
     set active(value: boolean);
     private isActive;
+    /** The host's HttpClient: a served region set's requests go through it (its auth). */
+    private readonly http;
     protected regions: Region[];
     protected selectedRegions: Region[];
     protected showShapeLabel: boolean;
@@ -348,7 +350,32 @@ export declare class RegionEditorComponent implements OnInit, OnDestroy {
     protected importPresets(event: Event): void;
     /** Validate and apply an imported annotation-classes JSON file. */
     private applyImportedPresets;
+    /** The files chosen in the import inputs: one GeoJSON, a label volume with its ontology, or a
+     *  folder of per-slice GeoJSON files. */
     protected importRois(event: Event): void;
+    /** Whether the host can pick regions on its server ("Import regions from server"). */
+    protected get canImportFromServer(): boolean;
+    /** An import from the server is in flight. */
+    protected importing: boolean;
+    /** "Import regions from server": the host picks files or a served region set; they import as chosen files do. */
+    protected importFromServer(): void;
+    /**
+     * Import `files`: one GeoJSON file as before (its regions, editable); anything else (see
+     * readAnnotationSlices) as one region source per slice, replacing the regions and sources of
+     * every slice: a label volume or an OME-Zarr label image traced the first time a slice is shown,
+     * its classes named (and treed) by its ontology; a folder as one source per slice file; a
+     * z-indexed GeoJSON one per plane; a zip of any of these.
+     */
+    private importRegionFiles;
+    /** A region set the host's server serves (jit-service's /regions/{id}/), read through its HttpClient. */
+    private importServedRegionSet;
+    /** An import that finished after another image was shown (or another import began): dropped. */
+    private importStale;
+    /** The table and selection after the regions were replaced by imported sources. */
+    private afterSourceImport;
+    /** Warn when an imported volume's slices are not the image's size: its outlines would not fit. */
+    private warnIfSizeDiffers;
+    private importFailed;
     /**
      * Replace the regions with an imported GeoJSON file's, and the slice's region source with them.
      * A large file becomes the slice's region source instead (drawn by level of detail; listed above

package/lib/region-editor/region-persistence.service.d.ts

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import { Region } from '../models/region';
 import { IRegionEditorApi } from '../contracts/region-editor-api.contract';
-import { RegionIoPort } from '../contracts/ports/region-io.port';
+import { RegionIoPort, ServerRegionPick } from '../contracts/ports/region-io.port';
 import * as i0 from "@angular/core";
 /** One slice-file's serialized regions (folder stack, jit-ui#93). */
 export interface SliceGeoJson {
@@ -67,6 +67,10 @@ export declare class RegionPersistenceService {
      * in it.
      */
     sliceGeoJsons(): Promise<SliceGeoJson[]>;
+    /** Whether the host can pick regions on its server (see RegionIoPort.pickServerRegions). */
+    canPickServerRegions(): boolean;
+    /** Let the user pick regions on the host's server; null when cancelled or unsupported. */
+    pickServerRegions(): Observable<ServerRegionPick | null>;
     /** Write per-slice geojsons through the host port. */
     saveSlices(slices: SliceGeoJson[]): Observable<void>;
     /** Read the file chosen in a file input's change event as text, then call

package/lib/region-import/label-classes.d.ts

@@ -0,0 +1,39 @@
+import type { RegionClassNode, RegionSourceStyle } from '../region-source/region-tiles';
+import type { LabelVolume } from './label-volume';
+/**
+ * The classes of a label volume's values: their names and colours and, when the volume comes
+ * with an ontology, their tree. Pure.
+ */
+export interface LabelClasses {
+    /** The class of label `value` (> 0); one without an ontology entry is `label <value>`. */
+    classOf(value: number): {
+        name: string;
+        color: string;
+        title?: string;
+    };
+    /** The class tree, when the ontology has one. */
+    hierarchy?: RegionClassNode[];
+    /** How the set wants to be drawn (an atlas's filled look), when the ontology says. */
+    style?: RegionSourceStyle;
+}
+/** The look the Allen atlas region sets carry (see the brain-atlas example's GeoJSON). */
+export declare const ATLAS_STYLE: RegionSourceStyle;
+/**
+ * The classes of a label volume from `ontology`, a parsed JSON document:
+ *
+ * - an **Allen structure graph** (`structure_graph_1.json`: `{ msg: [root] }`, or a node or a
+ *   list of nodes with `id`, `acronym`, `name`, `color_hex_triplet`, `graph_order` and
+ *   `children`): label = structure id, class = acronym, its tree the ontology's, drawn as the
+ *   atlas region sets are;
+ * - a **region set description** (a `regionset.json`: `classHierarchy`, optional `style`), whose
+ *   classes name their label as `value` (or `id`), or with a `labels` map of value → class name.
+ *
+ * Without one (or with another document), each label is its own class `label <value>`.
+ */
+export declare function labelClasses(ontology?: unknown): LabelClasses;
+/**
+ * Slice `z` of `volume` as a GeoJSON FeatureCollection string: one feature per label on the
+ * slice, its every piece (with holes) traced along pixel edges, in image pixels with y down;
+ * classified by `classes`, which also give the collection its class tree and style.
+ */
+export declare function labelSliceGeoJson(volume: LabelVolume, z: number, classes: LabelClasses): string;

package/lib/region-import/label-volume.d.ts

@@ -0,0 +1,35 @@
+/**
+ * A label volume (a NIfTI-1 `.nii` / `.nii.gz` or a NRRD `.nrrd` of integer structure ids, an
+ * atlas annotation say) read in the browser, sliced as the server opens the matching image:
+ *
+ * - **NRRD**: a 3D volume is cut along its FIRST axis, each section its third axis wide and its
+ *   second axis high, as jit-service opens a NRRD volume (`AtlasNrrdReader`: the Allen CCF's 528
+ *   coronal sections of 456 × 320, anterior first). A 2D NRRD is one slice.
+ * - **NIfTI**: along its third axis, each slice its first axis wide and its second axis high, as
+ *   Bio-Formats reads one (no row flip).
+ *
+ * Only what label volumes use: a single file (NRRD with attached data, NIfTI-1 `n+1`), integer
+ * or integer-valued float samples, either byte order, raw or gzip. Anything else throws rather
+ * than be read approximately. Pure: usable from workers.
+ */
+/** A label volume, sliced (see the module comment). Label 0 is background. */
+export interface LabelVolume {
+    format: 'nrrd' | 'nifti';
+    /** A slice's width and height, in voxels (the image's pixels). */
+    width: number;
+    height: number;
+    /** Number of slices. */
+    slices: number;
+    /** Size of a voxel along the slice's x, its y and across slices, in micrometres, when the file
+     *  says (NRRD `space directions`/`spacings`, micrometres unless `space units` says otherwise;
+     *  NIfTI `pixdim`, in its `xyzt_units`, millimetres when unset). */
+    spacing?: [number, number, number];
+    /** Slice `z`'s labels, row-major (`height` rows of `width`). */
+    sliceLabels(z: number): Uint32Array;
+}
+/** Decompress gzip bytes (default: the platform's `DecompressionStream`). */
+export type Gunzip = (bytes: Uint8Array) => Promise<Uint8Array>;
+/** Whether a file name is a label volume this reads. */
+export declare function isLabelVolumeName(name: string): boolean;
+/** Read the label volume in `bytes`, named `name` (`.nrrd`, `.nii`, `.nii.gz`). */
+export declare function readLabelVolume(name: string, bytes: Uint8Array, gunzip?: Gunzip): Promise<LabelVolume>;

package/lib/region-import/ome-zarr-labels.d.ts

@@ -0,0 +1,36 @@
+/**
+ * A label image of an OME-Zarr store (`labels/<name>/`, NGFF 0.4 on zarr v2 or 0.5 on zarr v3),
+ * read in the browser from the store's files (a folder chosen, or a zip's members): its full
+ * resolution level, sliced along z, with the classes its `image-label` metadata names and colours.
+ *
+ * Chunks are decoded when a slice that needs them is read, so a store is never decoded whole.
+ * Only what label images use: C-order chunks of integer (or integer-valued float) samples, through
+ * the codecs {@link decodeChunk} reads, a missing chunk being the fill value. Sharded or transposed
+ * arrays, F-order and filters throw rather than be read wrongly. Pure: usable from workers.
+ */
+import { LabelClasses } from './label-classes';
+import type { RegionImportFile } from './region-import';
+import { Inflate } from './zarr-codecs';
+/** A stack of label slices read on demand. Label 0 is background. */
+export interface LabelStack {
+    width: number;
+    height: number;
+    slices: number;
+    /** Size of a voxel, x, y, z, in micrometres, when the source says. */
+    spacing?: [number, number, number];
+    /** Slice `z`'s labels, row-major (`height` rows of `width`). */
+    labels(z: number): Promise<Uint32Array>;
+}
+/** An OME-Zarr label image: its name, its slices, its classes. */
+export interface OmeZarrLabels {
+    name: string;
+    stack: LabelStack;
+    classes: LabelClasses;
+}
+/** Whether `files` hold a zarr store (any zarr metadata among them). */
+export declare function hasZarrMetadata(files: readonly RegionImportFile[]): boolean;
+/**
+ * The first label image of the zarr store among `files` (the order `labels/`'s listing gives,
+ * else the first found), or null when the store has none.
+ */
+export declare function readOmeZarrLabels(files: readonly RegionImportFile[], inflate?: Inflate): Promise<OmeZarrLabels | null>;