@jax-data-science/sci-image-visualizer 0.17.0 → 0.18.1

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-Dph35S7m.mjs}

@@ -1,6 +1,6 @@
 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-DHrHO2ay.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-YrNqv8wH.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
@@ -238,4 +238,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-Dph35S7m.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-Dph35S7m.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.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 ?? 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'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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+{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-Dph35S7m.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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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 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, n as DEFAULT_VISIBLE_CHANNELS, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, o as INSTANCE_SEGMENTER, p as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, q as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, s as NAPARI_DEFAULT_DECIMATE, t as NO_CATEGORY, u as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, v as PLOT_MODE_SESSION, w as PLOT_TYPE_CONTRIBUTIONS, x as PLOT_TYPE_DESCRIPTORS, y as PREFERENCES_PORT, z as PlotType, B as Polygon, E as ProcessingImage, R as REGION_EDITOR_API, F as REGION_IO_PORT, G as REGION_SOURCE_MIN_CHARS, J as Rectangle, K as Region, O as RegionEditorComponent, Q as RoutingVisualizerService, S as SAM_MODELS, T as SEMANTIC_SEGMENTER, U as SPATIAL_DATA_PORT, V as SPATIAL_WIRE_VERSION, W as ShapeSelection, X as SpatialChartsComponent, Y as SpatialControlsComponent, Z as SpatialDataHttpService, _ as SpatialSelectionStore, $ as SupersededError, a0 as TILE_ACCESS_PORT, a1 as TOOLBAR_TOOLS, a2 as VISUALIZER, a3 as VIZ_ALERT_TOAST_KEY, a4 as VIZ_CONFIG, a5 as VIZ_TOAST_KEY, a6 as ViewerFeature, a7 as VisualizationModule, a8 as VisualizerComponent, a9 as assertManifestVersion, aa as benefitsFromGrouping, ab as buildOmicsTraces, ac as capabilitiesOf, ad as clearSamModelCache, ae as contrastWindow, af as contributedPlotTypeOption, ag as countMask, ah as cropImage, ai as datasetFromManifest, aj as decodeColumn, ak as decodeCoords, al as decodeFeatureVector, am as decodePolygons, an as decodeRadius, ao as defaultChannelVisible, ap as defaultPresetSet, aq as dialogToolContributions, ar as emptySelection, as as encodeCategorical, at as encodeContinuous, au as expandZips, av as findColumnMeta, aw as getDefaultSamModelId, g as getOrtWasmBase, ax as getPlotTypeDescriptor, ay as getSamModel, az as hasZarrMetadata, aA as hydrateBounds, aB as importFile, aC as isBuiltinPlotType, aD as isCanvasToolId, aE as isCategoricalColumn, aF as isContinuousColumn, aG as isDialogToolContribution, aH as isEmptyPresetSet, aI as isLabelVolumeName, aJ as isLittleEndian, aK as isNapari3d, aL as isNapariIsosurface, aM as isNapariScatter, aN as isNapariScatter3d, aO as isNapariSurface, aP as isNapariVolume, aQ as isSamModelReady, aR as isSpatialOmics, aS as isSpatialOmics3d, aT as isThreeDimensional, aU as isZipName, aV as labelClasses, aW as labelSliceGeoJson, aX as lutFor, aY as markerDiameters, aZ as maskToIndices, a_ as mutedFromSelection, a$ as omicsLayout, b0 as openAnnotations, b1 as openGeoJsonRegionSource, b2 as openHttpRegionSource, b3 as parsePresetSet, b4 as planRegionImport, b5 as pointInRing, b6 as provideVisualization, b7 as readAnnotationSlices, b8 as readLabelVolume, b9 as readOmeZarrLabels, ba as readZip, bb as rendererOwnsWheel, bc as resolveCategoryColors, bd as selectByCategory, be as selectInRegions, bf as setDefaultSamModel, bg as setOrtWasmBase, bh as setSamModelUrls, bi as sortToolContributions, bj as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-DHrHO2ay.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, n as DEFAULT_VISIBLE_CHANNELS, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, o as INSTANCE_SEGMENTER, p as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, q as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, s as NAPARI_DEFAULT_DECIMATE, t as NO_CATEGORY, u as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, v as PLOT_MODE_SESSION, w as PLOT_TYPE_CONTRIBUTIONS, x as PLOT_TYPE_DESCRIPTORS, y as PREFERENCES_PORT, z as PlotType, B as Polygon, E as ProcessingImage, R as REGION_EDITOR_API, F as REGION_IO_PORT, G as REGION_SOURCE_MIN_CHARS, J as Rectangle, K as Region, O as RegionEditorComponent, Q as RoutingVisualizerService, S as SAM_MODELS, T as SEMANTIC_SEGMENTER, U as SPATIAL_DATA_PORT, V as SPATIAL_WIRE_VERSION, W as ShapeSelection, X as SpatialChartsComponent, Y as SpatialControlsComponent, Z as SpatialDataHttpService, _ as SpatialSelectionStore, $ as SupersededError, a0 as TILE_ACCESS_PORT, a1 as TOOLBAR_TOOLS, a2 as VISUALIZER, a3 as VIZ_ALERT_TOAST_KEY, a4 as VIZ_CONFIG, a5 as VIZ_TOAST_KEY, a6 as ViewerFeature, a7 as VisualizationModule, a8 as VisualizerComponent, a9 as assertManifestVersion, aa as benefitsFromGrouping, ab as buildOmicsTraces, ac as capabilitiesOf, ad as clearSamModelCache, ae as contrastWindow, af as contributedPlotTypeOption, ag as countMask, ah as cropImage, ai as datasetFromManifest, aj as decodeColumn, ak as decodeCoords, al as decodeFeatureVector, am as decodePolygons, an as decodeRadius, ao as defaultChannelVisible, ap as defaultPresetSet, aq as dialogToolContributions, ar as emptySelection, as as encodeCategorical, at as encodeContinuous, au as expandZips, av as findColumnMeta, aw as getDefaultSamModelId, g as getOrtWasmBase, ax as getPlotTypeDescriptor, ay as getSamModel, az as hasZarrMetadata, aA as hydrateBounds, aB as importFile, aC as isBuiltinPlotType, aD as isCanvasToolId, aE as isCategoricalColumn, aF as isContinuousColumn, aG as isDialogToolContribution, aH as isEmptyPresetSet, aI as isLabelVolumeName, aJ as isLittleEndian, aK as isNapari3d, aL as isNapariIsosurface, aM as isNapariScatter, aN as isNapariScatter3d, aO as isNapariSurface, aP as isNapariVolume, aQ as isSamModelReady, aR as isSpatialOmics, aS as isSpatialOmics3d, aT as isThreeDimensional, aU as isZipName, aV as labelClasses, aW as labelSliceGeoJson, aX as lutFor, aY as markerDiameters, aZ as maskToIndices, a_ as mutedFromSelection, a$ as omicsLayout, b0 as openAnnotations, b1 as openGeoJsonRegionSource, b2 as openHttpRegionSource, b3 as parsePresetSet, b4 as planRegionImport, b5 as pointInRing, b6 as provideVisualization, b7 as readAnnotationSlices, b8 as readLabelVolume, b9 as readOmeZarrLabels, ba as readZip, bb as rendererOwnsWheel, bc as resolveCategoryColors, bd as selectByCategory, be as selectInRegions, bf as setDefaultSamModel, bg as setOrtWasmBase, bh as setSamModelUrls, bi as sortToolContributions, bj as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-YrNqv8wH.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';

package/fesm2022/region-source.worker.js

@@ -278,6 +278,75 @@ function ringBox(r) {
   return [x0, y0, x1, y1];
 }
 
+// src/lib/geometry/cell-meshes.ts
+function reconstructCells(cells, opts = {}) {
+  const parts = [];
+  let nv = 0;
+  let nf = 0;
+  for (const c of cells) {
+    if (!c.slices.length)
+      continue;
+    const mesh = reconstruct(c.slices, { smooth: 1, ...opts });
+    if (!mesh.faces.length)
+      continue;
+    parts.push({ cell: c.cell, vertices: mesh.vertices, faces: mesh.faces });
+    nv += mesh.vertices.length / 3;
+    nf += mesh.faces.length;
+  }
+  const vertices = new Float32Array(nv * 3);
+  const faces = new Uint32Array(nf);
+  const vertexCell = new Uint32Array(nv);
+  let v = 0;
+  let f = 0;
+  for (const p of parts) {
+    vertices.set(p.vertices, v * 3);
+    for (let i = 0; i < p.faces.length; i++)
+      faces[f + i] = p.faces[i] + v;
+    const n = p.vertices.length / 3;
+    vertexCell.fill(p.cell, v, v + n);
+    v += n;
+    f += p.faces.length;
+  }
+  return { vertices, faces, vertexCell, cells: Uint32Array.from(parts.map((p) => p.cell)) };
+}
+function cellsMeshBuffers(mesh) {
+  return [mesh.vertices.buffer, mesh.faces.buffer, mesh.vertexCell.buffer, mesh.cells.buffer];
+}
+
+// src/lib/geometry/place.ts
+function toWorld(vertices, frame) {
+  if (frame.planes)
+    return planesToWorld(vertices, frame.planes);
+  const [w, h, d] = frame.size;
+  const [ww, wh, wd] = frame.world;
+  const out = new Float32Array(vertices.length);
+  for (let i = 0; i < vertices.length; i += 3) {
+    out[i] = (vertices[i] / w - 0.5) * ww;
+    out[i + 1] = (vertices[i + 1] / h - 0.5) * wh;
+    out[i + 2] = ((vertices[i + 2] + 0.5) / d - 0.5) * wd;
+  }
+  return out;
+}
+function planesToWorld(vertices, planes) {
+  const { z, scale, offset } = planes;
+  const out = new Float32Array(vertices.length);
+  for (let i = 0; i < vertices.length; i += 3) {
+    out[i] = vertices[i] * scale[0] + offset[0];
+    out[i + 1] = vertices[i + 1] * scale[1] + offset[1];
+    out[i + 2] = sliceZ(z, vertices[i + 2]) + offset[2];
+  }
+  return out;
+}
+function sliceZ(z, k) {
+  const n = z.length;
+  if (!n)
+    return k;
+  if (n === 1)
+    return z[0] + k;
+  const i = Math.min(n - 2, Math.max(0, Math.floor(k)));
+  return z[i] + (k - i) * (z[i + 1] - z[i]);
+}
+
 // src/lib/contracts/color.ts
 function rgbToHex(rgb) {
   const h = (n) => clampByte(n).toString(16).padStart(2, "0");
@@ -1038,6 +1107,10 @@ var RegionSourceTables = class {
         return this.table(r.handle).classOutlines(r.classes, r.level, r.exclude);
       case "mesh":
         return reconstruct(r.slices, r.options);
+      case "cells":
+        return reconstructCells(r.cells, r.options);
+      case "place":
+        return toWorld(r.vertices, r.frame);
       case "export":
         return this.table(r.handle).exportGeoJson(r.exclude, r.extra);
       case "close":
@@ -1058,10 +1131,19 @@ var tables = new RegionSourceTables();
 self.onmessage = (event) => {
   const { id } = event.data;
   let reply;
+  let transfer = [];
   try {
-    reply = { id, ok: true, result: tables.run(event.data) };
+    const result = tables.run(event.data);
+    if (event.data.op === "cells")
+      transfer = cellsMeshBuffers(result);
+    else if (event.data.op === "mesh") {
+      const mesh = result;
+      transfer = [mesh.vertices.buffer, mesh.faces.buffer];
+    } else if (event.data.op === "place")
+      transfer = [result.buffer];
+    reply = { id, ok: true, result };
   } catch (err) {
     reply = { id, ok: false, error: err?.message ?? String(err) };
   }
-  self.postMessage(reply);
+  self.postMessage(reply, [...new Set(transfer)]);
 };

package/lib/contracts/display-types.d.ts

@@ -75,6 +75,83 @@ export interface SpatialColorBy {
 /** Display state for the spatial-omics plot mode. Lives in `VisualizerStore`
  *  alongside the colormap/channel state so the renderer reacts to edits the
  *  same way it does for an image. */
+/**
+ * How the spatial 3D view's individual cells stand (a 3D segmentation's cells, each its own
+ * surface): how many are shown, whether some are left out (the cap, or not built yet), whether
+ * they are being built.
+ */
+export interface Cells3dStatus {
+    shown: number;
+    capped: boolean;
+    building: boolean;
+}
+/**
+ * The transcripts of what is selected, by gene (the spatial dialog's "Transcripts in selection"):
+ * in spatial 3D those of the selected cells, or of the cells of the picked cell types, through the
+ * whole volume; in the 2D view of a sliced dataset only those on the plane shown, of the selected
+ * cells or inside the selected regions.
+ */
+export interface TranscriptsInSelection {
+    /** `empty`: nothing selected (or nothing it applies to); `loading`; `ready`; `error`. */
+    state: 'empty' | 'loading' | 'ready' | 'error';
+    /** What the counts are of: selected cells, the cells of picked types, or drawn regions. */
+    scope?: 'cells' | 'types' | 'regions';
+    /** The selection, for the heading ("Cell 1234", "Cell type: Goblet", "2 regions"). */
+    label?: string;
+    /** The plane counted (2D, a sliced dataset): its index and how many there are. */
+    plane?: {
+        index: number;
+        count: number;
+    } | null;
+    total?: number;
+    /** Distinct cells the counted transcripts lie in. */
+    cells?: number;
+    /** Genes by count, most first. */
+    genes?: {
+        name: string;
+        count: number;
+    }[];
+    /** The selection spans more of the section than is read: the counts are a lower bound. */
+    partial?: boolean;
+    /** Why the list is empty, or what failed. */
+    message?: string;
+}
+/**
+ * The observations of what is selected (the spatial dialog's "Observations in selection", in the
+ * Observations section): how many, by the grouping they are coloured by (else the cell types), with
+ * a few measurements' means — or, for one cell, its id, groupings and values. In spatial 3D every
+ * observation of the selection; in the 2D view of a sliced dataset those on the plane shown. The
+ * selection is the one {@link TranscriptsInSelection} follows.
+ */
+export interface ObservationsInSelection {
+    /** `empty`: nothing selected (or nothing it applies to); `loading`; `ready`; `error`. */
+    state: 'empty' | 'loading' | 'ready' | 'error';
+    scope?: 'cells' | 'types' | 'regions';
+    label?: string;
+    plane?: {
+        index: number;
+        count: number;
+    } | null;
+    total?: number;
+    /** The grouping counted by, or null. */
+    groupColumn?: string | null;
+    /** Groups by count, most first, in their legend colours. */
+    groups?: {
+        name: string;
+        count: number;
+        color: string;
+    }[];
+    /** Means over the selection (`mean`), or one cell's own values (text for a grouping). */
+    measures?: {
+        name: string;
+        value: string | number;
+        unit?: string;
+        mean: boolean;
+    }[];
+    /** The one cell's id, when one cell is selected. */
+    cellId?: string;
+    message?: string;
+}
 export interface SpatialViewState {
     /** Colour source; `null` renders every observation in one neutral colour
      *  (useful on its own — it shows where the tissue actually is). */
@@ -208,15 +285,24 @@ export interface SpatialViewState {
      * user's explicit choice.
      */
     showCells: boolean | null;
+    /**
+     * How the spatial 3D view draws a 3D segmentation's cells (the dataset's region set): one
+     * merged surface per cell type (`types`), or every cell its own surface in the Cell Color
+     * (`cells`). A class can be set the other way in the Region Editor.
+     */
+    cells3d: 'types' | 'cells';
     /** Which boundary set (`cell`, `nucleus`, or `both` — cells as set by
      *  {@link cellDraw}, nuclei outlined over them); null takes the dataset's default. */
     cellSet: string | null;
     /**
      * What colours the cells — Xenium Explorer's "Cell Color": the active group
-     * ({@link cellTypeColumn}), one gene's expression ({@link cellColorGene}), the cell's
-     * transcript density, one flat colour, or how the cell was segmented.
+     * ({@link cellTypeColumn}), one gene's expression ({@link cellColorGene}), the numeric column
+     * the observations are coloured by (`column`: {@link colorBy}, a measurement), the cell's
+     * transcript density, one flat colour ({@link cellSingleColor}, the markers' too while
+     * {@link colorBy} is null), or how the cell was segmented. The panel's "Colour by" sets it
+     * with {@link colorBy}, so the markers and the cells are coloured alike.
      */
-    cellColorMode: 'group' | 'gene' | 'transcriptDensity' | 'single' | 'segmentation';
+    cellColorMode: 'group' | 'gene' | 'column' | 'transcriptDensity' | 'single' | 'segmentation';
     cellColorGene: string | null;
     /** `#rrggbb` for {@link cellColorMode} `single`. */
     cellSingleColor: string;
@@ -247,7 +333,7 @@ export interface SpatialViewState {
     observationGeneGlyphs: Record<string, TranscriptGlyphName>;
     /** Draw the tissue image (the Images section's switch). */
     showImage: boolean;
-    /** Draw the annotation regions (the Annotations section's switch). Selecting from them
+    /** Draw the regions (the Regions section's switch; off by default). Selecting from them
      *  still works while they are hidden. */
     showAnnotations: boolean;
     /** Fill the cells with their colour, outline them, or both. */

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

@@ -62,6 +62,12 @@ export interface IImageInfo {
     showStack: boolean;
     scaleRatio: boolean;
     fileName: string;
+    /**
+     * The host's id of the image, as a spatial dataset's `SpatialImageRef.imageId` names it (jit-ui:
+     * its path in the bucket). Optional: given, the image is a dataset's own only when the two are
+     * equal; without it, only its file name can be compared (see `isDatasetImage`).
+     */
+    imageId?: string;
     roiJsonStr?: string;
     /** Per-slice ROI GeoJSON, aligned 1:1 with `urls`, for a folder stack where
      *  each slice is a separate file with its own sibling `<stem>.geojson`

package/lib/contracts/ports/spatial-data.port.d.ts

@@ -1,5 +1,6 @@
 import { InjectionToken } from '@angular/core';
 import { Observable } from 'rxjs';
+import type { RegionSource } from '../../region-source/region-source';
 import { SpatialColumn, SpatialDataset, SpatialDensityRaster, SpatialEmbedding, SpatialPolygonTile, CategoricalColumnMeta, SpatialMarkerGenes, SpatialPolygons, SpatialTranscriptCounts, SpatialTranscriptSummary, SpatialTranscriptTile } from '../spatial-dataset.contract';
 /** Options for {@link SpatialDataPort.getTranscriptTile}. */
 export interface TranscriptTileQuery {
@@ -145,6 +146,12 @@ export interface SpatialDataPort {
      * mode should never pay for it.
      */
     getVolume?(): Promise<Uint8Array>;
+    /**
+     * Open the region set a boundary set names (`SpatialPolygonTilesMeta.sets[i].regionSource`): a
+     * 3D segmentation's outlines, every plane of them, as a tiled region source. Optional: without
+     * it the set is drawn as boundaries only.
+     */
+    openRegionSet?(id: string): Promise<RegionSource>;
 }
 /**
  * DI token for the host's {@link SpatialDataPort}. Optional: a host that serves no

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

@@ -175,6 +175,15 @@ export interface IRegionEditorApi {
      * drawn or picked, and their surfaces in the volume view are hidden.
      */
     setClassesHidden?(classes: readonly string[], hidden: boolean): void;
+    /**
+     * The classes the spatial 3D view draws as individual cells (each cell its own surface) rather
+     * than as one surface per class, and every change of it. Optional.
+     */
+    getIndividualClasses3d$?(): Observable<ReadonlySet<string>>;
+    /** The classes that can be drawn as individual cells now (a 3D segmentation's, in spatial 3D). */
+    getCellableClasses3d$?(): Observable<ReadonlySet<string>>;
+    /** Draw these classes as individual cells in spatial 3D (or merged again). Optional. */
+    setClassesIndividual3d?(classes: readonly string[], individual: boolean): void;
     /** Select every region of these classes on the slice, the source's included (taken). */
     selectRegionClasses?(classes: readonly string[], additive?: boolean): Promise<void>;
     /** The classes the selection was picked as by {@link selectRegionClasses}; [] once anything

package/lib/contracts/region-store.contract.d.ts

@@ -84,6 +84,12 @@ export interface IRegionEditApi {
 export interface IRegionSourceApi {
     /** The current slice's source as a layer draws it, and every change of it; null without one. */
     getRegionSourceView$(): Observable<RegionSourceView | null>;
+    /**
+     * The source view the overlays draw: null while another layer draws the same outlines (see
+     * `RegionStore.setRegionSourceDrawn`). Optional: without it, the overlays draw
+     * {@link getRegionSourceView$}.
+     */
+    getDrawnRegionSourceView$?(): Observable<RegionSourceView | null>;
     /** Take source features into the working set as regions and select them (added to the
      *  selection with `additive`). Resolves the region ids. */
     selectSourceFeatures(ids: readonly string[], additive?: boolean): Promise<number[]>;

package/lib/contracts/spatial-dataset.contract.d.ts

@@ -262,10 +262,16 @@ export type SpatialBounds = [number, number, number, number];
 /** Tiled cell/nucleus boundaries. Level 0 is the finest (every vertex). */
 export interface SpatialPolygonTilesMeta {
     bounds: SpatialBounds;
-    /** Boundary sets on offer — typically `cell` and `nucleus`. */
+    /**
+     * Boundary sets on offer — typically `cell` and `nucleus`. A 3D segmentation's set (its cells
+     * outlined on every plane they span) also names its outlines as a region set by `regionSource`,
+     * an id the port opens (`SpatialDataPort.openRegionSet`): the visualizer attaches it to the
+     * dataset's image in the region editor, which reconstructs the cells in 3D.
+     */
     sets: {
         name: string;
         label: string;
+        regionSource?: string;
     }[];
     /** The set to draw when the user has not chosen. */
     defaultSet?: string;

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

@@ -7,8 +7,9 @@ import { Polygon, Region } from '../models/region';
 import { PlotType, PlotTypeDescriptor } from './plot-type';
 import { ViewerCapabilities } from './capabilities.contract';
 import { IRegionOverlay } from './region-overlay.contract';
+import type { RegionSource } from '../region-source/region-source';
 import { IHistogram } from './channel-histogram-api.contract';
-import { CanvasToolOptions, ColormapNode, IWandOptions, IBrushOptions, SpatialViewState, SpatialColorBy } from './display-types';
+import { CanvasToolOptions, ColormapNode, IWandOptions, IBrushOptions, SpatialViewState, SpatialColorBy, Cells3dStatus, ObservationsInSelection, TranscriptsInSelection } from './display-types';
 import { CategoricalColumnMeta, SpatialDataset, SpatialEmbedding, SpatialMarkerGenes, SpatialSelectionMask, SpatialTranscriptCounts } from './spatial-dataset.contract';
 import type { PlotModeViewport } from './plot-type-contribution.contract';
 /**
@@ -393,6 +394,26 @@ export interface ISpatialControls {
     /** True while the observation gene filter could not be applied (an expression read failed):
      *  the observations then still show the last filter that could be. */
     getGeneFilterFailed$?(): Observable<boolean>;
+    /** The 3D view's individual cells as they stand (null: none are drawn). Optional. */
+    getCells3dStatus$?(): Observable<Cells3dStatus | null>;
+    /**
+     * Whether the dataset's region set (a 3D segmentation's) is attached and placed among the
+     * observations, so the 3D view can show the cells: not until its source opened with its planes,
+     * and never when it could not be or was not attached. Optional: without it, the dataset naming a
+     * set is taken for it.
+     */
+    getCells3dAvailable$?(): Observable<boolean>;
+    /**
+     * The transcripts of the selection, by gene, kept up to date as the selection, the picked
+     * classes, the regions or the plane shown change (see {@link TranscriptsInSelection}). Optional:
+     * only a dataset with tiled transcripts has it.
+     */
+    getTranscriptsInSelection$?(): Observable<TranscriptsInSelection>;
+    /**
+     * The observations of the same selection, by group, kept up to date as it changes (see
+     * {@link ObservationsInSelection}). Optional.
+     */
+    getObservationsInSelection$?(): Observable<ObservationsInSelection>;
     /**
      * The z positions of the sections the dataset was imaged at, ascending — or
      * null when its z is continuous rather than sectioned (so there are no sections
@@ -517,6 +538,27 @@ export interface IVisualizer extends IDataRenderer, IRegionStore, IToolControlle
     /** This backend's region renderer. May be null until a plot is mounted
      *  (OpenSeadragon). Drives region draw/select modes uniformly. */
     getRegionOverlay(): IRegionOverlay | null;
+    /**
+     * Attach a spatial dataset's region set (a 3D segmentation's cells, see
+     * `SpatialDataPort.openRegionSet`) to its image, the one plotted, beside the image's own regions;
+     * once per image and `key`. Resolves whether it is attached. Optional: the router's.
+     */
+    attachDatasetRegionSet?(open: () => Promise<RegionSource>, key: string): Promise<boolean>;
+    /**
+     * The spatial dataset no longer names the attached region set (it was cleared, or another was
+     * selected) while its image is still plotted: take down what the set brought to the views (its
+     * planes, its cells and surfaces in 3D) unless `keep` is its key. Its regions stay the image's,
+     * with what was taken from or deleted in them, as on another image: the same set attached again
+     * is restored as it was. Optional: the router's.
+     */
+    releaseDatasetRegionSet?(keep: string | null): void;
+    /**
+     * The planes of that region set (its `sliceZ`) while they slice the plotted image, an image of
+     * one plane; null otherwise. The host's slice slider runs over them: each position shows that
+     * plane's regions and, in the 2D spatial view, its observations and transcripts. Optional: the
+     * router's.
+     */
+    getDatasetPlanes$?(): Observable<readonly number[] | null>;
     /** Split a volume view: the displayed slice, with every region tool, in the div `div` beside
      *  the 3D view; null closes it. Resolves whether the slice shows. Optional: the router's. */
     setSliceEditor?(div: string | null): Promise<boolean>;

package/lib/geometry/cell-meshes.d.ts

@@ -0,0 +1,27 @@
+import { ReconstructOptions, SliceOutlines } from './reconstruct';
+/**
+ * A 3D segmentation's cells reconstructed one by one: each cell's outlines on the planes it spans
+ * (see `SliceOutlines`, slice k at z = k) meshed by themselves ({@link reconstruct}), so two cells
+ * of one type that touch stay two surfaces, where a class's union merges them.
+ *
+ * The meshes are concatenated into one, which a single surface layer draws, with each vertex's
+ * cell ({@link CellsMesh.vertexCell}): what colours a cell, hides it, or names it under the pointer.
+ */
+/** One cell's outlines: the cell (an observation index) and its rings on each plane it spans. */
+export interface CellOutlines {
+    cell: number;
+    slices: SliceOutlines[];
+}
+/** Cells' surfaces in one mesh, in image px (x, y) and slice indices (z), each vertex's cell known. */
+export interface CellsMesh {
+    vertices: Float32Array;
+    faces: Uint32Array;
+    /** The cell (observation index) of each vertex. */
+    vertexCell: Uint32Array;
+    /** The cells meshed (those with an area on some plane), in order. */
+    cells: Uint32Array;
+}
+/** Each cell's surface by itself (one smoothing pass: a cell is a few voxels across). */
+export declare function reconstructCells(cells: readonly CellOutlines[], opts?: ReconstructOptions): CellsMesh;
+/** The buffers of a {@link CellsMesh}, to hand them across a worker boundary without a copy. */
+export declare function cellsMeshBuffers(mesh: CellsMesh): ArrayBuffer[];

package/lib/geometry/place.d.ts

@@ -0,0 +1,45 @@
+/**
+ * Where a stack's reconstructions sit in a 3D view's world (pure: the volume and spatial 3D views
+ * place region surfaces with it, on the main thread or in a worker).
+ */
+/** Where the stack sits in the volume's world: its full size, and the centred world box it fills. */
+export interface VolumeFrame {
+    /** Image width, height (px) and slice count. */
+    size: [number, number, number];
+    /** The world box (centred on the origin), Z as currently stretched. */
+    world: [number, number, number];
+    /**
+     * How much of {@link world}'s depth is the view's Z stretch (default 1). The region surfaces keep
+     * their geometry in the unstretched box and take the stretch as a GPU scale (`scale3d`), so
+     * dragging the Z handle re-uploads no mesh.
+     */
+    zScale?: number;
+    /**
+     * The slices at z of their own rather than spread over the box: a region set's planes (a 3D
+     * segmentation's, outlined on an image of one plane) placed where the observations are. Given,
+     * it places the surfaces and {@link size} and {@link world} do not.
+     */
+    planes?: PlanePlacement;
+}
+/**
+ * Image px and slices → world, slice by slice: `x * scale[0] + offset[0]`, `y * scale[1] +
+ * offset[1]`, and slice k at `z[k] + offset[2]` (unstretched): between two slices in proportion,
+ * past the ends by the nearest spacing (a surface's caps, half a slice out).
+ */
+export interface PlanePlacement {
+    /** Each slice's z, by slice index, ascending. */
+    z: readonly number[];
+    scale: [number, number];
+    offset: [number, number, number];
+}
+/**
+ * Image px / slice coordinates → the volume's centred world box: pixel x of a `w`-wide image
+ * spans the box's width, slice k sits at the middle of its share of the box's depth. With
+ * {@link VolumeFrame.planes}, as they place them instead.
+ */
+export declare function toWorld(vertices: Float32Array, frame: VolumeFrame): Float32Array;
+/**
+ * The z of slice `k` (fractional): between two slices in proportion, past the ends by the nearest
+ * spacing (one slice alone: a unit apart).
+ */
+export declare function sliceZ(z: readonly number[], k: number): number;

package/lib/implementations/napari-js/napari-camera-depth.d.ts

@@ -0,0 +1,23 @@
+import type { Camera3D } from 'napari-js';
+/**
+ * Keep the whole scene within the 3D camera's depth range, however close the camera comes.
+ *
+ * napari-js (0.20) puts the far plane at `4 · distance + 1` from the eye, so the closer the camera
+ * (the more one zooms in), the nearer the far plane: zoomed in on a long, flat specimen seen at an
+ * angle (a MERFISH section, 9,000 px long), everything farther than four distances is cut away and
+ * the canvas goes black past a straight edge — one cannot zoom close to a small part of it. Here the
+ * far plane is pushed out to the far side of the scene (`distance + |target| + radius`, the scene
+ * centred on the origin as the 3D views centre it), never nearer than napari-js's own; the near
+ * plane, the field of view and the view are napari-js's, as are the matrices (copied: napari-js does
+ * not export them). Its picking and projections read the same matrix, so they agree.
+ *
+ * TODO: napari-js should take the scene's extent itself (a far plane from the layers' bounds); this
+ * override is removed once it does.
+ *
+ * Returns the function that restores napari-js's own projection.
+ */
+export declare function keepSceneInDepth(camera: Camera3D, radius: () => number | null): () => void;
+/** The radius of a centred box `[w, h, d]` (half its diagonal). */
+export declare function boxRadius(w: number, h: number, d: number): number;
+/** WebGPU-style perspective (clip z in [0,1]). */
+export declare function perspective(fovy: number, aspect: number, near: number, far: number): Float32Array;

package/lib/implementations/napari-js/napari-loading-state.d.ts

@@ -1,5 +1,5 @@
 /** What the service itself counts on the badge; the spatial tile layers report their own names. */
-export type LoadingSource = 'Image' | 'Observations' | 'Transcripts';
+export type LoadingSource = 'Image' | 'Observations' | 'Transcripts' | 'Cells';
 /**
  * "x reloading…" at the bottom of the canvas, aggregated over everything that loads into one
  * scene: image tiles (the tile client), observation colourings (the spatial scenes) and the

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

@@ -39,6 +39,18 @@ export interface NapariScene {
     screenProjection?(obs: SpatialObservations): Float32Array | null;
     /** Show these region reconstructions in the 3D view (volume scenes only). */
     setRegionMeshes?(meshes: readonly RegionMesh3D[]): void;
+    /**
+     * Where the reconstructions' slices are, in the observations' units, when their region set says
+     * (a 3D segmentation's planes); null: they are the plotted stack's slices (spatial 3D only).
+     */
+    setRegionPlanes?(z: readonly number[] | null): void;
+    /**
+     * The plane of those (see {@link setRegionPlanes}) the 2D spatial view shows, over an image of
+     * one plane: its observations and transcripts are the ones drawn (spatial 2D only).
+     */
+    setRegionPlane?(k: number): void;
+    /** Draw these classes of the dataset's region set as individual cells (spatial 3D only). */
+    setRegionCells?(classes: readonly string[] | null): void;
     /** Highlight the reconstructions of these keys (none: all as usual). */
     setRegionHighlight?(keys: readonly string[]): void;
     /** Hide the reconstructions of these keys. */