@jax-data-science/sci-image-visualizer 0.15.0 → 0.17.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.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-qUeMuBb0.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-DHrHO2ay.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-U1ODcfYD.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-CKEUwNta.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.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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+{"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 ?? (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-qUeMuBb0.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-DHrHO2ay.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';

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

@@ -130,8 +130,8 @@ export interface SpatialViewState {
      * setting for a backdrop and a useless one for the measurement.
      */
     volumeOpacity: number;
-    /** Draw the observation markers — the 3D cloud, or the 2D circles. In 2D they also
-     *  stand in for cells too small on screen to outline. */
+    /** Draw the observation markers — the 3D cloud, or the 2D circles. In 2D they are drawn at
+     *  every zoom, never under a couple of screen pixels, with any cell outlines over them. */
     showPoints: boolean;
     /**
      * Restrict the cloud to ONE imaged section, by index into the dataset's sampled
@@ -267,6 +267,13 @@ export interface SpatialViewState {
     transcriptHiddenGenes: string[];
     /** Per-gene marker colour (`#rrggbb`); genes not listed take the palette by position. */
     transcriptGeneColors: Record<string, string>;
+    /**
+     * Colours the user chose for groups of a categorical column (`#rrggbb`), by column name and
+     * then category: they override the column's own and the palette's, wherever that grouping
+     * colours anything (cells, markers, transcripts by cell type, legends, charts). Groups not
+     * listed keep their colour. Cleared when the dataset changes.
+     */
+    groupColors: Record<string, Record<string, string>>;
     /** Named gene groups (e.g. marker genes per cell type) for the selected-genes tree. */
     transcriptGeneGroups: {
         name: string;

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';
+export type LoadingSource = 'Image' | 'Observations' | 'Transcripts';
 /**
  * "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

@@ -71,6 +71,8 @@ export interface NapariSettings {
     surfaceWireframe: boolean;
     /** The volume's user Z-height factor (1 = the volume's natural proportions). */
     volumeZScale: number;
+    /** The 3D spatial view's Z stretch (1 = the data's true proportions). */
+    spatialZScale: number;
 }
 /** The stack-loading flag and progress the host shows while frames load. */
 export interface StackProgress {

package/lib/implementations/napari-js/napari-spatial-2d-scene.d.ts

@@ -61,9 +61,9 @@ export declare class Spatial2dScene extends SpatialSceneBase implements NapariSc
      */
     protected pickObservation(clientX: number, clientY: number, slackPx: number): number;
     /**
-     * Whether the markers are drawn: when the user wants them, and not while cell outlines are on
-     * screen — then a cell IS its outline, and a circle on top of it is noise. Zoomed out past the
-     * outline threshold, the circles stand in for the cells.
+     * Whether the markers are drawn: whenever the user wants them, at every zoom. Cell outlines come
+     * and go with the zoom (their level of detail follows it) and are drawn over the markers; the
+     * observations themselves never disappear with them.
      */
     private pointsVisible;
     /**

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

@@ -1,17 +1,44 @@
+import type { AxisLabelSpec } from 'napari-js/overlays';
 import { IHistogram } from '../../contracts/channel-histogram-api.contract';
+import { ISurface3dControls } from '../../contracts/visualizer.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 { Box3 } from './napari-axes-gizmo';
 import { SpatialSceneBase, SpatialSession } from './napari-spatial-scene';
 import type { NapariScene, SceneContext } from './napari-scene';
+/** The least Z stretch: a tenth of the true depth. */
+export declare const SPATIAL_Z_SCALE_MIN = 0.1;
+/**
+ * The most a box's Z may be stretched: until it is twice as deep as it is wide, so even a section
+ * microns thick and millimetres wide can be stood up into a block — but never less than the
+ * Volume view's 10x, nor more than {@link SPATIAL_Z_SCALE_CEILING}.
+ */
+export declare function spatialZScaleMax(box: Box3): number;
+/**
+ * The Z handle's drag (px) per doubling: the Volume view's 180 px, less when the range is wider,
+ * so going from the true depth to the most stretch is about the same drag (~540 px) either way.
+ */
+export declare function spatialZPixelsPerDouble(maxScale: number): number;
+/**
+ * The X/Y/Z axis-end labels for a box (as drawn: Z stretched by `zScale`), its true lengths in µm
+ * when the dataset declares `micronsPerUnit`, else in its own units. A stretched Z says by how much,
+ * so its length is never read off the drawing.
+ */
+export declare function spatialAxesLabels(drawn: Box3, zScale: number, micronsPerUnit?: number): AxisLabelSpec[];
 /**
  * SPATIAL_OMICS_3D (review Appendix B, cluster K): observations as a 3D point cloud under the
  * orbit camera, with the dataset's reference volume around it, per-cluster density volumes and the
  * 3D gene map.
  *
+ * Everything sits in one box centred on the world origin (see {@link ensureFrame}): the reference
+ * volume's, else the density grid's. The Volume view's axes gizmo and Z-height handle are drawn on
+ * it, and the handle stretches Z: the cloud through its `scale3d`, every volume through its voxel
+ * size, so nothing is re-uploaded while dragging (see {@link setZScale}).
+ *
  * Thinner than the 2D scene: there is no tissue image to render (a registered volume like the
  * Allen CCF has no single reference plane), so no readback and no navigator; the 3D scale bar
  * follows the dataset (see {@link installScaleBar}). The region tools work in SCREEN space through
@@ -46,6 +73,14 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
     private geneMapKey;
     /** Offset applied to observation coordinates to sit them in the volume's box. */
     private origin;
+    /** The box everything sits in, before the Z stretch, centred on the origin (see ensureFrame). */
+    private box;
+    private boxKey;
+    /** The axes gizmo on {@link box} and the handle that stretches its Z (see setZScale). */
+    private gizmo;
+    private zHandle;
+    /** Each volume layer's own voxel size, before the Z stretch. */
+    private readonly baseVoxels;
     /**
      * napari-js's depth-aware pick over the cloud, and the projection the ROI selection reads. It
      * owns the caching policy: re-project lazily, on the first pick after the camera, the canvas or
@@ -68,6 +103,8 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
      * regions were drawn on is that volume's stack (see {@link placeRegionMeshes}).
      */
     private readonly regionMeshes;
+    /** The transcripts of the genes the Transcripts panel draws, at their own z (see Spatial3dTranscripts). */
+    private readonly transcripts3d;
     /** 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
@@ -106,6 +143,25 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
     setZ(): void;
     /** A cloud has no intensity distribution for the histogram pane. */
     histogram(): IHistogram | null;
+    /** The toolbar's 3D controls, as the Volume view's: drag mode, re-framing and the axes. */
+    surface3dControls(): ISurface3dControls | null;
+    /**
+     * Stretch Z by `factor` (1 = the data's true proportions), as the Z handle drags it: the cloud
+     * through its `scale3d`, each volume through its voxel size, the axes and the region surfaces
+     * with them — all about the world origin, which the box is centred on, so they stay aligned.
+     * Nothing is re-uploaded. Kept in the settings, so a re-plot keeps it.
+     */
+    setZScale(factor: number): void;
+    /** The Z stretch in effect: the setting, within what this box allows. */
+    zScale(): number;
+    private applyZScale;
+    /** `box` with its Z stretched as drawn. */
+    private drawnBox;
+    /**
+     * Add a volume layer with its Z stretched as the rest of the scene is, remembering its own
+     * voxel size so a later stretch can be applied to it.
+     */
+    private addVolume;
     /**
      * Every observation's position on the canvas under the current 3D camera (for the ROI
      * selection), indexed by observation with NaN for anything not drawn. Null before the cloud
@@ -224,18 +280,35 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
      */
     private densityGroups;
     /**
-     * Add (or keep) the dataset's reference volume, and derive the offset that sits the
-     * observations inside it.
+     * Add (or keep) the dataset's reference volume. The offset that sits the observations inside
+     * it is {@link ensureFrame}'s.
      *
-     * `VolumeLayer` has no translate: napari-js maps the volume's unit cube to a world box
-     * **centred on the origin**, sized `dims x voxelSize`. The observations, by contract, are in
-     * the volume's own frame with its near corner at the coordinate origin. So the two only line
-     * up if the POINTS move — by half the box — which is what {@link origin} is.
-     *
-     * A failed or absent volume is not fatal: the cloud renders on its own, at its own
-     * coordinates, and the camera frames the points instead.
+     * A failed or absent volume is not fatal: the cloud renders on its own, in the same box, and
+     * the camera frames the points instead.
      */
     private ensureVolume;
+    /**
+     * The box everything sits in, centred on the world origin, and the offset that sits the
+     * observations in it; with the axes gizmo and the Z handle on it.
+     *
+     * `VolumeLayer` has no translate: napari-js maps a volume's unit cube to a world box centred on
+     * the origin, sized `dims x voxelSize`. The observations, by contract, are in the reference
+     * volume's frame with its near corner at the coordinate origin, and the density grid is measured
+     * from the coordinate origin the same way (`densityGrid`), so its box is the reference volume's
+     * when there is one. So the POINTS move by half that box — {@link origin} — and every volume, the
+     * reference, the densities and the gene map, lines up with them and with each other. Without a
+     * reference volume this centres the cloud too, which the axes and the Z stretch need: both work
+     * about the origin.
+     */
+    private ensureFrame;
+    /**
+     * The Volume view's axes gizmo and Z-height handle, on {@link box}. The handle floats past the
+     * top of the Z axis (the box's min-XY corner, where the blue axis and its label are), by a share
+     * of the box's largest side rather than of its depth, so it clears the label even while a thin
+     * section is drawn flat.
+     */
+    private installAxes;
+    private removeAxes;
     /** Drop every layer of the cloud (the dataset went away, or has no z). */
     private removeLayers;
     /**

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

@@ -0,0 +1,62 @@
+import type { Points3DLayer, Viewer } from 'napari-js';
+import { type SpatialDataPort } from '../../contracts/ports/spatial-data.port';
+import type { SpatialViewState } from '../../contracts/display-types';
+import { type SpatialDataset } from '../../contracts/spatial-dataset.contract';
+/** Most transcripts drawn in the 3D view: past it, every k-th one is drawn (and the console says so). */
+export declare const TRANSCRIPTS_3D_MAX = 2000000;
+/** Most level-0 tiles read for the 3D view: a dataset needing more is too large to draw whole. */
+export declare const TRANSCRIPTS_3D_MAX_TILES = 4096;
+/** A transcript's marker in the 3D view, in screen pixels at a transcript scale of 1. */
+export declare const TRANSCRIPT_3D_BASE_SIZE = 2;
+/** What the 3D transcripts need of the scene: where the cloud sits and how Z is stretched. */
+export interface Transcripts3dFrame {
+    /** Offset applied to observation coordinates to sit them in the scene's box. */
+    origin: readonly [number, number, number];
+    zScale: number;
+}
+/** The genes a view draws in 3D, as the tile query takes them, or null when it draws none. */
+export declare function transcripts3dGenes(dataset: SpatialDataset, view: SpatialViewState): {
+    query: string[];
+    allGenes: boolean;
+} | null;
+/**
+ * Each loaded transcript's colour, packed RGBA, as the 2D markers colour them by gene: a gene's
+ * chosen colour, else the palette's by its slot (the selection's order, or with "All genes" the
+ * dataset's gene code).
+ */
+export declare function transcripts3dColors(view: SpatialViewState, names: readonly string[] | null, gene: Uint16Array, count: number): Float32Array;
+/**
+ * How the panel's "Colour by" applies in 3D, as it does to the 2D markers (`colorViewFor`): by
+ * cell type when the dataset has one (else by gene), by cluster for the selected genes (with "All
+ * genes" a cluster is its gene), by gene otherwise.
+ */
+export declare function transcripts3dColorBy(dataset: SpatialDataset, view: SpatialViewState, allGenes: boolean): 'cellType' | 'cluster' | 'gene';
+/**
+ * The transcripts of the 3D spatial view: every molecule of the genes the Transcripts panel draws
+ * (its selected genes, or "All genes"), at its own x, y and z, in the cloud's box and Z stretch.
+ *
+ * The 2D view reads transcripts by level of detail for the camera; a 3D orbit has no such window,
+ * so this reads the whole level 0 once per gene selection (a few hundred thousand molecules for a
+ * MERFISH section) and only restyles after that. Drawn only for a dataset whose transcripts carry z.
+ */
+export declare class Spatial3dTranscripts {
+    private readonly viewer;
+    private readonly begin;
+    private layer;
+    /** What {@link layer} was loaded from (dataset, genes, quality), and styled with. */
+    private loadKey;
+    private styleKey;
+    private loaded;
+    private readonly loads;
+    constructor(viewer: Viewer, begin: (label: 'Transcripts') => () => void);
+    /** The layer drawn, if any (for tests and the scene's Z stretch). */
+    get drawn(): Points3DLayer | null;
+    /** Draw what `view` asks for, loading the molecules when the genes changed. */
+    sync(dataset: SpatialDataset, view: SpatialViewState, port: SpatialDataPort | null, frame: Transcripts3dFrame): Promise<void>;
+    /** Follow the scene's Z stretch (nothing is re-uploaded). */
+    setZScale(s: number): void;
+    /** Take the layer down and forget what it showed. */
+    remove(): void;
+    private clearLayer;
+    private draw;
+}

package/lib/implementations/napari-js/napari-spatial-encoding.d.ts

@@ -2,7 +2,7 @@ import type { Colormap } from 'napari-js';
 import { Rgb } from '../../contracts/colormap-lut';
 import { CategoricalColumn } from '../../contracts/spatial-dataset.contract';
 import { SpatialViewState } from '../../contracts/display-types';
-import { type RGBA } from '../../spatial/spatial-encoding';
+import { GroupColorOverrides, type RGBA } from '../../spatial/spatial-encoding';
 import { SpatialSelectionMask } from '../../spatial/spatial-selection';
 /**
  * The spatial scenes' pure colour and grouping math: what the 2D markers, the 3D cloud and the
@@ -16,6 +16,13 @@ export declare const SPATIAL_FALLBACK_RADIUS = 4;
  *  40 µm/px template, so drawing them to scale would put every cell a fifth of a pixel wide
  *  and the section would come up empty. The point-size control scales up from this floor. */
 export declare const SPATIAL_SLICE_MIN_DIAMETER_PX = 1.5;
+/**
+ * Smallest drawn marker diameter in the 2D view, in SCREEN pixels, at any zoom. A marker's size is
+ * the cell's own (data units), so zoomed out over a whole Cytos plate or Xenium section every cell
+ * fell below a pixel and the observations vanished; with the floor they stay a dense field of
+ * dots, coloured as they are, at every zoom (the GPU applies it per frame: no rebuild on zoom).
+ */
+export declare const SPATIAL_MARKER_MIN_SCREEN_PX = 2;
 /** Longest side of the gene-map raster, in field pixels. A gene map is a smooth
  *  field read as territory, so it gains nothing from matching a 2 Gpx slide's
  *  resolution — and the estimate costs one pass over this many pixels. */
@@ -116,4 +123,4 @@ export declare function totalDensityGroup(selection: SpatialSelectionMask): Dens
  * {@link DENSITY_MAX_CLUSTERS}, each with its legend colour — restricted to the selection when
  * there is one, so "select a region, check the box" answers which clusters live there.
  */
-export declare function rankDensityGroups(columnName: string, column: CategoricalColumn, count: number, selection: SpatialSelectionMask): DensityGroup[];
+export declare function rankDensityGroups(columnName: string, column: CategoricalColumn, count: number, selection: SpatialSelectionMask, groupColors?: GroupColorOverrides | null): DensityGroup[];

package/lib/implementations/napari-js/napari-spatial-tiles.d.ts

@@ -48,11 +48,10 @@ export interface SpatialTileHost {
  * -----------
  * Cell fill, cell outline, nucleus outline, the transcript density, then transcripts on top
  * ({@link TILE_LAYER_ORDER}); a plan restores the order once, after all its groups are in
- * place. The service's observation markers sit under all of them; while outlines are drawn the
- * markers are hidden (a cell is its outline then, not a dot), so the cells never have to
- * be ordered against them. The density goes OVER the markers on purpose: under 10^5
- * dots it would only show in the gaps between cells. {@link afterObservations} restores
- * the order after the service re-adds its markers.
+ * place. The service's observation markers sit under all of them, drawn at every zoom: once
+ * cells are big enough to outline, their outlines go over their markers. The density goes
+ * OVER the markers on purpose: under 10^5 dots it would only show in the gaps between cells.
+ * {@link afterObservations} restores the order after the service re-adds its markers.
  *
  * ONE LAYER PER GROUP
  * -------------------
@@ -95,7 +94,7 @@ export declare class NapariSpatialTileLayers {
     hoverAt(wx: number, wy: number, radiusWorld: number, onDetails: (lines: string[]) => void): string[] | null;
     /** Whether `layer` is one of the overlays drawn here (density, cells, transcripts). */
     owns(layer: Layer): boolean;
-    /** True while outlines are on screen — the service hides its dots then. */
+    /** True while outlines are on screen. */
     get outlinesShown(): boolean;
     /** The density window in use and the densest bin, for the panel's threshold control. */
     get densityStats(): DensityStats | null;

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

@@ -16,6 +16,12 @@ export interface VolumeFrame {
     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;
 }
 /** Opacity of a region's surface in the volume. */
 export declare const REGION_MESH_OPACITY = 0.55;
@@ -26,8 +32,10 @@ export declare const REGION_MESH_DIMMED_OPACITY = 0.12;
 /**
  * The region reconstructions shown in a volume view: one translucent surface per region, in its
  * colour, placed in the volume's world box (pixel x, y and slice z mapped onto it the way the
- * volume maps its voxels) and re-placed when the volume's Z is stretched. A surface is updated in
- * place (`setData`, `color`) rather than added again, and picked by napari-js (`pickSurface`).
+ * volume maps its voxels). The box's Z stretch is the surfaces' `scale3d` (a uniform), so a stretch
+ * alone changes no geometry; a new box re-places them. A surface is updated in place (`setData`,
+ * `color`, `scale3d`) rather than added again, and picked by napari-js (`pickSurface`), which
+ * picks it where it is drawn.
  *
  * Highlighting is focus + context: the highlighted surfaces turn near opaque and the others fade
  * to a ghost, so the selection stands out while staying in place among its neighbours.
@@ -43,8 +51,13 @@ export declare class VolumeRegionMeshes {
     constructor(viewer: Viewer);
     /** Show exactly `meshes` (adding, keeping or removing surfaces). */
     set(meshes: readonly RegionMesh3D[]): void;
-    /** Follow the volume's frame (it opened, or its Z was stretched): re-place every surface. */
+    /**
+     * Follow the volume's frame. A new box (it opened, another volume) re-places every surface; a Z
+     * stretch of the same box only sets their `scale3d`, so nothing is re-uploaded while dragging.
+     */
     setFrame(frame: VolumeFrame): void;
+    /** The surfaces' GPU scale: the frame's Z stretch. */
+    private scale3d;
     /** Highlight the surfaces of these keys (none: every surface as usual). */
     setHighlight(keys: Iterable<string>): void;
     /** Hide the surfaces of these keys (they are kept, so showing them again is instant). */

package/lib/implementations/napari-js/spatial-tiles/cell-layers.d.ts

@@ -40,7 +40,7 @@ export declare class CellLayers {
      *  value, and a selection or opacity change recolours with the vector unchanged (SPATIAL-12). */
     private readonly contrastWindows;
     constructor(port: SpatialDataPort, groups: OrderedLayerGroups<TileGroup>, lookup: CategoricalLookup, host: CellLayersHost);
-    /** True while outlines are on screen — the service hides its dots then. */
+    /** True while outlines are on screen. */
     get outlinesShown(): boolean;
     /** The viewer went away (its layers with it): the outlines are no longer shown. */
     detached(): void;

package/lib/spatial/spatial-encoding.d.ts

@@ -73,6 +73,16 @@ export declare function parseHex(hex: string): Rgb;
  * 40-cluster column still gets stable, distinct-ish colours.
  */
 export declare function resolveCategoryColors(meta: CategoricalColumnMeta, palette?: string[]): string[];
+/** The user's group colours: by column name, then category (see `SpatialViewState.groupColors`). */
+export type GroupColorOverrides = Readonly<Record<string, Readonly<Record<string, string>>>>;
+/**
+ * Categorical column `column`'s colours ({@link resolveCategoryColors}) with the user's choices
+ * for its groups over them. Every place a grouping is coloured goes through this, so a group
+ * recoloured in the list is that colour on the cells, the markers, the legend and the charts.
+ */
+export declare function categoryColorsFor(column: string, meta: CategoricalColumnMeta, overrides?: GroupColorOverrides | null): string[];
+/** What a cache keyed on a grouping's colours must include of the user's choices for it. */
+export declare function groupColorsKey(column: string | null, overrides?: GroupColorOverrides | null): string;
 /** Categorical column → flat per-point RGBA (length `4 * codes.length`). */
 export declare function encodeCategorical(codes: Uint16Array, opts: CategoricalEncodingOptions): Float32Array;
 /** Continuous column / gene vector → flat per-point RGBA. */

package/lib/spatial-controls/spatial-controls.component.d.ts

@@ -139,6 +139,8 @@ export declare class SpatialControlsComponent implements OnInit {
     protected get hasCells(): boolean;
     /** Transcripts on offer: tiles to draw, or a density map. */
     protected get hasTranscripts(): boolean;
+    /** Whether the 3D cloud can draw the transcripts too: they carry z (a MERFISH volume's do). */
+    protected get hasTranscripts3d(): boolean;
     protected onShowImage(on: boolean): void;
     protected onShowAnnotations(on: boolean): void;
     /** Which collapsible sections are open. Per dialog instance, not persisted. */

package/lib/spatial-controls/spatial-gene-style/spatial-gene-style.component.d.ts

@@ -17,6 +17,8 @@ export declare class SpatialGeneStyleComponent {
     glyph: TranscriptGlyphName;
     /** A note under the icons, e.g. where they show; none when null. */
     iconHint: string | null;
+    /** False for a colour alone (a cell group, or every gene drawn with one icon): no icon grid. */
+    showIcons: boolean;
     readonly colorChange: EventEmitter<string>;
     readonly glyphChange: EventEmitter<TranscriptGlyphName>;
     /** Back to the gene's default icon and colour. */
@@ -26,5 +28,5 @@ export declare class SpatialGeneStyleComponent {
     /** A typed hex colour, accepted as `#rrggbb` or `rrggbb`; anything else is ignored. */
     protected onHex(text: string): void;
     static ɵfac: i0.ɵɵFactoryDeclaration<SpatialGeneStyleComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialGeneStyleComponent, "spatial-gene-style", never, { "gene": { "alias": "gene"; "required": false; }; "what": { "alias": "what"; "required": false; }; "color": { "alias": "color"; "required": false; }; "glyph": { "alias": "glyph"; "required": false; }; "iconHint": { "alias": "iconHint"; "required": false; }; }, { "colorChange": "colorChange"; "glyphChange": "glyphChange"; "resetStyle": "resetStyle"; }, never, never, true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialGeneStyleComponent, "spatial-gene-style", never, { "gene": { "alias": "gene"; "required": false; }; "what": { "alias": "what"; "required": false; }; "color": { "alias": "color"; "required": false; }; "glyph": { "alias": "glyph"; "required": false; }; "iconHint": { "alias": "iconHint"; "required": false; }; "showIcons": { "alias": "showIcons"; "required": false; }; }, { "colorChange": "colorChange"; "glyphChange": "glyphChange"; "resetStyle": "resetStyle"; }, never, never, true, never>;
 }

package/lib/spatial-controls/spatial-gene-tree/spatial-gene-tree.component.d.ts

@@ -4,6 +4,8 @@ import type { SpatialDataset } from '../../contracts/spatial-dataset.contract';
 import { SpatialViewState, TranscriptGlyphName } from '../../contracts/display-types';
 import { GeneTreeNode } from '../../spatial/spatial-panel-model';
 import * as i0 from "@angular/core";
+/** How the gene rows are ordered: by name, or by their transcripts in view, most first. */
+export type GeneSort = 'name' | 'count';
 /** One gene row as the template draws it, derived once per input change. */
 interface GeneRowView {
     shown: boolean;
@@ -19,6 +21,8 @@ interface AllGeneRowView {
     shown: boolean;
     /** Its colour when coloured by gene, or null when the dataset's code order is unknown. */
     swatch: string | null;
+    /** Its code in the dataset's gene list (what its palette colour is picked by). */
+    code: number;
     count: number | null;
 }
 /**
@@ -29,6 +33,11 @@ interface AllGeneRowView {
  * expands to every gene of the dataset, each with its eye when the dataset lists its genes
  * in code order (`transcriptTiles.genes`), filtered by name past a few hundred.
  *
+ * Both lists are ordered by name, or by their transcripts in view, most first (the
+ * sort switch, offered once the renderer reports counts). The all-genes list is sorted
+ * before it is cut to its first rows, so by count those are the genes with the most
+ * transcripts in view.
+ *
  * Writes only through `controls.setViewState`.
  */
 export declare class SpatialGeneTreeComponent implements OnChanges {
@@ -47,6 +56,10 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     /** Swatches in the picker: the categorical palette genes are coloured from by default. */
     /** The tree, rebuilt when the view changes — never per change-detection pass. */
     protected geneTree: GeneTreeNode[];
+    /** {@link geneTree} with each node's genes in {@link geneSort} order: what the template draws. */
+    protected sortedTree: GeneTreeNode[];
+    /** The rows' order. By count only while the renderer reports counts (see {@link sortShown}). */
+    protected geneSort: GeneSort;
     /** Per gene: its eye, swatch, glyph and count — rebuilt with the inputs (and when the
      *  cells' group colours arrive), so the template does no per-row lookups per check. */
     protected rows: Map<string, GeneRowView>;
@@ -78,6 +91,13 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     constructor(zone: NgZone, cdr: ChangeDetectorRef);
     ngOnChanges(changes: SimpleChanges): void;
     private rebuildRows;
+    /** Whether the rows are ordered by count: chosen, and counts to order by. */
+    protected get byCount(): boolean;
+    /** The sort switch is offered once there are counts to sort by. */
+    protected get sortShown(): boolean;
+    protected onGeneSort(sort: GeneSort): void;
+    /** `genes` in the rows' order: by count, most first (ties by name), else by name. */
+    private sorted;
     /**
      * The all-genes list's rows: the genes matching the filter, up to the cap. Built only while
      * the list is open: the counts in view change with every pan, and the list can be thousands.
@@ -113,6 +133,11 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     /** The colour gene `slot` is drawn in when transcripts are coloured by gene. */
     geneColor(slot: number): string;
     protected geneColorOf(gene: string): string;
+    /**
+     * The colour the open picker shows: with "All genes", the gene's colour among every gene (its
+     * chosen one, else the palette's by its code), as its row and its markers have it.
+     */
+    protected styleColorOf(gene: string): string;
     /** In Cluster colouring, a gene's swatch is its cluster's colour, as its markers are. */
     protected geneSwatchOf(gene: string): string;
     protected geneCountOf(gene: string): number | null;