@jax-data-science/sci-image-visualizer 0.13.0 → 0.15.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-D0IQ6PjZ.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.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-DURPqs5a.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-qUeMuBb0.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
@@ -38,6 +38,7 @@ import 'primeng/selectbutton';
 import 'primeng/treeselect';
 import 'plotly.js-dist-min';
 import 'primeng/multiselect';
+import 'primeng/inputswitch';
 import 'image-js';
 import 'buffer';
 import 'openseadragon';
@@ -237,4 +238,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-D0IQ6PjZ.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-D0IQ6PjZ.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-U1ODcfYD.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-D0IQ6PjZ.mjs","sources":["../../src/lib/toolbar/segmentation/pending-calls.ts","../../src/lib/toolbar/segmentation/onnx-sam-session.ts"],"sourcesContent":["/** A reply from the SAM worker: progress for, or the result of, call `id`. */\nexport interface WorkerReply {\n  id: number;\n  type: string;\n  /** Present on `type: 'progress'` replies. */\n  fraction?: number;\n  /** Present on `type: 'error'` replies. */\n  error?: string;\n  [key: string]: unknown;\n}\n\ninterface Pending {\n  resolve: (reply: WorkerReply) => void;\n  reject: (err: Error) => void;\n  onProgress?: (fraction: number) => void;\n}\n\n/**\n * Request/response bookkeeping for a worker RPC: each call gets an id and a\n * promise that its reply settles. Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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package/fesm2022/jax-data-science-sci-image-visualizer.mjs

@@ -1,4 +1,4 @@
-export { A as ALL_GENES, b as ALL_TOOLBAR_TOOLS, c as ANNOTATION_IMAGE_MAX_DIM, C as CANVAS_TOOL_IDS, d as CELL_SEGMENTER, e as CHANNEL_HISTOGRAM_API, h as CellposeSegmenterService, i as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, j as DEFAULT_FALLBACK_PALETTE, k as DEFAULT_MUTED_OPACITY, l as DEFAULT_SAM_MODEL_ID, m as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, n as INSTANCE_SEGMENTER, o as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, p as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, q as NAPARI_DEFAULT_DECIMATE, s as NO_CATEGORY, t as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, u as PLOT_MODE_SESSION, v as PLOT_TYPE_CONTRIBUTIONS, w as PLOT_TYPE_DESCRIPTORS, x as PREFERENCES_PORT, y as PlotType, z as Polygon, B as ProcessingImage, R as REGION_EDITOR_API, E as REGION_IO_PORT, F as REGION_SOURCE_MIN_CHARS, G as Rectangle, J as Region, K as RegionEditorComponent, O as RoutingVisualizerService, S as SAM_MODELS, Q as SEMANTIC_SEGMENTER, T as SPATIAL_DATA_PORT, U as SPATIAL_WIRE_VERSION, V as ShapeSelection, W as SpatialChartsComponent, X as SpatialControlsComponent, Y as SpatialDataHttpService, Z as SpatialSelectionStore, _ as SupersededError, $ as TILE_ACCESS_PORT, a0 as TOOLBAR_TOOLS, a1 as VISUALIZER, a2 as VIZ_ALERT_TOAST_KEY, a3 as VIZ_CONFIG, a4 as VIZ_TOAST_KEY, a5 as ViewerFeature, a6 as VisualizationModule, a7 as VisualizerComponent, a8 as assertManifestVersion, a9 as benefitsFromGrouping, aa as buildOmicsTraces, ab as capabilitiesOf, ac as clearSamModelCache, ad as contrastWindow, ae as contributedPlotTypeOption, af as countMask, ag as cropImage, ah as datasetFromManifest, ai as decodeColumn, aj as decodeCoords, ak as decodeFeatureVector, al as decodePolygons, am as decodeRadius, an as defaultPresetSet, ao as dialogToolContributions, ap as emptySelection, aq as encodeCategorical, ar as encodeContinuous, as as expandZips, at as findColumnMeta, au as getDefaultSamModelId, g as getOrtWasmBase, av as getPlotTypeDescriptor, aw as getSamModel, ax as hasZarrMetadata, ay as hydrateBounds, az as importFile, aA as isBuiltinPlotType, aB as isCanvasToolId, aC as isCategoricalColumn, aD as isContinuousColumn, aE as isDialogToolContribution, aF as isEmptyPresetSet, aG as isLabelVolumeName, aH as isLittleEndian, aI as isNapari3d, aJ as isNapariIsosurface, aK as isNapariScatter, aL as isNapariScatter3d, aM as isNapariSurface, aN as isNapariVolume, aO as isSamModelReady, aP as isSpatialOmics, aQ as isSpatialOmics3d, aR as isThreeDimensional, aS as isZipName, aT as labelClasses, aU as labelSliceGeoJson, aV as lutFor, aW as markerDiameters, aX as maskToIndices, aY as mutedFromSelection, aZ as omicsLayout, a_ as openAnnotations, a$ as openGeoJsonRegionSource, b0 as openHttpRegionSource, b1 as parsePresetSet, b2 as planRegionImport, b3 as pointInRing, b4 as provideVisualization, b5 as readAnnotationSlices, b6 as readLabelVolume, b7 as readOmeZarrLabels, b8 as readZip, b9 as rendererOwnsWheel, ba as resolveCategoryColors, bb as selectByCategory, bc as selectInRegions, bd as setDefaultSamModel, be as setOrtWasmBase, bf as setSamModelUrls, bg as sortToolContributions, bh as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-DURPqs5a.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-qUeMuBb0.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';
@@ -38,6 +38,7 @@ import 'primeng/selectbutton';
 import 'primeng/treeselect';
 import 'plotly.js-dist-min';
 import 'primeng/multiselect';
+import 'primeng/inputswitch';
 import 'image-js';
 import 'buffer';
 import 'openseadragon';

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

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

package/lib/channel-histogram/channel-histogram.component.d.ts

@@ -1,5 +1,6 @@
 import { EventEmitter, OnDestroy, OnInit } from '@angular/core';
 import { TreeNode } from 'primeng/api';
+import { ChannelGroupRow, ChannelTreeRow } from './channel-tree';
 import { IChannelHistogramApi, IChannelState, IHistogram } from '../contracts/channel-histogram-api.contract';
 import * as i0 from "@angular/core";
 /**
@@ -27,7 +28,11 @@ export declare class ChannelHistogramComponent implements OnInit, OnDestroy {
         color: string;
     }[];
     protected channels: IChannelState[];
+    /** The channels as the table lists them: in their groups when the image groups them, else flat. */
+    protected rows: ChannelTreeRow[];
     protected selected: IChannelState | null;
+    /** The groups folded shut, by key; kept across emissions and images with the same groups. */
+    private readonly collapsed;
     protected invert: boolean;
     protected logScale: boolean;
     /** Bounded retries while the (async) histogram sampling resolves. */
@@ -80,6 +85,15 @@ export declare class ChannelHistogramComponent implements OnInit, OnDestroy {
      *  dragging, since each change resets the timer). */
     private markBusy;
     protected onVisibleToggle(ch: IChannelState, value: boolean): void;
+    /** The table row of the selected channel, for its highlight. */
+    protected get selectedRow(): ChannelTreeRow | null;
+    /** A row was selected: a channel's selects the channel (a group's row cannot be). */
+    protected onRowSelect(row: ChannelTreeRow): void;
+    /** Fold a group shut, or open it. */
+    protected toggleGroup(row: ChannelGroupRow): void;
+    /** Show or hide every channel of a group. */
+    protected onGroupVisibleToggle(row: ChannelGroupRow, value: boolean): void;
+    protected trackRow(_: number, row: ChannelTreeRow): string;
     protected onColorChange(ch: IChannelState, color: string): void;
     protected onColormap(node: TreeNode): void;
     protected onInvert(value: boolean): void;

package/lib/channel-histogram/channel-tree.d.ts

@@ -0,0 +1,30 @@
+import { IChannelState } from '../contracts/channel-histogram-api.contract';
+/** A group of channels in the Channels pane: its label, how many channels it holds, how many show. */
+export interface ChannelGroupRow {
+    kind: 'group';
+    /** The group's path, its labels joined: stable across emissions, so it keys the row and its folding. */
+    key: string;
+    label: string;
+    depth: number;
+    /** The channels below it, at any depth, by index. */
+    channels: number[];
+    /** How many of them are visible. */
+    shown: number;
+    expanded: boolean;
+}
+/** A channel in the Channels pane, below its groups. */
+export interface ChannelRow {
+    kind: 'channel';
+    key: string;
+    depth: number;
+    channel: IChannelState;
+}
+export type ChannelTreeRow = ChannelGroupRow | ChannelRow;
+/** Whether any channel says which group it is in. */
+export declare function hasChannelGroups(channels: readonly IChannelState[]): boolean;
+/**
+ * The Channels pane's rows: each group (as the image's metadata groups its channels, outermost
+ * first) followed by what is in it, in channel order — a group where its first channel is — and
+ * the channels in no group where they are. A group in `collapsed` (by key) hides what is in it.
+ */
+export declare function channelTreeRows(channels: readonly IChannelState[], collapsed?: ReadonlySet<string>): ChannelTreeRow[];

package/lib/contracts/channel-histogram-api.contract.d.ts

@@ -17,7 +17,23 @@ export interface IChannelState {
     max: number;
     gamma: number;
     visible: boolean;
+    /** The groups the channel is in, outermost first (`IChannelInfo.group`); absent when it is in none. */
+    group?: string[];
 }
+/**
+ * How many channels of a multichannel image start visible. Each visible channel is drawn
+ * from tiles of its own, so a 22-channel plate showed every channel at once and asked the
+ * server for 22 tiles per position on every pan and zoom. Channels past these start hidden
+ * (one click shows them), and a hidden channel fetches no tiles.
+ */
+export declare const DEFAULT_VISIBLE_CHANNELS = 4;
+/**
+ * Whether channel `index` of `count` starts visible: as the image says when its
+ * `channelInfo` does, else every channel of an image with at most
+ * {@link DEFAULT_VISIBLE_CHANNELS}, and the first {@link DEFAULT_VISIBLE_CHANNELS} of one with more.
+ * Only a boolean says: a descriptor's `null` (a JSON field left empty) leaves the default.
+ */
+export declare function defaultChannelVisible(index: number, count: number, specified?: boolean | null): boolean;
 /** The standard LUT pseudo-colours (mirrors Fiji's Merge Channels palette) for
  *  quick per-channel assignment. */
 export declare const LUT_COLORS: ReadonlyArray<{

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

@@ -225,6 +225,26 @@ export interface SpatialViewState {
      * not drawn, nor the transcripts inside them. Cleared when the group column changes.
      */
     hiddenGroups: string[];
+    /**
+     * Genes whose observations are drawn: with any set, only the observations that express
+     * them (a value above 0) are drawn — the markers, the cell outlines and the transcripts
+     * inside them, in 2D and in the 3D cloud — and the rest are hidden. Empty draws every
+     * observation. Cleared when the dataset changes.
+     */
+    observationGenes: string[];
+    /** Whether an observation must express any of {@link observationGenes}, or all of them. */
+    observationGenesMatch: 'any' | 'all';
+    /**
+     * Colour (and mark) the filtered observations by their gene: each drawn observation in the
+     * colour and icon of the picked gene it expresses most (relative to that gene's highest
+     * value), in place of {@link colorBy}. Off, {@link colorBy} colours them as before.
+     */
+    observationGenesColorBy: boolean;
+    /** `#rrggbb` per gene of {@link observationGenes}; a gene left out takes the palette's colour
+     *  for its place in the list. */
+    observationGeneColors: Record<string, string>;
+    /** The icon per gene of {@link observationGenes} (2D); a gene left out is drawn as a circle. */
+    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
@@ -258,6 +278,13 @@ export interface SpatialViewState {
      * marker per transcript once those fit {@link transcriptBudget}.
      */
     transcriptAllGenes: boolean;
+    /**
+     * Genes of "All genes" switched off with their eye toggle — its own list, so hiding a gene
+     * there leaves the selection's {@link transcriptHiddenGenes} alone, and the other way round.
+     * Led by `'*'` (`ALL_GENES`), it lists the genes still shown instead: `['*']` hides every
+     * gene, `['*', 'KRT5']` shows KRT5 alone, without naming the thousands of others.
+     */
+    transcriptAllGenesHidden: string[];
     /**
      * Most transcript markers drawn at once. The level of detail is chosen to stay under it,
      * which is what keeps pan and zoom responsive however dense the data is.

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

@@ -21,6 +21,14 @@ export interface IChannelInfo {
     minAllowed?: number;
     /** Pixel-type maximum (e.g. 65535 for unsigned 16-bit). Native-unit ceiling. */
     maxAllowed?: number;
+    /** Whether the channel starts visible; else the first `DEFAULT_VISIBLE_CHANNELS` do. */
+    visible?: boolean;
+    /**
+     * The groups the channel is in, outermost first, as the image's metadata describes them (an
+     * instrument panel's kind of target, then the panel: `['Protein IF', 'Cell Signaling']`); the
+     * Channels pane lists the channels as a tree of them. Absent or empty for a channel in none.
+     */
+    group?: string[] | null;
 }
 /** Per-series image metadata (physical size + dimensions). */
 export interface IImageMetadata {

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

@@ -278,6 +278,13 @@ export interface SpatialTranscriptTilesMeta {
     count?: number;
     /** Real genes (control probes excluded). Names come from the feature search. */
     geneCount: number;
+    /**
+     * The genes an all-gene tile's `gene` codes index, in code order (the port's
+     * `TranscriptTileQuery.genes` with `[ALL_GENES]`); an empty name is a code those tiles never
+     * carry (a control probe). Optional: without it "All genes" still draws, but cannot hide one
+     * of its genes.
+     */
+    genes?: string[];
     hasZ: boolean;
     levels: (SpatialTileLevel & {
         /** True when an entry stands for several transcripts (see {@link SpatialTranscriptTile.weight}). */

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

@@ -390,6 +390,9 @@ export interface ISpatialControls {
         hi: number;
         max: number;
     } | null>;
+    /** 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 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

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

@@ -101,6 +101,13 @@ export declare class Image2dScene implements NapariScene {
     /** Channel states + grayscale colormap → live-apply to the rendered layers (no re-fetch; only z
      *  changes re-fetch), and recolour the navigator thumbnail. */
     private followDisplayState;
+    /**
+     * Put the current channel states back on the rendered layers: each channel's visibility, window,
+     * gamma and tint, and which of an RGB image's layers draw it. For a caller that changed the
+     * layers' visibility wholesale (the spatial view showing its tissue again), so the channels
+     * the user or the defaults switched off stay off. Nothing to do before the image is drawn.
+     */
+    reapplyDisplayState(): void;
     /** Apply the current channel states / colormap to the live layers (no re-fetch), delegating the
      *  per-channel layer mutations to the {@link MultiChannelImageView}. */
     private applyDisplayState;

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

@@ -1,7 +1,7 @@
 import type { ImageLayer, Viewer } from 'napari-js';
 import { IHistogram } from '../../contracts/channel-histogram-api.contract';
 import { SpatialDataset } from '../../contracts/spatial-dataset.contract';
-import { SpatialViewState } from '../../contracts/display-types';
+import { SpatialViewState, TranscriptGlyphName } from '../../contracts/display-types';
 import { SpatialSelectionMask } from '../../spatial/spatial-selection';
 import { NapariSpatialTileLayers } from './napari-spatial-tiles';
 import { Image2dScene } from './napari-image-2d-scene';
@@ -157,7 +157,18 @@ export declare class Spatial2dScene extends SpatialSceneBase implements NapariSc
      * selected to colour by. Categorical columns use the column's own palette; continuous columns
      * and gene vectors go through the active colormap with a percentile-clipped window.
      */
-    private faceColors;
+    /** The observations the view's gene filter keeps (1 = drawn), or null when it has none.
+     *  Rejects when an expression read fails. */
+    private filterMask;
+    /** The markers' colours (and icons, by gene) before the gene filter hides any of them. */
+    private markerStyle;
+    /** {@link faceColors} before the gene filter: what the colour source and the selection make of them. */
+    private sourceColors;
     /** Continuous values → RGBA through the active colormap and a clipped window. */
     encodeContinuous(values: Float32Array, view: SpatialViewState, muted?: Uint8Array | null): Float32Array;
 }
+/** Per-observation napari-js symbol codes: each observation's gene's icon (`codes` index
+ *  `glyphs`), a disc where it has none. */
+export declare function glyphSymbols(codes: Uint16Array, glyphs: readonly TranscriptGlyphName[]): Uint8Array;
+/** The symbols of the drawn subset (all of them when `indices` is undefined). */
+export declare function gatherSymbols(symbols: Uint8Array | null, indices?: Uint32Array): Uint8Array | null;

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

@@ -94,6 +94,11 @@ export declare function encodeSpatialContinuous(values: Float32Array, view: Spat
 export type PointColors = Float32Array | RGBA;
 /** Whether a colour input is one RGBA per point rather than one broadcast RGBA. */
 export declare function isPerPoint(colors: PointColors): colors is Float32Array;
+/**
+ * `colors` with every observation `shown` leaves at 0 made transparent: the observations a gene
+ * filter leaves out. A broadcast colour becomes per-point, since the points now differ.
+ */
+export declare function hideUnshown(colors: PointColors, shown: Uint8Array): Float32Array;
 /** Per-point colours for the drawn subset. A broadcast tuple stays broadcast —
  *  it is one colour for every point either way. */
 export declare function gatherColors(colors: PointColors, indices?: Uint32Array): PointColors;

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

@@ -26,6 +26,8 @@ export interface SpatialTileSinks {
         max: number;
     }): void;
     loadingChanged(layers: string[]): void;
+    /** Whether the observation gene filter could be applied; see {@link SpatialSession.reportGeneFilter}. */
+    geneFilterFailed?(failed: boolean): void;
 }
 /** The 2D scene the tile layers currently draw into. */
 export interface SpatialTileOwner {
@@ -64,6 +66,8 @@ export declare class SpatialSession {
     private tileLayers;
     private tileOwner;
     constructor(port: SpatialDataPort | null, selection: SpatialSelectionStore | null, sinks: SpatialTileSinks);
+    /** Tell the panel whether the observation gene filter could be applied this rebuild. */
+    reportGeneFilter(failed: boolean): void;
     /** The tile layers, if they were ever built. */
     get tiles(): NapariSpatialTileLayers | null;
     /**

package/lib/implementations/napari-js/napari-visualizer.service.d.ts

@@ -80,6 +80,8 @@ export declare class NapariVisualizerService extends BaseStoreVisualizer impleme
         hi: number;
         max: number;
     } | null>;
+    /** The observation gene filter could not be applied (an expression read failed). */
+    readonly geneFilterFailed$: BehaviorSubject<boolean>;
     /** "x reloading…" at the bottom of the canvas: the tile layers' loads and the observations'. */
     private readonly badge;
     /** The store's display state (colormap, reverse, invert) and the colormaps derived from it. */

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

@@ -21,6 +21,11 @@ export declare class CategoricalLookup {
     constructor(port: SpatialDataPort);
     /** Codes of the column `name`, or null when it is not categorical. */
     codes(name: string): Promise<CategoricalCodes | null>;
-    /** Codes of the group column that are switched off, or null when none are. */
+    /**
+     * The observations not drawn: those of the groups switched off, and those the gene filter
+     * leaves out. Null when nothing is hidden.
+     */
     hiddenCodes(dataset: SpatialDataset, view: SpatialViewState): Promise<HiddenCodes | null>;
+    /** Codes of the group column that are switched off, or null when none are. */
+    private hiddenGroupCodes;
 }

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

@@ -62,6 +62,10 @@ export interface DrawnTranscripts {
     merged: SpatialTranscriptTile;
     /** The layer the entries are drawn in, one marker per entry in the same order. */
     layer: PointsLayer;
+    /**
+     * The genes the entries' `gene` codes index: the selection's, or for every gene's individual
+     * transcripts the dataset's gene list (`transcriptTiles.genes`; empty without one).
+     */
     genes: string[];
     /** For a grouped gene selection: each entry's group, and the groups' names. */
     entryGroup?: Int32Array;

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

@@ -6,7 +6,7 @@ import { TranscriptGlyph } from '../../../spatial/glyphs';
 import type { CategoricalLookup } from './categorical-lookup';
 import type { OrderedLayerGroups, TileGroup } from './layer-groups';
 import type { PlanContext } from './plan-context';
-import type { TranscriptHover } from './transcript-hover';
+import type { TranscriptHover, TranscriptKind } from './transcript-hover';
 import { type TranscriptJobPlanner } from './transcript-jobs';
 /**
  * The napari-js point symbol each transcript icon is drawn as. Every icon has a counterpart of
@@ -14,6 +14,8 @@ import { type TranscriptJobPlanner } from './transcript-jobs';
  * differs.
  */
 export declare const GLYPH_SYMBOLS: Readonly<Record<TranscriptGlyph, PointSymbol>>;
+/** The view the markers are coloured by, for what was loaded. */
+export declare function colorViewFor(view: SpatialViewState, kind: TranscriptKind, clustered: boolean, hasCellTypes: boolean): SpatialViewState;
 /**
  * The transcript markers of the 2D spatial view: runs the planner's job, drops hidden groups
  * and genes, groups a selection under the marker budget, colours the entries and draws them as

package/lib/spatial/lod.d.ts

@@ -12,7 +12,7 @@
  * `zoom · scale`. For a Xenium bundle the data unit is the micron and the world unit the
  * morphology pixel.
  */
-import type { SpatialBounds, SpatialDataset, SpatialImageRef, SpatialTileLevel } from '../contracts/spatial-dataset.contract';
+import type { SpatialBounds, SpatialDataset, SpatialImageRef, SpatialPolygonTilesMeta, SpatialTileLevel } from '../contracts/spatial-dataset.contract';
 import type { SpatialViewState } from '../contracts/display-types';
 /** A rectangle in observation coordinates. */
 export interface DataRect {
@@ -29,13 +29,25 @@ export interface TileKey {
 }
 /** Whether cell outlines are drawn: the user's choice, else on when the dataset has any. */
 export declare function cellsShown(dataset: Pick<SpatialDataset, 'polygonTiles' | 'polygons'> | null, view: Pick<SpatialViewState, 'showCells'>): boolean;
+/**
+ * The boundary sets drawn for the view's `cellSet`: that set when the dataset has it, else the
+ * dataset's default, else its first; for "both", that one with the other set beside it. Null when
+ * the dataset has no set. The renderer and the Cells panel's switches both read it, so a set kept
+ * from another dataset shows as what is actually drawn.
+ */
+export declare function drawnCellSets(tiled: Pick<SpatialPolygonTilesMeta, 'sets' | 'defaultSet'> | null | undefined, cellSet: string | null | undefined): {
+    set: string;
+    nucleusSet?: string;
+} | null;
 /** A column holding a hand-curated cell-type annotation, by naming convention. */
 export declare function isCuratedColumn(name: string): boolean;
 /**
  * The categorical column that names each cell's type: the view's choice when it is a
  * column of this dataset, else the first categorical column that is not a curated
  * annotation (a pipeline's clustering is the default; curation is opted into), else
- * any categorical column.
+ * any categorical column. A column of one category, such as the `region` a SpatialData
+ * table links its cells to their shapes with, names no type and is only used when chosen;
+ * a dataset with nothing else has no cell types (null).
  */
 export declare function cellTypeColumnFor(dataset: SpatialDataset, view: Pick<SpatialViewState, 'cellTypeColumn'>): string | null;
 /** A stable string id for a tile key, `level/gx/gy` — usable as a Map key. */

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

@@ -24,6 +24,9 @@ export interface SpatialRendererFeeds {
             max: number;
         } | null>;
     };
+    readonly geneFilterFailed$?: {
+        asObservable(): Observable<boolean>;
+    };
     /** Observations projected to canvas pixels by the 3D camera, or null when the cloud is not mounted. */
     getSpatialScreenProjection(obs: SpatialObservations): Float32Array | null;
     /** The ids of the regions drawn over the 3D cloud in screen space (its lassos). */

package/lib/spatial/spatial-gene-filter.d.ts

@@ -0,0 +1,44 @@
+import type { SpatialViewState, TranscriptGlyphName } from '../contracts/display-types';
+/** One gene's value for every observation: the port's `getFeatureVector`. */
+export type FeatureVectorSource = (gene: string) => Promise<Float32Array>;
+type GeneFilterView = Pick<SpatialViewState, 'observationGenes' | 'observationGenesMatch'>;
+/** Whether the view draws only the observations expressing some genes. */
+export declare function hasGeneFilter(view: Partial<GeneFilterView>): boolean;
+/** What decides the gene filter, for the layers' cache keys: '' when there is none. */
+export declare function geneFilterKey(view: Partial<GeneFilterView>): string;
+/**
+ * 1 for each of `count` observations that expresses the genes — a value above 0 in any of
+ * `vectors`, or in all of them — else 0. A missing value (NaN) is not expressed.
+ */
+export declare function expressingMask(vectors: readonly Float32Array[], count: number, match: 'any' | 'all'): Uint8Array;
+/**
+ * The view's gene filter as a per-observation mask (1 = drawn), or null when it has none. Every
+ * layer asks on every rebuild, so the mask of the same vectors is built once.
+ */
+export declare function observationGeneMask(view: GeneFilterView, count: number, read: FeatureVectorSource): Promise<Uint8Array | null>;
+/** The colour a gene of the observation filter is drawn in: the view's own, else the palette's
+ *  for its place in the list. */
+export declare function observationGeneColor(view: Pick<SpatialViewState, 'observationGenes' | 'observationGeneColors'>, gene: string): string;
+/** The icon a gene of the observation filter is drawn as (2D): the view's own, else a circle. */
+export declare function observationGeneGlyph(view: Pick<SpatialViewState, 'observationGeneGlyphs'>, gene: string): TranscriptGlyphName;
+/** Whether the filtered observations are coloured by their gene (rather than by `colorBy`). */
+export declare function colorsByObservationGene(view: Pick<SpatialViewState, 'observationGenes' | 'observationGenesColorBy'>): boolean;
+/**
+ * Each observation's gene among `vectors`: the index of the one it expresses most relative to
+ * that gene's own highest value — so a gene expressed at low counts everywhere is not always
+ * outvoted by a highly expressed one — or {@link NO_CATEGORY} where it expresses none.
+ */
+export declare function dominantGenes(vectors: readonly Float32Array[], count: number): Uint16Array;
+/**
+ * How the filtered observations are drawn, by gene: each observation's gene (an index into the
+ * view's genes, see {@link dominantGenes}) with the genes' colours and icons. Null when the view
+ * does not colour by them.
+ */
+export declare function observationGeneStyle(view: GeneFilterView & Pick<SpatialViewState, 'observationGenesColorBy' | 'observationGeneColors' | 'observationGeneGlyphs'>, count: number, read: FeatureVectorSource): Promise<{
+    codes: Uint16Array;
+    colors: string[];
+    glyphs: TranscriptGlyphName[];
+} | null>;
+/** What decides how the filtered observations are drawn by gene, for cache keys. */
+export declare function observationGeneStyleKey(view: Pick<SpatialViewState, 'observationGenes' | 'observationGenesColorBy' | 'observationGeneColors' | 'observationGeneGlyphs'>): string;
+export {};

package/lib/spatial/spatial-tile-merge.d.ts

@@ -15,6 +15,23 @@ export declare function filterRings(rings: SpatialPolygonTile, hidden: {
 } | null): SpatialPolygonTile;
 /** Slots (indices into the selected genes) switched off with their eye toggle. */
 export declare function hiddenGeneSlots(view: SpatialViewState): Uint8Array | null;
+/**
+ * Whether "All genes" is switched off as a whole with the gene tree's root eye: its hidden
+ * list is `[ALL_GENES]` (every gene hidden, none excepted). Hiding every gene by name would
+ * need the gene list, which a dataset need not have.
+ */
+export declare function allGenesHidden(view: Pick<SpatialViewState, 'transcriptAllGenes' | 'transcriptAllGenesHidden'>): boolean;
+/** Whether an "All genes" hidden list hides every gene, none excepted. */
+export declare function everyGeneOff(off: readonly string[]): boolean;
+/** Whether a gene of "All genes" is drawn, by its hidden list (see `transcriptAllGenesHidden`). */
+export declare function allGeneShownBy(off: readonly string[]): (gene: string) => boolean;
+/** "All genes"'s hidden list with `gene` shown (`on`) or hidden, in the list's own form. */
+export declare function toggleAllGeneHidden(off: readonly string[], gene: string, on: boolean): string[];
+/**
+ * Codes (indices into `genes`, the dataset's all-gene code order) switched off with their eye
+ * toggle while every gene is drawn; null when none is, or without the gene list.
+ */
+export declare function hiddenAllGeneCodes(view: Pick<SpatialViewState, 'transcriptAllGenesHidden'>, genes: readonly string[] | undefined): Uint8Array | null;
 /** Entries in a hidden group's cell, or of a hidden gene, removed (with their sizes). */
 export declare function filterTranscripts(t: SpatialTranscriptTile, px: Float32Array, hidden: {
     codes: Uint16Array;

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

@@ -39,6 +39,15 @@ export declare class SpatialCellsPanelComponent implements OnChanges {
      * its buttons whenever the array identity changes — which made them impossible to click.
      */
     protected cellSetOptions: PanelOption<string>[];
+    /**
+     * The boundary sets, the cells' first, each with a switch when there are at most two (as
+     * CytoCanvas's "Cell Boundaries" and "Nuclear Boundaries"): either, both or neither drawn.
+     * More sets keep the one-of choice.
+     */
+    protected boundarySets: {
+        name: string;
+        label: string;
+    }[];
     /** Cell colour modes on offer (Xenium Explorer's "Cell Color"). */
     protected cellColorOptions: PanelOption<SpatialViewState['cellColorMode']>[];
     /** The density colour bar, rebuilt only when its colormap changes (a 256-entry LUT). */
@@ -47,12 +56,20 @@ export declare class SpatialCellsPanelComponent implements OnChanges {
     ngOnChanges(changes: SimpleChanges): void;
     /** Whether outlines are on — the explicit choice, or automatically for data that has them. */
     protected get cellsOn(): boolean;
-    /** The boundary set drawn: the view's choice, else the dataset's default, else its first. */
+    /** The boundary set drawn, or "both", as the renderer resolves the view's choice: a set this
+     *  dataset has, else its default, else its first. */
     protected get activeCellSet(): string | null;
     /** Fill opacity as a 0–100 number, for the box beside the slider. */
     protected get cellOpacityPercent(): number;
     protected onShowCells(on: boolean): void;
     protected onCellSet(set: string): void;
+    /** Whether boundary set `name` is drawn: outlines on, and that set or both. */
+    protected boundaryOn(name: string): boolean;
+    /**
+     * A set's switch: on draws it with the other when that one is drawn ("both"), else alone;
+     * off leaves the other drawn, or no outlines at all.
+     */
+    protected onBoundary(name: string, on: boolean): void;
     protected onCellDraw(draw: SpatialViewState['cellDraw']): void;
     protected onCellOpacity(value: number | undefined): void;
     protected onCellOpacityPercent(v: number | null): void;