@jax-data-science/sci-image-visualizer 0.14.0 → 0.16.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-D7lSUAM1.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-DaZVXq1s.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-DvFp1jNH.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-CYsPzX3J.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-D7lSUAM1.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-DaZVXq1s.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-D7lSUAM1.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-DaZVXq1s.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-D7lSUAM1.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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'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-DvFp1jNH.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-CYsPzX3J.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

@@ -17,6 +17,8 @@ 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

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

@@ -23,6 +23,12 @@ export interface IChannelInfo {
     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/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-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
@@ -106,6 +141,25 @@ 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 +278,35 @@ 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/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 {
@@ -29,6 +29,16 @@ 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;
 /**

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;

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;
@@ -29,6 +31,11 @@ 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 +54,10 @@ 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 +89,13 @@ 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.

package/lib/store/visualizer-store.service.d.ts

@@ -33,6 +33,10 @@ export declare class VisualizerStore {
     private defaultChannelStates;
     /** The image the current channel states were derived for (see setImageMeta). */
     private channelImageKey;
+    /** The channel info the host gave with the image (see setImageMeta), apart from what a tile
+     *  descriptor added since: each adoption merges against this, so a later descriptor can change
+     *  or clear what an earlier one put in. */
+    private hostChannelInfo;
     private readonly grayscale$;
     private readonly invert$;
     private presetSet;
@@ -82,11 +86,13 @@ export declare class VisualizerStore {
      * "Actin" or "Cell-Membrane"), where a host's metadata (jit-ui's `/metadata`) carries none, so
      * the Channels pane showed "Channel 1", "Channel 2"… The host's own names and tints win; only a
      * channel still showing its derived default takes the descriptor's, so an edit made in the pane
-     * stays. A no-op when the channel counts differ, or for RGB.
+     * stays. A no-op when the channel counts differ, or for RGB. Each adoption replaces the last
+     * one's names, tints and groups: only the host's own count as overrides.
      */
     adoptChannelInfo(info: ReadonlyArray<{
         name?: string;
         color?: string;
+        group?: string[] | null;
     }> | null | undefined): void;
     /**
      * Publish the current image's metadata and derive its channels.

package/lib/toolbar/toolbar.component.d.ts

@@ -216,6 +216,12 @@ export declare class ToolbarComponent {
     protected get isNapariMode(): boolean;
     /** ISOSURFACE (Plotly or napari-js WebGPU, either resolution) shows the isovalue range slider. */
     protected get isIsosurfaceMode(): boolean;
+    /**
+     * The views that draw the 3D axes gizmo (an `Axes3dGizmo`): napari-js's volume, isosurface and
+     * surface, and the 3D spatial cloud. Not every napari-js view: its 2D image and scatter and its
+     * 3D scatter draw none, and a toggle there would do nothing.
+     */
+    protected get showsAxesToggle(): boolean;
     /** The napari-js WebGPU surface — shows the wireframe toggle. */
     protected get isNapariSurfaceMode(): boolean;
     /** Any napari-js WebGPU 3D type (volume/isosurface/surface) — shows the Resolution control. */

package/lib/toolbar/view-controls/view-controls.component.d.ts

@@ -16,12 +16,12 @@ export declare class ViewControlsComponent {
     activeDragMode: string | null;
     /** The 3D camera mode (`turntable` / `orbit` / …). */
     activeSurface3dMode: string;
-    /** A napari-js WebGPU view (axes toggle, napari camera). */
-    isNapariMode: boolean;
     /** The napari-js surface (shows the wireframe toggle). */
     isNapariSurfaceMode: boolean;
     /** A napari-js 3D view (shows the Resolution dropdown). */
     isNapari3dMode: boolean;
+    /** Whether the view draws the 3D axes gizmo (shows its toggle). */
+    axesToggle: boolean;
     /** The napari 3D axes gizmo is shown. */
     axesVisible: boolean;
     /** The napari surface wireframe is on. */
@@ -50,5 +50,5 @@ export declare class ViewControlsComponent {
         value: number;
     }[];
     static ɵfac: i0.ɵɵFactoryDeclaration<ViewControlsComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<ViewControlsComponent, "toolbar-view-controls", never, { "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "zoomTools": { "alias": "zoomTools"; "required": false; }; "isImageView": { "alias": "isImageView"; "required": false; }; "activeDragMode": { "alias": "activeDragMode"; "required": false; }; "activeSurface3dMode": { "alias": "activeSurface3dMode"; "required": false; }; "isNapariMode": { "alias": "isNapariMode"; "required": false; }; "isNapariSurfaceMode": { "alias": "isNapariSurfaceMode"; "required": false; }; "isNapari3dMode": { "alias": "isNapari3dMode"; "required": false; }; "axesVisible": { "alias": "axesVisible"; "required": false; }; "wireframeActive": { "alias": "wireframeActive"; "required": false; }; "resolutionScale": { "alias": "resolutionScale"; "required": false; }; }, { "toggleDragMode": "toggleDragMode"; "zoomIn": "zoomIn"; "zoomOut": "zoomOut"; "toggleSurface3dMode": "toggleSurface3dMode"; "resetSurfaceCamera": "resetSurfaceCamera"; "toggleAxes": "toggleAxes"; "toggleWireframe": "toggleWireframe"; "selectResolution": "selectResolution"; }, never, never, true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<ViewControlsComponent, "toolbar-view-controls", never, { "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "zoomTools": { "alias": "zoomTools"; "required": false; }; "isImageView": { "alias": "isImageView"; "required": false; }; "activeDragMode": { "alias": "activeDragMode"; "required": false; }; "activeSurface3dMode": { "alias": "activeSurface3dMode"; "required": false; }; "isNapariSurfaceMode": { "alias": "isNapariSurfaceMode"; "required": false; }; "isNapari3dMode": { "alias": "isNapari3dMode"; "required": false; }; "axesToggle": { "alias": "axesToggle"; "required": false; }; "axesVisible": { "alias": "axesVisible"; "required": false; }; "wireframeActive": { "alias": "wireframeActive"; "required": false; }; "resolutionScale": { "alias": "resolutionScale"; "required": false; }; }, { "toggleDragMode": "toggleDragMode"; "zoomIn": "zoomIn"; "zoomOut": "zoomOut"; "toggleSurface3dMode": "toggleSurface3dMode"; "resetSurfaceCamera": "resetSurfaceCamera"; "toggleAxes": "toggleAxes"; "toggleWireframe": "toggleWireframe"; "selectResolution": "selectResolution"; }, never, never, true, never>;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.14.0",
+  "version": "0.16.0",
   "engines": {
     "node": ">=20.9.0"
   },
@@ -40,7 +40,7 @@
     "cellpose-js": "^0.6.0",
     "fast-png": "^6.4.0",
     "fzstd": "^0.1.1",
-    "napari-js": "^0.18.0",
+    "napari-js": "^0.19.0",
     "openseadragon": "^6.0.2",
     "plotly.js-dist-min": "^3.0.1",
     "tslib": "^2.3.0"