@jax-data-science/sci-image-visualizer 0.2.19 → 0.3.1

package/index.d.ts

@@ -16,6 +16,7 @@ export * from './lib/contracts/viz-config';
 export * from './lib/contracts/image.contract';
 export * from './lib/contracts/plot-type';
 export * from './lib/contracts/toolbar-config';
+export * from './lib/contracts/toolbar-tool.contract';
 export * from './lib/contracts/capabilities.contract';
 export * from './lib/contracts/region-overlay.contract';
 export * from './lib/contracts/display-types';
@@ -23,17 +24,11 @@ export * from './lib/contracts/sam.contract';
 export * from './lib/contracts/cell-segmenter.contract';
 export { CellposeSegmenterService } from './lib/toolbar/segmentation/cellpose-segmenter.service';
 export * from './lib/contracts/instance-segmenter.contract';
-export { YoloSegmenterService } from './lib/toolbar/segmentation/yolo-segmenter.service';
-export { YoloDetectToolService, YOLO_REGION_SOURCE } from './lib/toolbar/segmentation/yolo-detect-tool.service';
 export * from './lib/contracts/semantic-segmenter.contract';
-export { RetinalSegmenterService } from './lib/toolbar/segmentation/retinal-segmenter.service';
-export { RetinalLayerToolService, RETINAL_REGION_SOURCE, } from './lib/toolbar/segmentation/retinal-layer-tool.service';
 export { ProcessingImage } from './lib/processing/processing-image';
 export { cropImage, CropImageOptions } from './lib/processing/image-crop';
 export { ImageConverterService } from './lib/processing/image-converter.service';
 export { SAM_MODELS, DEFAULT_SAM_MODEL_ID, getSamModel, isSamModelReady, setSamModelUrls, setDefaultSamModel, getDefaultSamModelId, } from './lib/toolbar/segmentation/sam-model-registry';
-export { YOLO_MODELS, DEFAULT_YOLO_MODEL_ID, getYoloModel, isYoloModelReady, setYoloModelUrls, setDefaultYoloModel, getDefaultYoloModelId, YoloModelDef, } from './lib/toolbar/segmentation/yolo-model-registry';
-export { RETINAL_MODELS, DEFAULT_RETINAL_MODEL_ID, getRetinalModel, isRetinalModelReady, readyRetinalModels, setRetinalModelUrls, setDefaultRetinalModel, getDefaultRetinalModelId, RetinalModelDef, } from './lib/toolbar/segmentation/retinal-model-registry';
 export { setOrtWasmBase, getOrtWasmBase } from './lib/toolbar/segmentation/ort-runtime-config';
 export * from './lib/models/region';
 export * from './lib/models/class-preset';

package/lib/contracts/instance-segmenter.contract.d.ts

@@ -128,8 +128,12 @@ export interface IInstanceSegmenter {
     }, opts?: InstanceSegmentOptions, progress?: InstanceSegmentProgress): Promise<InstanceSegmentation>;
 }
 /**
- * DI token for the automatic instance segmenter. Defaults to the in-library
- * {@link YoloSegmenterService} (yolo-segdetect-js, lazy-loaded); override it in
- * the host to swap implementations — for example to delegate to the server.
+ * DI token for the automatic instance segmenter.
+ *
+ * **No default.** It used to fall back to an in-library YOLO service, and that
+ * factory was what pulled `yolo-segdetect-js` into every bundle of this package
+ * — which is not shippable while the checkpoints are closed. A host provides an
+ * implementation (see `@jax-data-science/sci-image-visualizer-jax-tools`), or
+ * nothing does and no tool needing it is registered.
  */
 export declare const INSTANCE_SEGMENTER: InjectionToken<IInstanceSegmenter>;

package/lib/contracts/semantic-segmenter.contract.d.ts

@@ -99,7 +99,12 @@ export interface ISemanticSegmenter {
     }, opts?: SemanticSegmentOptions, progress?: SemanticSegmentProgress): Promise<SemanticSegmentation>;
 }
 /**
- * DI token for the semantic segmenter, defaulting to the in-library
- * jax-ai-js-backed implementation. Hosts override it to supply their own.
+ * DI token for the semantic segmenter.
+ *
+ * **No default.** It used to fall back to an in-library jax-ai-js service, and
+ * that factory was what pulled `jax-ai-js` into every bundle of this package —
+ * which is not shippable while the checkpoints are closed. A host provides an
+ * implementation (see `@jax-data-science/sci-image-visualizer-jax-tools`), or
+ * nothing does and no tool needing it is registered.
  */
 export declare const SEMANTIC_SEGMENTER: InjectionToken<ISemanticSegmenter>;

package/lib/contracts/toolbar-tool.contract.d.ts

@@ -0,0 +1,190 @@
+/**
+ * How a tool gets into the toolbar without this library knowing what it is.
+ *
+ * WHY THIS EXISTS
+ * The YOLO detector and the retinal-layer segmenter used to be built in: their
+ * buttons were hardcoded in the toolbar template, their model registries named
+ * JAX checkpoints, and the `INSTANCE_SEGMENTER` / `SEMANTIC_SEGMENTER` tokens
+ * defaulted to in-library services that imported `yolo-segdetect-js` and
+ * `jax-ai-js`. Those default factories were the only thing pulling either
+ * package into the bundle — the contracts themselves were already clean.
+ *
+ * That arrangement cannot ship in an open library while the models are closed.
+ * So the tools move out, into a package that depends on this one, and arrive
+ * back through {@link TOOLBAR_TOOLS}. This library keeps the contracts, the
+ * chrome and the region plumbing; it no longer knows that YOLO exists.
+ *
+ * A host registers tools with a multi-provider:
+ *
+ *     { provide: TOOLBAR_TOOLS, useExisting: YoloToolContribution, multi: true }
+ *
+ * Register nothing and the toolbar has no segmentation tools, the help dialog
+ * lists none, and neither model package is in the graph.
+ *
+ * WHY PARAMS ARE DECLARED, NOT RENDERED
+ * A contribution describes its parameters ({@link ToolParamSpec}) instead of
+ * supplying a component to draw them. The toolbar renders one generic dialog
+ * from that description. The alternative — each plugin shipping its own dialog
+ * component — would make every plugin depend on this library's exact PrimeNG
+ * version and styling internals to look like the rest of the toolbar, and the
+ * two dialogs that exist today are entirely numbers and one checkbox. A schema
+ * covers them, and it is the same shape jit-ui already uses for its pipeline
+ * step parameters, so the vocabulary is familiar.
+ *
+ * If a tool ever needs a control this cannot express, add a variant here rather
+ * than an escape hatch that returns a component — the moment one tool draws
+ * itself, the toolbar stops being able to lay tools out consistently.
+ *
+ * WHY AN EMPTY MODEL LIST HIDES THE TOOL
+ * {@link ToolbarToolContribution.models} returning `[]` removes the tool from
+ * the toolbar entirely. This preserves the behaviour the built-in tools already
+ * had (their buttons were `*ngIf`'d on a filtered registry), and it gives a host
+ * one switch for "the weights are not configured in this deployment" that does
+ * not require unregistering the provider.
+ */
+import { InjectionToken } from '@angular/core';
+import type { Observable } from 'rxjs';
+import type { IVisualizer } from './visualizer.contract';
+/** A number field. Rendered as a stepper, matching the built-in dialogs. */
+export interface NumberParamSpec {
+    id: string;
+    label: string;
+    type: 'number';
+    min?: number;
+    max?: number;
+    step?: number;
+    /** Decimal places to show. Omit for integers. */
+    fractionDigits?: number;
+    /** Hover help. Plain text; it is not rendered as HTML. */
+    tooltip?: string;
+}
+/** A checkbox. `label` sits beside it and may run to a sentence or two. */
+export interface BooleanParamSpec {
+    id: string;
+    label: string;
+    type: 'boolean';
+    tooltip?: string;
+}
+/** A fixed set of choices. */
+export interface SelectParamSpec {
+    id: string;
+    label: string;
+    type: 'select';
+    options: {
+        label: string;
+        value: string | number;
+    }[];
+    tooltip?: string;
+}
+export type ToolParamSpec = NumberParamSpec | BooleanParamSpec | SelectParamSpec;
+/** One selectable checkpoint. */
+export interface ToolModelOption {
+    id: string;
+    label: string;
+    /**
+     * Describes the checkpoint in the picker's hover tooltip — size, speed,
+     * training domain, accuracy. **Rendered as HTML**, so it is trusted content
+     * from the contributing package, never anything user-supplied.
+     */
+    info?: string;
+    /**
+     * Parameter values this checkpoint wants, merged over
+     * {@link ToolbarToolContribution.defaultParams} when it is selected. Defaults
+     * belong to the model rather than the tool — a detector trained on native 40x
+     * patches wants different tiling from one trained on thumbnails.
+     */
+    defaults?: Record<string, unknown>;
+}
+/**
+ * The `status$` / `busy$` / `progress$` surface the toolbar drives its sticky
+ * toast and progress bar from. `progress$` is a 0..1 fraction, or -1 for
+ * indeterminate.
+ */
+export interface ToolProgress {
+    status$: Observable<string>;
+    busy$: Observable<boolean>;
+    progress$: Observable<number>;
+}
+/** Toolbar icon: a published asset, or a PrimeIcon class name. */
+export type ToolIcon = {
+    src: string;
+    pi?: never;
+} | {
+    pi: string;
+    src?: never;
+};
+/**
+ * A tool contributed to the toolbar.
+ *
+ * Implement it on an `@Injectable()` service in the contributing package, so it
+ * can inject its own segmenter and model registry — this library provides
+ * neither and must not learn to.
+ */
+export interface ToolbarToolContribution {
+    /** Stable identity, used for tracking and persisted preferences. */
+    id: string;
+    /** Short name, used in the toast and the help dialog heading. */
+    label: string;
+    icon: ToolIcon;
+    /** Tooltip on the run button — say what it does to the current view. */
+    runTooltip: string;
+    /** Tooltip on the checkpoint picker. Defaults to "Pick the model". */
+    modelTooltip?: string;
+    /** Tooltip on the parameters button. Defaults to "Parameters". */
+    paramsTooltip?: string;
+    /**
+     * Where it sits among the segmentation tools. Lower sorts first; ties fall
+     * back to registration order. The built-in prompted tools occupy 0-99, so
+     * contributed tools should start at 100 to land after them.
+     */
+    order?: number;
+    /** Selectable checkpoints. **Empty hides the tool.** */
+    models(): ToolModelOption[];
+    /** Which checkpoint runs when the user has not chosen. */
+    defaultModelId(): string;
+    /**
+     * Called when the user picks a checkpoint, before parameters are re-seeded.
+     * Use it to record the choice in the contributing package's own registry.
+     */
+    onModelChange?(modelId: string): void;
+    /** Parameter fields, in dialog order. Empty hides the parameters button. */
+    params: ToolParamSpec[];
+    /**
+     * Baseline parameter values for a checkpoint. Called on first use and again
+     * on "Reset to model defaults", so it must be pure and must return every key
+     * the tool reads — a parameter the dialog shows but this omits renders as
+     * empty and reaches `run` as undefined.
+     */
+    defaultParams(modelId: string): Record<string, unknown>;
+    /**
+     * Entry for the help dialog's tool list. `body` is rendered as HTML and may
+     * reference published assets (e.g. the tool's own icon).
+     */
+    help?: {
+        body: string;
+    };
+    /** Progress surface for the toast. */
+    progress: ToolProgress;
+    /**
+     * Run over what is currently displayed, and write whatever it finds through
+     * `viz`. Resolves with the number of regions added.
+     *
+     * Everything the tool needs is on {@link IVisualizer}, which is part of this
+     * library's public surface — a contribution never reaches into internals.
+     * Region writes go through the same path the built-in tools use, so the
+     * index-based overlays and the Regions table stay consistent.
+     */
+    run(viz: IVisualizer, params: Record<string, unknown>): Promise<number>;
+}
+/**
+ * Multi-provider token for contributed tools.
+ *
+ * Deliberately has no `factory`: unregistered means no tools, which is what
+ * makes this library shippable without the closed model packages. Inject it
+ * `{ optional: true }` and treat null as empty.
+ */
+export declare const TOOLBAR_TOOLS: InjectionToken<readonly ToolbarToolContribution[]>;
+/** Sort contributed tools into display order. */
+export declare function sortToolContributions(tools: readonly ToolbarToolContribution[]): ToolbarToolContribution[];
+/** The tools a toolbar should actually show: those with at least one model. */
+export declare function visibleToolContributions(tools: readonly ToolbarToolContribution[] | null | undefined): ToolbarToolContribution[];

package/lib/toolbar/model-info.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Per-model descriptions for the info icon beside each item of the SAM / YOLO /
+ * retinal model dropdowns, keyed by registry model id.
+ *
+ * Lives in the toolbar layer rather than in the model registries for two
+ * reasons: the toolbar receives only `{ id, label }` from its host, so registry
+ * copy would have to be threaded through every host; and this text was already
+ * owned here — the SAM entries are the prose from the "About the SAM models"
+ * overlay panel this replaced, moved next to the model it describes.
+ *
+ * The quoted numbers come from the registries (`sizeMb`, `miou`, `patchSize`,
+ * per-model tiling `defaults`) — keep them in step when those change.
+ *
+ * Rendered with `[escape]="false"`, so `<b>` / `<br>` / entities are honoured.
+ * A model with no entry here simply gets no info icon.
+ */
+export declare const MODEL_INFO: Record<string, string>;

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

@@ -3,6 +3,7 @@ import { MenuItem } from 'primeng/api';
 import { IImageInfo } from '../contracts/image.contract';
 import { PlotType, PlotTypeDescriptor } from '../contracts/plot-type';
 import { ToolbarToolVisibility } from '../contracts/toolbar-config';
+import { ToolbarToolContribution } from '../contracts/toolbar-tool.contract';
 import * as i0 from "@angular/core";
 /**
  * Presentational toolbar for the plotting viewport.
@@ -66,18 +67,14 @@ export declare class ToolbarComponent implements OnChanges {
         label: string;
     }[];
     samModelId: string;
-    /** YOLO checkpoints offered by the host's registry, and the active one. */
-    yoloModels: {
-        id: string;
-        label: string;
-    }[];
-    yoloModelId: string;
-    /** Retinal-layer checkpoints offered by the host's registry, and the active one. */
-    retinalModels: {
-        id: string;
-        label: string;
-    }[];
-    retinalModelId: string;
+    /**
+     * Tools contributed through {@link TOOLBAR_TOOLS}, already filtered to the
+     * ones with models and sorted. The host resolves them so it can own the
+     * per-tool parameter state; this component only draws them.
+     */
+    contributedTools: ToolbarToolContribution[];
+    /** Active checkpoint per contributed tool, keyed by tool id. */
+    toolModelIds: Record<string, string>;
     selectPlotType: EventEmitter<PlotType>;
     /** Intensity (LINE) mode: add another colored line ROI + inset trace. */
     addProfileLine: EventEmitter<void>;
@@ -117,18 +114,15 @@ export declare class ToolbarComponent implements OnChanges {
     segmentRegions: EventEmitter<void>;
     /** Run cellpose-SAM (auto) inside each drawn rectangle's crop (jit-ui#90). */
     segmentCellpose: EventEmitter<void>;
-    /** Run YOLO detection over the current view. */
-    detectYolo: EventEmitter<void>;
-    /** Pick the YOLO checkpoint. */
-    yoloModelChange: EventEmitter<string>;
-    /** Open the YOLO parameter dialog. */
-    openYoloParams: EventEmitter<void>;
-    /** Run retinal-layer segmentation over the current view. */
-    segmentRetinal: EventEmitter<void>;
-    /** Pick the retinal-layer checkpoint. */
-    retinalModelChange: EventEmitter<string>;
-    /** Open the retinal-layer parameter dialog. */
-    openRetinalParams: EventEmitter<void>;
+    /** Run a contributed tool over the current view, by tool id. */
+    runTool: EventEmitter<string>;
+    /** Pick a contributed tool's checkpoint. */
+    toolModelChange: EventEmitter<{
+        toolId: string;
+        modelId: string;
+    }>;
+    /** Open a contributed tool's parameter dialog, by tool id. */
+    openToolParams: EventEmitter<string>;
     /** SAM model picker (jit-ui#90 P1). */
     samModelChange: EventEmitter<string>;
     wandSensitivityChange: EventEmitter<number | undefined>;
@@ -155,15 +149,44 @@ export declare class ToolbarComponent implements OnChanges {
      *  Held as a stable array (rebuilt only when `samModels`/`samModelId` change),
      *  NOT a getter: a getter returns a fresh array with new `command` closures on
      *  every change-detection tick, which makes the bound `p-menu` overlay rebuild
-     *  its DOM mid-interaction and swallow the click on a menu item. */
+     *  its DOM mid-interaction and swallow the click on a menu item.
+     *
+     *  `tooltip` carries the model's description from {@link MODEL_INFO}; the
+     *  menus' shared item template turns it into the hover info icon. p-menu's own
+     *  rendering ignores the field (it reads `item.title`), so it is free to use. */
     samMenuItems: MenuItem[];
-    /** Same stable-array reasoning as {@link samMenuItems}. */
-    yoloMenuItems: MenuItem[];
-    /** Same stable-array reasoning as {@link samMenuItems}. */
-    retinalMenuItems: MenuItem[];
+    /**
+     * Model menus for the contributed tools, keyed by tool id. Same stable-array
+     * reasoning as {@link samMenuItems} — and it is why this is a map rebuilt in
+     * `ngOnChanges` rather than a method called from the template, which would
+     * hand `p-menu` a new array every tick.
+     *
+     * A contributed tool supplies its own per-model description, so unlike the
+     * SAM menu these do not consult {@link MODEL_INFO}: this library has no
+     * copy for checkpoints it does not know about.
+     */
+    toolMenuItems: Record<string, MenuItem[]>;
     /** Rebuild the SAM model menu when the model list or active selection
      *  changes (keeps the array reference stable across other CD ticks). */
     ngOnChanges(changes: SimpleChanges): void;
+    /**
+     * Strip markup from a model description so it can be read aloud.
+     *
+     * The copy in MODEL_INFO and in a contribution's `ToolModelOption.info` is
+     * written for a visual tooltip rendered with `[escape]="false"`, so it carries
+     * `<b>` and `<br>`. Passed to `aria-label` verbatim a screen reader announces
+     * the tags, so they are removed and `<br>` becomes a sentence break. Entities
+     * used in that copy (`&nbsp;`, `&times;`, `&amp;`) are decoded for the same
+     * reason.
+     */
+    plainText(html: string): string;
+    /** Contributed tool names for the help dialog's prompted/no-prompt contrast,
+     *  e.g. "YOLO, Retinal layers". Empty when nothing is registered, which is
+     *  why the sentence that uses it is itself conditional. */
+    get contributedToolNames(): string;
+    /** Keeps each contributed tool's `p-menu` overlay alive across CD ticks —
+     *  re-creating it mid-interaction swallows the click on a menu item. */
+    trackToolById(_index: number, tool: ToolbarToolContribution): string;
     /** The Image plot type renders as a natively pan/zoom-able raster, so the
      *  generic zoom/pan tools are hidden. */
     get isImageView(): boolean;
@@ -191,5 +214,5 @@ export declare class ToolbarComponent implements OnChanges {
     get isIntensityCapable(): boolean;
     showHelp(): void;
     static ɵfac: i0.ɵɵFactoryDeclaration<ToolbarComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<ToolbarComponent, "plotting-toolbar", never, { "imageInfo": { "alias": "imageInfo"; "required": false; }; "plotTypeOptions": { "alias": "plotTypeOptions"; "required": false; }; "selectedPlotType": { "alias": "selectedPlotType"; "required": false; }; "isoRange": { "alias": "isoRange"; "required": false; }; "maxIndex": { "alias": "maxIndex"; "required": false; }; "zIndex": { "alias": "zIndex"; "required": false; }; "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "activeDragMode": { "alias": "activeDragMode"; "required": false; }; "activeSurface3dMode": { "alias": "activeSurface3dMode"; "required": false; }; "axesVisible": { "alias": "axesVisible"; "required": false; }; "wireframeActive": { "alias": "wireframeActive"; "required": false; }; "resolutionScale": { "alias": "resolutionScale"; "required": false; }; "wandSensitivity": { "alias": "wandSensitivity"; "required": false; }; "brushSize": { "alias": "brushSize"; "required": false; }; "vertexEraserRadius": { "alias": "vertexEraserRadius"; "required": false; }; "canUndo": { "alias": "canUndo"; "required": false; }; "canRedo": { "alias": "canRedo"; "required": false; }; "stackOptions": { "alias": "stackOptions"; "required": false; }; "tools": { "alias": "tools"; "required": false; }; "imageSmoothingEnabled": { "alias": "imageSmoothingEnabled"; "required": false; }; "samModels": { "alias": "samModels"; "required": false; }; "samModelId": { "alias": "samModelId"; "required": false; }; "yoloModels": { "alias": "yoloModels"; "required": false; }; "yoloModelId": { "alias": "yoloModelId"; "required": false; }; "retinalModels": { "alias": "retinalModels"; "required": false; }; "retinalModelId": { "alias": "retinalModelId"; "required": false; }; }, { "selectPlotType": "selectPlotType"; "addProfileLine": "addProfileLine"; "toggleImageSmoothing": "toggleImageSmoothing"; "isoRangeChange": "isoRangeChange"; "openChannelHistogram": "openChannelHistogram"; "openRegionEditor": "openRegionEditor"; "selectStackOption": "selectStackOption"; "zScrub": "zScrub"; "zSlide": "zSlide"; "zIndexInput": "zIndexInput"; "reloadAndPlot": "reloadAndPlot"; "downloadImage": "downloadImage"; "autoscaleImage": "autoscaleImage"; "toggleDragMode": "toggleDragMode"; "zoomIn": "zoomIn"; "zoomOut": "zoomOut"; "toggleSurface3dMode": "toggleSurface3dMode"; "resetSurfaceCamera": "resetSurfaceCamera"; "toggleAxes": "toggleAxes"; "toggleWireframe": "toggleWireframe"; "selectResolution": "selectResolution"; "deleteRegion": "deleteRegion"; "undoRegion": "undoRegion"; "redoRegion": "redoRegion"; "segmentRegions": "segmentRegions"; "segmentCellpose": "segmentCellpose"; "detectYolo": "detectYolo"; "yoloModelChange": "yoloModelChange"; "openYoloParams": "openYoloParams"; "segmentRetinal": "segmentRetinal"; "retinalModelChange": "retinalModelChange"; "openRetinalParams": "openRetinalParams"; "samModelChange": "samModelChange"; "wandSensitivityChange": "wandSensitivityChange"; "brushSizeChange": "brushSizeChange"; "vertexEraserRadiusChange": "vertexEraserRadiusChange"; }, never, ["*"], false, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<ToolbarComponent, "plotting-toolbar", never, { "imageInfo": { "alias": "imageInfo"; "required": false; }; "plotTypeOptions": { "alias": "plotTypeOptions"; "required": false; }; "selectedPlotType": { "alias": "selectedPlotType"; "required": false; }; "isoRange": { "alias": "isoRange"; "required": false; }; "maxIndex": { "alias": "maxIndex"; "required": false; }; "zIndex": { "alias": "zIndex"; "required": false; }; "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "activeDragMode": { "alias": "activeDragMode"; "required": false; }; "activeSurface3dMode": { "alias": "activeSurface3dMode"; "required": false; }; "axesVisible": { "alias": "axesVisible"; "required": false; }; "wireframeActive": { "alias": "wireframeActive"; "required": false; }; "resolutionScale": { "alias": "resolutionScale"; "required": false; }; "wandSensitivity": { "alias": "wandSensitivity"; "required": false; }; "brushSize": { "alias": "brushSize"; "required": false; }; "vertexEraserRadius": { "alias": "vertexEraserRadius"; "required": false; }; "canUndo": { "alias": "canUndo"; "required": false; }; "canRedo": { "alias": "canRedo"; "required": false; }; "stackOptions": { "alias": "stackOptions"; "required": false; }; "tools": { "alias": "tools"; "required": false; }; "imageSmoothingEnabled": { "alias": "imageSmoothingEnabled"; "required": false; }; "samModels": { "alias": "samModels"; "required": false; }; "samModelId": { "alias": "samModelId"; "required": false; }; "contributedTools": { "alias": "contributedTools"; "required": false; }; "toolModelIds": { "alias": "toolModelIds"; "required": false; }; }, { "selectPlotType": "selectPlotType"; "addProfileLine": "addProfileLine"; "toggleImageSmoothing": "toggleImageSmoothing"; "isoRangeChange": "isoRangeChange"; "openChannelHistogram": "openChannelHistogram"; "openRegionEditor": "openRegionEditor"; "selectStackOption": "selectStackOption"; "zScrub": "zScrub"; "zSlide": "zSlide"; "zIndexInput": "zIndexInput"; "reloadAndPlot": "reloadAndPlot"; "downloadImage": "downloadImage"; "autoscaleImage": "autoscaleImage"; "toggleDragMode": "toggleDragMode"; "zoomIn": "zoomIn"; "zoomOut": "zoomOut"; "toggleSurface3dMode": "toggleSurface3dMode"; "resetSurfaceCamera": "resetSurfaceCamera"; "toggleAxes": "toggleAxes"; "toggleWireframe": "toggleWireframe"; "selectResolution": "selectResolution"; "deleteRegion": "deleteRegion"; "undoRegion": "undoRegion"; "redoRegion": "redoRegion"; "segmentRegions": "segmentRegions"; "segmentCellpose": "segmentCellpose"; "runTool": "runTool"; "toolModelChange": "toolModelChange"; "openToolParams": "openToolParams"; "samModelChange": "samModelChange"; "wandSensitivityChange": "wandSensitivityChange"; "brushSizeChange": "brushSizeChange"; "vertexEraserRadiusChange": "vertexEraserRadiusChange"; }, never, ["*"], false, never>;
 }

package/lib/visualizer.component.d.ts

@@ -12,10 +12,7 @@ import { IVisualizer } from './contracts/visualizer.contract';
 import { SamToolService } from './toolbar/segmentation/sam-tool.service';
 import { SamPointToolService } from './toolbar/segmentation/sam-point-tool.service';
 import { CellSegmentToolService } from './toolbar/segmentation/cell-segment-tool.service';
-import { YoloDetectToolService } from './toolbar/segmentation/yolo-detect-tool.service';
-import type { IInstanceSegmenter, InstanceSegmentOptions } from './contracts/instance-segmenter.contract';
-import { RetinalLayerToolService } from './toolbar/segmentation/retinal-layer-tool.service';
-import type { ISemanticSegmenter, SemanticSegmentOptions } from './contracts/semantic-segmenter.contract';
+import { NumberParamSpec, SelectParamSpec, ToolParamSpec, ToolbarToolContribution } from './contracts/toolbar-tool.contract';
 import { ToolbarToolVisibility } from './contracts/toolbar-config';
 import { VizConfig } from './contracts/viz-config';
 import * as i0 from "@angular/core";
@@ -28,10 +25,6 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     private session;
     private samTool;
     private cellSegmentTool;
-    private yoloDetectTool;
-    private instanceSegmenter;
-    private semanticSegmenter;
-    private retinalLayerTool;
     private samPointTool;
     private regionOps;
     private vizConfig?;
@@ -131,28 +124,22 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
         label: string;
     }[];
     samModelId: string;
-    /** YOLO checkpoints with a configured URL, and the active one. */
-    yoloModels: {
-        id: string;
-        label: string;
-    }[];
-    yoloModelId: string;
-    /** Parameter dialog state. Seeded from the active model's own defaults, which
-     *  encode the scale and crowding each checkpoint was trained for. */
-    showYoloParams: boolean;
-    yoloParams: InstanceSegmentOptions;
-    /** Retinal-layer checkpoints with a configured URL, and the active one.
-     *  Only VNet ships — see the registry for why the ResUNet-a entries are off. */
-    retinalModels: {
-        id: string;
-        label: string;
-    }[];
-    retinalModelId: string;
-    showRetinalParams: boolean;
-    retinalParams: SemanticSegmentOptions;
-    /** Download size of the active retinal model, surfaced in the dialog because
-     *  ~590 MB is worth knowing before clicking Run rather than after. */
-    get retinalModelSizeMb(): number;
+    /**
+     * No-prompt tools registered through {@link TOOLBAR_TOOLS}, filtered to those
+     * with configured models and sorted. This library registers none — a host
+     * supplies them — so an open build has an empty array here and the toolbar
+     * and help dialog simply omit that group.
+     */
+    contributedTools: ToolbarToolContribution[];
+    /** Active checkpoint per contributed tool. */
+    toolModelIds: Record<string, string>;
+    /**
+     * Parameter values per contributed tool, seeded from each tool's own defaults
+     * — which encode the scale and crowding its checkpoint was trained for.
+     */
+    toolParams: Record<string, Record<string, unknown>>;
+    /** Which tool's parameter dialog is open, or null. */
+    openParamsToolId: string | null;
     /** SAM download/segment toast state (bound by the `sam` p-toast template). */
     samStatus: string;
     samProgress: number;
@@ -263,7 +250,7 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     private wheelListener?;
     /** Debounced z-slice scrubbing (see SliceScrubber — refactoring plan Step 7). */
     private readonly scrubber;
-    constructor(state: ImageStatePort, plotService: IVisualizer, messageService: MessageService, ngZone: NgZone, cdr: ChangeDetectorRef, session: VisualizerStore, samTool: SamToolService, cellSegmentTool: CellSegmentToolService, yoloDetectTool: YoloDetectToolService, instanceSegmenter: IInstanceSegmenter, semanticSegmenter: ISemanticSegmenter, retinalLayerTool: RetinalLayerToolService, samPointTool: SamPointToolService, regionOps: RegionOpsService, vizConfig?: VizConfig | undefined);
+    constructor(state: ImageStatePort, plotService: IVisualizer, messageService: MessageService, ngZone: NgZone, cdr: ChangeDetectorRef, session: VisualizerStore, samTool: SamToolService, cellSegmentTool: CellSegmentToolService, samPointTool: SamPointToolService, regionOps: RegionOpsService, vizConfig?: VizConfig | undefined, toolContributions?: readonly ToolbarToolContribution[]);
     /**
      * Plot types offered in the selector for the current image:
      *  - Outside **test mode**, only the curated default set (descriptors with a
@@ -411,37 +398,41 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
      *  (jit-ui#90). Each box is cropped (browser slide-crop) then run through the
      *  cellpose-js model; the same sticky `sam` toast + progress bar is reused. */
     segmentCellpose(): Promise<void>;
-    /** Per-model defaults from the registry — what the checkpoint was trained for. */
-    private defaultYoloParams;
+    /**
+     * Parameters currently bound by the generic parameter dialog, for whichever
+     * tool is open. Seeded lazily: a tool's defaults are only asked for when the
+     * user first touches it, so registering a tool costs nothing until used.
+     */
+    paramsFor(toolId: string): Record<string, unknown>;
+    /** Active checkpoint for a tool, falling back to the tool's own default. */
+    modelIdFor(tool: ToolbarToolContribution): string;
     /** Switching checkpoint re-seeds the parameters, since the defaults belong to
      *  the model rather than to the tool. */
-    onYoloModelChange(id: string): void;
-    openYoloParams(): void;
-    resetYoloParams(): void;
-    /** Detect objects across the current view. No prompt: a detector finds objects
-     *  in a field rather than being pointed at one. Reuses the shared segmentation
-     *  toast so progress and status read the same as the SAM/cellpose tools. */
-    detectYolo(): Promise<void>;
+    onToolModelChange(e: {
+        toolId: string;
+        modelId: string;
+    }): void;
+    /** A tool's defaults for a checkpoint, with that checkpoint's own overrides
+     *  applied on top — per-model defaults beat per-tool ones. */
+    private seedParams;
     /**
-     * Defaults for the retinal tool.
+     * Narrow a param spec for the template.
      *
-     * `classThreshold` is 0.5 to match the reference worker, which thresholds each
-     * class channel independently rather than taking an argmax — with a softmax
-     * output that makes it argmax plus a confidence floor.
-     *
-     * `downsamplingFactor` is 1 rather than YOLO's 5: these checkpoints were
-     * trained on native 40x patches, so the model wants full resolution and
-     * downsampling actively hurts.
+     * `*ngSwitchCase` does not narrow a discriminated union in Angular's template
+     * type checker the way a `switch` does in TypeScript, so the template asks for
+     * the variant it has already matched on.
      */
-    private defaultRetinalParams;
-    /** Switching checkpoint re-seeds the parameters, since the defaults belong to
-     *  the model rather than to the tool. */
-    onRetinalModelChange(id: string): void;
-    openRetinalParams(): void;
-    resetRetinalParams(): void;
-    /** Segment retinal layers across the current view. Like YOLO this takes no
-     *  prompt — it labels every pixel — and reuses the shared segmentation toast. */
-    segmentRetinal(): Promise<void>;
+    numberParam(p: ToolParamSpec): NumberParamSpec;
+    selectParam(p: ToolParamSpec): SelectParamSpec;
+    openToolParams(toolId: string): void;
+    /** The tool whose parameter dialog is open, for the generic dialog's header
+     *  and field list. */
+    get openParamsTool(): ToolbarToolContribution | undefined;
+    resetToolParams(toolId: string): void;
+    /** Run a contributed tool over the current view. No prompt: these sweep the
+     *  whole view rather than being pointed at something. Reuses the shared
+     *  segmentation toast so progress reads the same as the SAM/cellpose tools. */
+    runTool(toolId: string): Promise<void>;
     /** Shared driver for the box-prompt segment tools: wires the tool's status +
      *  download progress into the sticky `sam` toast, runs `op`, and reports the
      *  region count. Keeps the toast open until the run settles (bar hits 100%). */
@@ -485,6 +476,6 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     onSelectPlotType(type: PlotType): void;
     /** Deactivate whatever tool is armed and clear every tool mode. */
     private deactivateActiveTool;
-    static ɵfac: i0.ɵɵFactoryDeclaration<VisualizerComponent, [null, null, null, null, null, null, null, null, null, null, null, null, null, null, { optional: true; }]>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<VisualizerComponent, [null, null, null, null, null, null, null, null, null, null, { optional: true; }, { optional: true; }]>;
     static ɵcmp: i0.ɵɵComponentDeclaration<VisualizerComponent, "visualizer", never, { "toolbarTools": { "alias": "toolbarTools"; "required": false; }; "testMode": { "alias": "testMode"; "required": false; }; }, { "isStackEvent": "isStackEvent"; "isGrayscaleEvent": "isGrayscaleEvent"; }, never, ["*"], false, never>;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.2.19",
+  "version": "0.3.1",
   "description": "Browser-based scientific image visualization for Angular — gigapixel whole-slide (OpenSeadragon), 2D/3D (Plotly) and WebGPU (napari-js) rendering, with region/annotation editing and in-browser SAM segmentation.",
   "keywords": [
     "angular",
@@ -34,14 +34,12 @@
     "access": "public"
   },
   "dependencies": {
-    "cellpose-js": "^0.4.1",
+    "cellpose-js": "^0.5.0",
     "fast-png": "^6.4.0",
-    "jax-ai-js": "^0.2.0",
     "napari-js": "^0.11.0",
     "openseadragon": "^6.0.2",
     "plotly.js-dist-min": "^3.0.1",
-    "tslib": "^2.3.0",
-    "yolo-segdetect-js": "^0.1.2"
+    "tslib": "^2.3.0"
   },
   "peerDependencies": {
     "@angular/animations": "^17.3.0",

package/src/lib/assets/cell-detection.svg

@@ -0,0 +1,37 @@
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+     inkscape:deskcolor="#d1d1d1"
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