@jax-data-science/sci-image-visualizer 0.2.12 → 0.2.13

package/index.d.ts

@@ -24,6 +24,7 @@ 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 } from './lib/toolbar/segmentation/yolo-detect-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';

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

@@ -52,6 +52,17 @@ export interface InstanceSegmentation {
 export interface InstanceSegmentOptions {
     /** Which registered model to run. Defaults to the registry's default. */
     modelId?: string;
+    /**
+     * Scale to run at, as a divisor of full resolution — the same meaning the
+     * server gives it.
+     *
+     * This is what puts objects at the size the checkpoint was trained on, and it
+     * matters more than any threshold: run a detector at the wrong object scale
+     * and it finds nothing. A caller that can re-crop the source (a tile-backed
+     * viewer) should honour it rather than accepting whatever the display happens
+     * to show.
+     */
+    downsamplingFactor?: number;
     /** Minimum detection confidence, per tile. */
     confidence?: number;
     /** NMS IoU within a single tile. */

package/lib/toolbar/segmentation/yolo-detect-tool.service.d.ts

@@ -0,0 +1,49 @@
+import { BehaviorSubject } from 'rxjs';
+import { type TileAccessPort } from '../../contracts/ports/tile-access.port';
+import type { IVisualizer } from '../../contracts/visualizer.contract';
+import type { IInstanceSegmenter, InstanceSegmentOptions } from '../../contracts/instance-segmenter.contract';
+import * as i0 from "@angular/core";
+/**
+ * YOLO object detection over the current view.
+ *
+ * The complement to {@link CellSegmentToolService}: cellpose auto-segments cells
+ * inside a box you draw, whereas a detector is meant to find objects across a
+ * field. So this takes no prompt — it runs on whatever is on screen and turns
+ * every detection into a region.
+ *
+ * Detections come back in the displayed image's pixels; they are mapped onto
+ * the full-resolution image through the viewer's own source rect, so the regions
+ * land where the objects actually are rather than at view-local coordinates.
+ *
+ * Exposes the same `status$` / `busy$` / `progress$` surface as the cellpose
+ * tool so the host's shared segmentation toast drives it unchanged.
+ */
+export declare class YoloDetectToolService {
+    /** Server-side crop, so detection can run at the model's scale rather than
+     *  the viewer's. Optional: without it the tool falls back to the displayed
+     *  pixels, which is correct but scale-dependent. */
+    private tileAccess;
+    readonly status$: BehaviorSubject<string>;
+    readonly busy$: BehaviorSubject<boolean>;
+    readonly progress$: BehaviorSubject<number>;
+    constructor(
+    /** Server-side crop, so detection can run at the model's scale rather than
+     *  the viewer's. Optional: without it the tool falls back to the displayed
+     *  pixels, which is correct but scale-dependent. */
+    tileAccess?: TileAccessPort | null);
+    /**
+     * Detect in the current view and append the results as regions.
+     *
+     * @returns the number of regions added.
+     */
+    detectInView(viz: IVisualizer, segmenter: IInstanceSegmenter, opts?: InstanceSegmentOptions): Promise<number>;
+    /**
+     * Re-crop `rect` at `1/target` of full resolution. Returns null on any
+     * failure, so the caller falls back to the displayed pixels — a coarser crop
+     * beats a failed run.
+     */
+    private fetchCropAtScale;
+    private makeRegion;
+    static ɵfac: i0.ɵɵFactoryDeclaration<YoloDetectToolService, [{ optional: true; }]>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<YoloDetectToolService>;
+}

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

@@ -66,6 +66,12 @@ 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;
     selectPlotType: EventEmitter<PlotType>;
     /** Intensity (LINE) mode: add another colored line ROI + inset trace. */
     addProfileLine: EventEmitter<void>;
@@ -105,6 +111,12 @@ 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>;
     /** SAM model picker (jit-ui#90 P1). */
     samModelChange: EventEmitter<string>;
     wandSensitivityChange: EventEmitter<number | undefined>;
@@ -133,6 +145,8 @@ export declare class ToolbarComponent implements OnChanges {
      *  every change-detection tick, which makes the bound `p-menu` overlay rebuild
      *  its DOM mid-interaction and swallow the click on a menu item. */
     samMenuItems: MenuItem[];
+    /** Same stable-array reasoning as {@link samMenuItems}. */
+    yoloMenuItems: 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;
@@ -163,5 +177,5 @@ 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; }; }, { "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"; "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; }; "yoloModels": { "alias": "yoloModels"; "required": false; }; "yoloModelId": { "alias": "yoloModelId"; "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"; "samModelChange": "samModelChange"; "wandSensitivityChange": "wandSensitivityChange"; "brushSizeChange": "brushSizeChange"; "vertexEraserRadiusChange": "vertexEraserRadiusChange"; }, never, ["*"], false, never>;
 }

package/lib/visualizer.component.d.ts

@@ -12,6 +12,8 @@ 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 { ToolbarToolVisibility } from './contracts/toolbar-config';
 import { VizConfig } from './contracts/viz-config';
 import * as i0 from "@angular/core";
@@ -24,6 +26,8 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     private session;
     private samTool;
     private cellSegmentTool;
+    private yoloDetectTool;
+    private instanceSegmenter;
     private samPointTool;
     private regionOps;
     private vizConfig?;
@@ -123,6 +127,16 @@ 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;
     /** SAM download/segment toast state (bound by the `sam` p-toast template). */
     samStatus: string;
     samProgress: number;
@@ -233,7 +247,7 @@ 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, samPointTool: SamPointToolService, regionOps: RegionOpsService, vizConfig?: VizConfig | undefined);
+    constructor(state: ImageStatePort, plotService: IVisualizer, messageService: MessageService, ngZone: NgZone, cdr: ChangeDetectorRef, session: VisualizerStore, samTool: SamToolService, cellSegmentTool: CellSegmentToolService, yoloDetectTool: YoloDetectToolService, instanceSegmenter: IInstanceSegmenter, samPointTool: SamPointToolService, regionOps: RegionOpsService, vizConfig?: VizConfig | undefined);
     /**
      * Plot types offered in the selector for the current image:
      *  - Outside **test mode**, only the curated default set (descriptors with a
@@ -381,6 +395,17 @@ 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;
+    /** 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>;
     /** 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%). */
@@ -424,6 +449,6 @@ 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, { optional: true; }]>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<VisualizerComponent, [null, null, null, null, null, null, null, null, null, null, null, null, { 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": "0.2.12",
+  "version": "0.2.13",
   "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",