@jax-data-science/sci-image-visualizer 0.16.0 → 0.18.0

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

@@ -0,0 +1,64 @@
+import { EventEmitter, OnChanges, SimpleChanges } from '@angular/core';
+import type { ISpatialControls } from '../../contracts/visualizer.contract';
+import type { SpatialDataset } from '../../contracts/spatial-dataset.contract';
+import { ColormapNode, SpatialViewState } from '../../contracts/display-types';
+import type { PanelOption } from '../../spatial/spatial-panel-model';
+import type { GenePickerModel } from '../spatial-gene-picker';
+import type { SpatialLegendEntry } from '../spatial-key/spatial-key.model';
+import * as i0 from "@angular/core";
+/** What colours the observations: a grouping, a gene, a measurement, or one colour. */
+export type ColorByMode = 'group' | 'gene' | 'measure' | 'single';
+/**
+ * The Observations section's "Colour by": one colouring for the markers and the cells alike —
+ * a grouping (the {@link SpatialGroupsPanelComponent groups} with their colours and switches),
+ * one gene's expression, a measurement (a numeric column), or one colour. Each choice writes
+ * the markers' colour source (`colorBy`) and the cells' (`cellColorMode` and its own fields)
+ * together, so the two cannot disagree.
+ *
+ * Writes only through `controls.setViewState`.
+ */
+export declare class SpatialColorByComponent implements OnChanges {
+    /** The spatial controls this panel reads and writes through; null without a `SPATIAL_DATA_PORT`. */
+    controls: ISpatialControls | null;
+    /** The dataset on offer, or null. */
+    dataset: SpatialDataset | null;
+    /** The current spatial view state. */
+    view: SpatialViewState;
+    /** The gene list the gene colouring picks from, shared with the other gene dropdowns. */
+    genes: GenePickerModel | null;
+    /** The key's categorical legend, or null (continuous). */
+    legend: SpatialLegendEntry[] | null;
+    /** The key's continuous colour bar (a CSS gradient), or null. */
+    colorBarCss: string | null;
+    /** The selected category (its code), for highlighting its group. */
+    selectedCategory: number | null;
+    /** Colormap tree for the continuous colour scale. */
+    colormapOptions: ColormapNode[];
+    /** A group was clicked: its category's code, to select its observations. */
+    readonly categoryClicked: EventEmitter<number>;
+    /** Virtual-scrolled only past this many options (see the gene dropdowns elsewhere). */
+    protected readonly geneVirtualScrollFrom = 200;
+    /** The modes the dataset can be coloured in. */
+    protected modeOptions: PanelOption<ColorByMode>[];
+    /** The dataset's numeric columns. */
+    protected measureOptions: PanelOption<string>[];
+    /** A mode picked before its gene or measurement is: shown, nothing written yet. */
+    private pending;
+    ngOnChanges(changes: SimpleChanges): void;
+    /** The mode on show: one picked and waiting for its value, else what the view is coloured by. */
+    protected get mode(): ColorByMode | null;
+    /** What the view is coloured by, as a mode; null for the flat default. */
+    private get viewMode();
+    /** The gene the observations are coloured by, or null. */
+    protected get selectedGene(): string | null;
+    /** The measurement the observations are coloured by, or null. */
+    protected get selectedMeasure(): string | null;
+    protected onMode(mode: ColorByMode | null): void;
+    /** Colour the markers and the cells by gene `name`. */
+    protected onGene(name: string | null): void;
+    /** Colour the markers and the cells by measurement `name`. */
+    protected onMeasure(name: string | null): void;
+    protected onSingleColor(hex: string): void;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SpatialColorByComponent, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialColorByComponent, "spatial-color-by", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; "genes": { "alias": "genes"; "required": false; }; "legend": { "alias": "legend"; "required": false; }; "colorBarCss": { "alias": "colorBarCss"; "required": false; }; "selectedCategory": { "alias": "selectedCategory"; "required": false; }; "colormapOptions": { "alias": "colormapOptions"; "required": false; }; }, { "categoryClicked": "categoryClicked"; }, never, never, true, never>;
+}

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

@@ -1,7 +1,7 @@
 import { EventEmitter, NgZone, OnInit } from '@angular/core';
 import { IVisualizer, ISpatialControls, RoiSelectionMode } from '../contracts/visualizer.contract';
 import { SpatialDataset } from '../contracts/spatial-dataset.contract';
-import { ColormapNode, SpatialViewState } from '../contracts/display-types';
+import { Cells3dStatus, ColormapNode, SpatialViewState } from '../contracts/display-types';
 import { PanelOption, parseGeneGroups } from '../spatial/spatial-panel-model';
 import { SpatialSelectionMask } from '../spatial/spatial-selection';
 import { GenePickerModel } from './spatial-gene-picker';
@@ -137,12 +137,29 @@ export declare class SpatialControlsComponent implements OnInit {
     protected get hasSelection(): boolean;
     /** Boundaries on offer: tiled (level-of-detail) or whole-dataset rings. */
     protected get hasCells(): boolean;
+    /** The 3D view's individual cells as they stand (null: none drawn). */
+    protected cells3dStatus: Cells3dStatus | null;
+    /**
+     * Whether the router has the dataset's region set attached and placed (null: it does not say).
+     * See {@link hasCells3d}.
+     */
+    protected cells3dAvailable: boolean | null;
+    /**
+     * The dataset's cells can be drawn in 3D: its boundaries name a 3D segmentation's region set, and
+     * it is attached with its planes (else the 3D view draws no cells, and the markers stay).
+     */
+    protected get hasCells3d(): boolean;
     /** Transcripts on offer: tiles to draw, or a density map. */
     protected get hasTranscripts(): boolean;
+    /** Whether the 3D cloud can draw the transcripts too: they carry z (a MERFISH volume's do). */
+    protected get hasTranscripts3d(): boolean;
     protected onShowImage(on: boolean): void;
+    /** The reference volume, in 3D (the Volume section's switch). */
+    protected onShowVolume(on: boolean): void;
+    protected onVolumeOpacity(value: number | undefined): void;
     protected onShowAnnotations(on: boolean): void;
     /** Which collapsible sections are open. Per dialog instance, not persisted. */
-    protected open: Record<'images' | 'cells' | 'transcripts' | 'annotations' | 'observations', boolean>;
+    protected open: Record<'images' | 'volume' | 'transcripts' | 'annotations' | 'observations', boolean>;
     protected toggleSection(name: keyof SpatialControlsComponent['open']): void;
     /** Expand or collapse a section — what a panel's header asks for. */
     protected setOpen(name: keyof SpatialControlsComponent['open'], on: boolean): void;

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

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

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

@@ -21,6 +21,8 @@ interface AllGeneRowView {
     shown: boolean;
     /** Its colour when coloured by gene, or null when the dataset's code order is unknown. */
     swatch: string | null;
+    /** Its code in the dataset's gene list (what its palette colour is picked by). */
+    code: number;
     count: number | null;
 }
 /**
@@ -131,6 +133,11 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     /** The colour gene `slot` is drawn in when transcripts are coloured by gene. */
     geneColor(slot: number): string;
     protected geneColorOf(gene: string): string;
+    /**
+     * The colour the open picker shows: with "All genes", the gene's colour among every gene (its
+     * chosen one, else the palette's by its code), as its row and its markers have it.
+     */
+    protected styleColorOf(gene: string): string;
     /** In Cluster colouring, a gene's swatch is its cluster's colour, as its markers are. */
     protected geneSwatchOf(gene: string): string;
     protected geneCountOf(gene: string): number | null;

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

@@ -1,16 +1,18 @@
-import { ChangeDetectorRef, NgZone, OnChanges, SimpleChanges } from '@angular/core';
+import { ChangeDetectorRef, EventEmitter, NgZone, OnChanges, SimpleChanges } from '@angular/core';
 import type { ISpatialControls } from '../../contracts/visualizer.contract';
 import type { SpatialDataset } from '../../contracts/spatial-dataset.contract';
 import { SpatialViewState } from '../../contracts/display-types';
 import { GroupOptionSection, GroupRow, PanelOption } from '../../spatial/spatial-panel-model';
 import * as i0 from "@angular/core";
 /**
- * The cells' grouping, as Xenium Explorer's Groups section: the group picker (columns under
- * their section heading, a k-means family once, with its k beside it), CSV import of a new
- * grouping, and the grouping's categories with their colours, cell counts and show/hide
- * switches.
+ * The observations' grouping, as Xenium Explorer's Groups section: the group picker (columns
+ * under their section heading, a k-means family once, with its k beside it), CSV import of a new
+ * grouping, and the grouping's categories with their colours (each one's swatch opens a colour
+ * picker), cell counts and show/hide switches. A group's name selects its observations.
  *
- * Writes only through `controls.setViewState` (`cellTypeColumn`, `hiddenGroups`).
+ * The Observations section's "Colour by" in Group mode: the grouping colours the markers and the
+ * cells alike. Writes only through `controls.setViewState` (`cellTypeColumn` with `colorBy` and
+ * `cellColorMode`, `hiddenGroups`, `groupColors`).
  */
 export declare class SpatialGroupsPanelComponent implements OnChanges {
     private readonly zone;
@@ -21,6 +23,10 @@ export declare class SpatialGroupsPanelComponent implements OnChanges {
     dataset: SpatialDataset | null;
     /** The current spatial view state: what is drawn, and how. */
     view: SpatialViewState;
+    /** The category selected (its code in the grouping), for highlighting its row. */
+    selectedCategory: number | null;
+    /** A group's name was clicked: its category's code in the grouping, to select its observations. */
+    readonly categoryClicked: EventEmitter<number>;
     /**
      * The group picker: categorical columns under their section heading, a family of
      * variants (k-means at k = 2…10) listed once. Values are a column name, or
@@ -42,6 +48,8 @@ export declare class SpatialGroupsPanelComponent implements OnChanges {
     private readonly groupRowsLoad;
     protected groupImportError: string | null;
     protected groupImporting: boolean;
+    /** The group the open colour picker edits. */
+    protected styleGroup: string | null;
     constructor(zone: NgZone, cdr: ChangeDetectorRef);
     ngOnChanges(changes: SimpleChanges): void;
     /** The categorical column the cells are grouped by. */
@@ -51,12 +59,25 @@ export declare class SpatialGroupsPanelComponent implements OnChanges {
     protected onGroupEntry(value: string): void;
     protected onGroupVariant(name: string): void;
     onCellTypeColumn(name: string | null): void;
+    /** Group `label`'s category code in the active grouping, or -1. */
+    protected codeOf(label: string): number;
+    /** Select (or, selected already, clear) group `label`'s observations. */
+    protected onGroupClicked(label: string): void;
     /** {@link SpatialViewState.hiddenGroups} as a set, for the per-row checks. */
     private hiddenGroups;
     protected isGroupShown(label: string): boolean;
     protected get allGroupsShown(): boolean;
     protected onGroupShown(label: string, on: boolean): void;
     protected onAllGroupsShown(on: boolean): void;
+    protected openGroupStyle(event: Event, label: string, panel: {
+        toggle(e: Event): void;
+        hide(): void;
+    }): void;
+    /** The colour group `label` is drawn in now (the user's, else the column's or the palette's). */
+    protected groupColorOf(label: string): string;
+    protected onGroupColor(label: string, hex: string): void;
+    /** Back to the group's own colour (the column's, else the palette's). */
+    protected resetGroupColor(label: string): void;
     protected get canImportGroups(): boolean;
     /** '+': a CSV/TSV of `cell_id` and group, named after the file. */
     protected onImportGroupsFile(input: HTMLInputElement): Promise<void>;
@@ -68,5 +89,5 @@ export declare class SpatialGroupsPanelComponent implements OnChanges {
     /** Apply an async result inside the zone and re-render this OnPush panel. */
     private apply;
     static ɵfac: i0.ɵɵFactoryDeclaration<SpatialGroupsPanelComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialGroupsPanelComponent, "spatial-groups-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; }, {}, never, never, true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialGroupsPanelComponent, "spatial-groups-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; "selectedCategory": { "alias": "selectedCategory"; "required": false; }; }, { "categoryClicked": "categoryClicked"; }, never, never, true, never>;
 }

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

@@ -8,16 +8,6 @@ import { PanelOption } from '../../spatial/spatial-panel-model';
 import type { GenePickerModel } from '../spatial-gene-picker';
 import type { SpatialLegendEntry } from '../spatial-key/spatial-key.model';
 import * as i0 from "@angular/core";
-/**
- * The Observations section — one marker per observation (cell centroid, Visium spot) — and
- * what else draws them: what colours them (a column or a gene, mutually exclusive, with
- * the {@link SpatialKeyComponent key}), point size and opacity, the gene map, the 3D scene
- * (volume, cloud, sections, density volumes) and the continuous-only knobs.
- *
- * Renders the section and the sections after it as siblings in the dialog body
- * (`display: contents`). Writes only through the port: `setViewState`, and the colour
- * source's own `colorByColumn` / `colorByFeature` / `clearColorBy`.
- */
 export declare class SpatialObservationsPanelComponent implements OnChanges {
     /** The spatial controls this panel reads and writes through; null without a `SPATIAL_DATA_PORT`. */
     controls: ISpatialControls | null;
@@ -43,6 +33,11 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     open: boolean;
     /** Asks to open or close it; two-way with `open`. */
     readonly openChange: EventEmitter<boolean>;
+    /**
+     * Whether the dataset's cells can be drawn here (a cell segmentation, and in 3D a 3D one): the
+     * observations are shown as Markers or as Cell segmentations.
+     */
+    cellsAvailable: boolean;
     /** A legend row was clicked (see the key). */
     readonly categoryClicked: EventEmitter<number>;
     protected readonly clipOptions: PanelOption<[number, number]>[];
@@ -50,10 +45,10 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     protected readonly matchOptions: PanelOption<SpatialViewState['observationGenesMatch']>[];
     /** Virtual-scrolled only past this many options (see the cells panel's gene dropdown). */
     protected readonly geneVirtualScrollFrom = 200;
-    /** Colour-by column choices — "None" plus every column the dataset declares. */
-    protected columnOptions: PanelOption<string | null>[];
-    protected selectedColumn: string | null;
-    protected selectedGene: string | null;
+    /** What the observations are shown as, with a cell segmentation. */
+    protected readonly showAsOptions: PanelOption<'markers' | 'cells'>[];
+    /** The choice of Markers or Cell segmentations, kept while the observations are hidden. */
+    private chosenShownAs;
     /**
      * The dataset's imaged section positions, or null when its z is continuous rather than
      * sectioned. Read once per dataset — the scan walks the z of every observation, so it
@@ -61,10 +56,22 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
      */
     protected sections: Float32Array | null;
     ngOnChanges(changes: SimpleChanges): void;
-    /** Column dropdown. Choosing a column supersedes any gene selection. */
-    protected onColumn(name: string | null): void;
-    /** A gene was picked; it supersedes any column selection. */
-    protected onGene(name: string | null): void;
+    /** Whether the cells are drawn (the explicit choice, or automatically for data that has them). */
+    private get cellsOn();
+    /** Whether the observations are shown at all, as markers or as cells. */
+    protected get observationsShown(): boolean;
+    /** What the observations are shown as (the toggle): the cells while they are drawn, else the
+     *  markers, or, hidden, what was last chosen. */
+    protected get shownAs(): 'markers' | 'cells';
+    /** Show or hide the observations, as what they were shown as. */
+    protected onShowObservations(on: boolean): void;
+    protected onShownAs(as: 'markers' | 'cells' | null): void;
+    /**
+     * Draw the observations as the markers, or as the cells: one or the other, never both (the
+     * renderers draw no markers while the cells are drawn). The markers stay switched on under the
+     * cells, so a view without them (spatial 3D of a 2D segmentation) still shows the markers.
+     */
+    private showAs;
     /** Genes picked for the observation filter; none draws every observation. */
     protected onObservationGenes(genes: string[] | null): void;
     protected onObservationGenesMatch(match: SpatialViewState['observationGenesMatch'] | null): void;
@@ -94,8 +101,6 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     protected resetGeneStyle(gene: string): void;
     /** What the filter hides, in words. */
     protected get geneFilterHint(): string;
-    /** Cell outlines on offer, which changes what the circles mean. */
-    protected get hasCells(): boolean;
     /** True while a selection is active — everything else renders muted. */
     get hasSelection(): boolean;
     /** Whether log/clip apply — they are continuous-only knobs. */
@@ -122,8 +127,6 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     protected get geneMapVolumeNote(): string;
     /** True while a gene is the colour source — the only thing a gene map can map. */
     protected get canMapGene(): boolean;
-    protected onShowVolume(on: boolean): void;
-    protected onVolumeOpacity(value: number | undefined): void;
     protected onShowPoints(on: boolean): void;
     /** The "one section at a time" switch: null restores the whole stack. */
     protected onOneSection(on: boolean): void;
@@ -145,5 +148,5 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     private static readonly DENSITY_MAX_CLUSTERS;
     protected onClip(value: [number, number]): void;
     static ɵfac: i0.ɵɵFactoryDeclaration<SpatialObservationsPanelComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialObservationsPanelComponent, "spatial-observations-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; "genes": { "alias": "genes"; "required": false; }; "legend": { "alias": "legend"; "required": false; }; "colorBarCss": { "alias": "colorBarCss"; "required": false; }; "selection": { "alias": "selection"; "required": false; }; "selectedCategory": { "alias": "selectedCategory"; "required": false; }; "colormapOptions": { "alias": "colormapOptions"; "required": false; }; "is3d": { "alias": "is3d"; "required": false; }; "open": { "alias": "open"; "required": false; }; }, { "openChange": "openChange"; "categoryClicked": "categoryClicked"; }, never, never, true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialObservationsPanelComponent, "spatial-observations-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; "genes": { "alias": "genes"; "required": false; }; "legend": { "alias": "legend"; "required": false; }; "colorBarCss": { "alias": "colorBarCss"; "required": false; }; "selection": { "alias": "selection"; "required": false; }; "selectedCategory": { "alias": "selectedCategory"; "required": false; }; "colormapOptions": { "alias": "colormapOptions"; "required": false; }; "is3d": { "alias": "is3d"; "required": false; }; "open": { "alias": "open"; "required": false; }; "cellsAvailable": { "alias": "cellsAvailable"; "required": false; }; }, { "openChange": "openChange"; "categoryClicked": "categoryClicked"; }, never, ["spatial-cells-panel"], true, never>;
 }

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

@@ -0,0 +1,48 @@
+import { ChangeDetectorRef, NgZone, OnChanges, OnDestroy, SimpleChanges } from '@angular/core';
+import type { ISpatialControls } from '../../contracts/visualizer.contract';
+import type { ObservationsInSelection } from '../../contracts/display-types';
+import * as i0 from "@angular/core";
+/**
+ * "Observations in selection", in the Observations section: the observations of what is selected —
+ * a cell, a cell type picked on the canvas, the selected regions — by the grouping they are coloured
+ * by (else the cell types), with a few measurements' means, or one cell's id, groupings and values.
+ * Every observation in spatial 3D; in 2D those on the plane shown. See
+ * `ISpatialControls.getObservationsInSelection$`.
+ *
+ * Collapsible; followed only while expanded (and while the Observations section, which holds it, is
+ * open).
+ */
+export declare class SpatialSelectionObservationsComponent implements OnChanges, OnDestroy {
+    private readonly zone;
+    private readonly cdr;
+    /** The spatial controls the list is read through; null without a `SPATIAL_DATA_PORT`. */
+    controls: ISpatialControls | null;
+    /** In spatial 3D: the list is of the whole volume. */
+    is3d: boolean;
+    /** Expanded: the list is followed and shown. */
+    protected expanded: boolean;
+    /** The selection's observations (null until the first answer). */
+    protected list: ObservationsInSelection | null;
+    private sub;
+    constructor(zone: NgZone, cdr: ChangeDetectorRef);
+    ngOnChanges(changes: SimpleChanges): void;
+    ngOnDestroy(): void;
+    /** Whether there is a list to offer. */
+    protected get available(): boolean;
+    /** The largest group, for the bars. */
+    protected get max(): number;
+    protected toggle(): void;
+    private watch;
+    /** A measurement as shown: a number to 3 significant figures (with its unit), text as it is. */
+    protected format(m: {
+        value: string | number;
+        unit?: string;
+    }): string;
+    /** The groups as tab-separated text (group, observations), for a spreadsheet. */
+    protected copy(): void;
+    protected trackGroup(_i: number, g: {
+        name: string;
+    }): string;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SpatialSelectionObservationsComponent, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialSelectionObservationsComponent, "spatial-selection-observations", never, { "controls": { "alias": "controls"; "required": false; }; "is3d": { "alias": "is3d"; "required": false; }; }, {}, never, never, true, never>;
+}

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

@@ -0,0 +1,43 @@
+import { ChangeDetectorRef, NgZone, OnChanges, OnDestroy, SimpleChanges } from '@angular/core';
+import type { ISpatialControls } from '../../contracts/visualizer.contract';
+import type { TranscriptsInSelection } from '../../contracts/display-types';
+import * as i0 from "@angular/core";
+/**
+ * "Transcripts in selection", in the Transcripts section: the transcripts of what is selected, by
+ * gene, most frequent first — through the volume in spatial 3D (a cell, or a cell type picked on the
+ * canvas), on the plane shown in 2D (the selected cells or regions). See
+ * `ISpatialControls.getTranscriptsInSelection$`.
+ *
+ * Collapsible; counted only while expanded (and while the Transcripts section, which holds it, is
+ * open): the counts read the finest transcript tiles of the selection.
+ */
+export declare class SpatialSelectionTranscriptsComponent implements OnChanges, OnDestroy {
+    private readonly zone;
+    private readonly cdr;
+    /** The spatial controls the list is read through; null without a `SPATIAL_DATA_PORT`. */
+    controls: ISpatialControls | null;
+    /** In spatial 3D: the list is of the whole volume. */
+    is3d: boolean;
+    /** Expanded: the list is counted and shown. */
+    protected expanded: boolean;
+    /** The selection's transcripts by gene (null until the first answer). */
+    protected list: TranscriptsInSelection | null;
+    private sub;
+    constructor(zone: NgZone, cdr: ChangeDetectorRef);
+    ngOnChanges(changes: SimpleChanges): void;
+    ngOnDestroy(): void;
+    /** Whether there is a list to offer: the controls count transcripts. */
+    protected get available(): boolean;
+    /** The largest gene count, for the bars. */
+    protected get max(): number;
+    protected toggle(): void;
+    /** Subscribe while expanded, else not (a collapsed list reads nothing). */
+    private watch;
+    /** The list as tab-separated text (gene, count), for a spreadsheet. */
+    protected copy(): void;
+    protected trackGene(_i: number, g: {
+        name: string;
+    }): string;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SpatialSelectionTranscriptsComponent, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialSelectionTranscriptsComponent, "spatial-selection-transcripts", never, { "controls": { "alias": "controls"; "required": false; }; "is3d": { "alias": "is3d"; "required": false; }; }, {}, never, never, true, never>;
+}

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

@@ -29,6 +29,8 @@ export declare class SpatialTranscriptsPanelComponent implements OnChanges {
     controls: ISpatialControls | null;
     /** The dataset on offer, or null. */
     dataset: SpatialDataset | null;
+    /** In spatial 3D (the transcripts in selection are then the whole volume's). */
+    is3d: boolean;
     /** The current spatial view state: what is drawn, and how. */
     view: SpatialViewState;
     /** The gene list the transcript genes are picked from, shared with the other gene dropdowns. */
@@ -150,5 +152,5 @@ export declare class SpatialTranscriptsPanelComponent implements OnChanges {
     /** '⋮' menu. */
     private buildGeneMenu;
     static ɵfac: i0.ɵɵFactoryDeclaration<SpatialTranscriptsPanelComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialTranscriptsPanelComponent, "spatial-transcripts-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "view": { "alias": "view"; "required": false; }; "genes": { "alias": "genes"; "required": false; }; "estimate": { "alias": "estimate"; "required": false; }; "densityStats": { "alias": "densityStats"; "required": false; }; "geneCounts": { "alias": "geneCounts"; "required": false; }; "colormapOptions": { "alias": "colormapOptions"; "required": false; }; "open": { "alias": "open"; "required": false; }; }, { "openChange": "openChange"; }, never, never, true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialTranscriptsPanelComponent, "spatial-transcripts-panel", never, { "controls": { "alias": "controls"; "required": false; }; "dataset": { "alias": "dataset"; "required": false; }; "is3d": { "alias": "is3d"; "required": false; }; "view": { "alias": "view"; "required": false; }; "genes": { "alias": "genes"; "required": false; }; "estimate": { "alias": "estimate"; "required": false; }; "densityStats": { "alias": "densityStats"; "required": false; }; "geneCounts": { "alias": "geneCounts"; "required": false; }; "colormapOptions": { "alias": "colormapOptions"; "required": false; }; "open": { "alias": "open"; "required": false; }; }, { "openChange": "openChange"; }, never, never, true, never>;
 }

package/lib/store/region-source-scope.d.ts

@@ -51,6 +51,10 @@ export declare class RegionSourceScope {
     slicesWithSource(image: string | undefined): number[];
     /** Whether `image` has one source over all its slices. */
     hasPlanesSource(image: string | undefined): boolean;
+    /** The opener of `image`'s source over all its slices (as attached), or null without one. */
+    planesOpener(image: string | undefined): RegionSourceOpener | null;
+    /** Whether `image` has any source: one over all its slices, or one of a slice's own. */
+    hasAny(image: string | undefined): boolean;
     /**
      * The source behind `slice` of `image`, opening it if needed. Resolves null when there is
      * none, and rejects when it cannot be opened.

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

@@ -92,6 +92,8 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
      */
     private readonly sources;
     private readonly sourceView$;
+    /** Whether the overlays draw the source (see setRegionSourceDrawn). */
+    private readonly sourceDrawn$;
     /** The region look the user chose (overrides the source's hint), field by field. */
     private userStyle;
     /** The current source's style hint. */
@@ -355,10 +357,29 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
     dropSliceRegionSource(): Promise<void>;
     /** Whether the slice shown has a region source. */
     hasRegionSource(): boolean;
+    /** Whether the current image has any region source, over all its slices or a slice's own. */
+    hasAnyRegionSource(): boolean;
+    /**
+     * The opener of the current image's source over all its slices, as attached (see
+     * {@link attachRegionSource}), or null without one: tells whose source it still is.
+     */
+    getPlanesSourceOpener(): RegionSourceOpener | null;
     /** The slice's region source as a source layer draws it; null without one (or until it opens). */
     getRegionSourceView(): RegionSourceView | null;
     /** {@link getRegionSourceView} and every change of it (slice, taken ids, class colours). */
     getRegionSourceView$(): Observable<RegionSourceView | null>;
+    /**
+     * The source view the overlays draw: {@link getRegionSourceView$}, or null while the source is
+     * drawn by another layer instead (see {@link setRegionSourceDrawn}). The Region Editor's list
+     * and the source's other uses keep reading the source itself.
+     */
+    getDrawnRegionSourceView$(): Observable<RegionSourceView | null>;
+    /**
+     * Whether the overlays draw the region source (default), or leave it to another layer that draws
+     * the same outlines (the 2D spatial view's cells, from a 3D segmentation's region set), so they
+     * are not drawn twice. Only the drawing: the source stays attached, listed and editable.
+     */
+    setRegionSourceDrawn(drawn: boolean): void;
     /**
      * Take source features into the working set for editing: their exact geometry becomes
      * ordinary regions (minted, coloured and slice-tagged as any region entering the store) and

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

@@ -41,6 +41,11 @@ export declare class ToolbarComponent {
     isoRange: number[];
     /** The last slice index of a stack. */
     maxIndex: number;
+    /**
+     * The image is one plane, but a spatial dataset's region set slices it into planes: the live
+     * views offer the slider over them ({@link maxIndex} is the last plane), as over a stack.
+     */
+    planeSlices: boolean;
     /** The current slice (0-based). */
     zIndex: number;
     /** True for any 2D (non Surface-3D) plot type. */
@@ -231,5 +236,5 @@ export declare class ToolbarComponent {
     protected get isIntensityCapable(): boolean;
     protected showHelp(): void;
     static ɵfac: i0.ɵɵFactoryDeclaration<ToolbarComponent, never>;
-    static ɵcmp: i0.ɵɵComponentDeclaration<ToolbarComponent, "plotting-toolbar", never, { "imageInfo": { "alias": "imageInfo"; "required": false; }; "hasSpatialDataset": { "alias": "hasSpatialDataset"; "required": false; }; "plotTypeOptions": { "alias": "plotTypeOptions"; "required": false; }; "selectedPlotType": { "alias": "selectedPlotType"; "required": false; }; "basePlotType": { "alias": "basePlotType"; "required": false; }; "isoRange": { "alias": "isoRange"; "required": false; }; "maxIndex": { "alias": "maxIndex"; "required": false; }; "zIndex": { "alias": "zIndex"; "required": false; }; "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "is3dRegions": { "alias": "is3dRegions"; "required": false; }; "isVolumeView": { "alias": "isVolumeView"; "required": false; }; "sliceEditor": { "alias": "sliceEditor"; "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; }; "dialogTools": { "alias": "dialogTools"; "required": false; }; "openDialogToolId": { "alias": "openDialogToolId"; "required": false; }; "toolModelIds": { "alias": "toolModelIds"; "required": false; }; }, { "selectPlotType": "selectPlotType"; "addProfileLine": "addProfileLine"; "toggleImageSmoothing": "toggleImageSmoothing"; "isoRangeChange": "isoRangeChange"; "openChannelHistogram": "openChannelHistogram"; "openSpatialControls": "openSpatialControls"; "openRegionEditor": "openRegionEditor"; "toggleSliceEditor": "toggleSliceEditor"; "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"; "toggleDialogTool": "toggleDialogTool"; "toolModelChange": "toolModelChange"; "openToolParams": "openToolParams"; "samModelChange": "samModelChange"; "wandSensitivityChange": "wandSensitivityChange"; "brushSizeChange": "brushSizeChange"; "vertexEraserRadiusChange": "vertexEraserRadiusChange"; }, never, ["*"], true, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<ToolbarComponent, "plotting-toolbar", never, { "imageInfo": { "alias": "imageInfo"; "required": false; }; "hasSpatialDataset": { "alias": "hasSpatialDataset"; "required": false; }; "plotTypeOptions": { "alias": "plotTypeOptions"; "required": false; }; "selectedPlotType": { "alias": "selectedPlotType"; "required": false; }; "basePlotType": { "alias": "basePlotType"; "required": false; }; "isoRange": { "alias": "isoRange"; "required": false; }; "maxIndex": { "alias": "maxIndex"; "required": false; }; "planeSlices": { "alias": "planeSlices"; "required": false; }; "zIndex": { "alias": "zIndex"; "required": false; }; "isHeatmap": { "alias": "isHeatmap"; "required": false; }; "is3dRegions": { "alias": "is3dRegions"; "required": false; }; "isVolumeView": { "alias": "isVolumeView"; "required": false; }; "sliceEditor": { "alias": "sliceEditor"; "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; }; "dialogTools": { "alias": "dialogTools"; "required": false; }; "openDialogToolId": { "alias": "openDialogToolId"; "required": false; }; "toolModelIds": { "alias": "toolModelIds"; "required": false; }; }, { "selectPlotType": "selectPlotType"; "addProfileLine": "addProfileLine"; "toggleImageSmoothing": "toggleImageSmoothing"; "isoRangeChange": "isoRangeChange"; "openChannelHistogram": "openChannelHistogram"; "openSpatialControls": "openSpatialControls"; "openRegionEditor": "openRegionEditor"; "toggleSliceEditor": "toggleSliceEditor"; "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"; "toggleDialogTool": "toggleDialogTool"; "toolModelChange": "toolModelChange"; "openToolParams": "openToolParams"; "samModelChange": "samModelChange"; "wandSensitivityChange": "wandSensitivityChange"; "brushSizeChange": "brushSizeChange"; "vertexEraserRadiusChange": "vertexEraserRadiusChange"; }, never, ["*"], true, never>;
 }

package/lib/visualizer/spatial-region-set.d.ts

@@ -0,0 +1,55 @@
+import { Observable } from 'rxjs';
+import { IImageInfo } from '../contracts/image.contract';
+import { SpatialDataPort } from '../contracts/ports/spatial-data.port';
+import { SpatialDataset } from '../contracts/spatial-dataset.contract';
+import type { RegionSourceOpener } from '../store/region-source-scope';
+/** What {@link SpatialRegionSetLink} attaches a dataset's region set through (the router). */
+export interface DatasetRegionSetTarget {
+    attachDatasetRegionSet?(open: RegionSourceOpener, key: string): Promise<boolean>;
+    releaseDatasetRegionSet?(keep: string | null): void;
+}
+/**
+ * The region set a spatial dataset's boundaries name (a 3D segmentation's cells, see
+ * `SpatialPolygonTilesMeta.sets`): the default set's when it names one, else the first that does.
+ */
+export declare function datasetRegionSet(dataset: SpatialDataset | null | undefined): string | null;
+/**
+ * Whether `info` is the dataset's own image, the one its `imageRef` names. Exactly, when the host
+ * gives the image's id ({@link IImageInfo.imageId}); otherwise by the file name the id ends in (the
+ * host opens the image by that id, a path), which images of other datasets can share: then the link
+ * only takes an image that landed after the dataset was selected (see {@link SpatialRegionSetLink}).
+ * Not the reference volume's stack, which a dataset without an `imageRef` is drawn over: the region
+ * set's coordinates are not its pixels.
+ */
+export declare function isDatasetImage(info: IImageInfo | null | undefined, dataset: SpatialDataset | null | undefined): boolean;
+/**
+ * Attaches a spatial dataset's region set to its image in the region editor, once both are there:
+ * the dataset (the port's) and its image, landed. Each time either changes it asks again; the
+ * target attaches once per image and set.
+ *
+ * An image that landed while another dataset was selected is not taken for this one by its file name,
+ * only by its id ({@link IImageInfo.imageId}): a host selects the dataset and then opens its image,
+ * and until that lands the image on screen is the previous dataset's, though its file name may be the
+ * same (every converted bundle's is `plate.ome.tif`). One that landed with no dataset selected may be.
+ */
+export declare class SpatialRegionSetLink {
+    private readonly port;
+    private readonly target;
+    private dataset;
+    private image;
+    /** The dataset selected when the image landed (its id), or null: none was. */
+    private imageDataset;
+    /** The region set last asked to be attached, until the dataset stops naming it. */
+    private asked;
+    constructor(port: SpatialDataPort | undefined, target: DatasetRegionSetTarget);
+    /** Follow the port's dataset until `until$` emits. */
+    bind(until$: Observable<unknown>): void;
+    /** An image landed (its render settled): the dataset's own, perhaps. */
+    imageLanded(info: IImageInfo): void;
+    /**
+     * Whether the landed image may be the dataset's: by its id when the host gives one, else only when
+     * it landed under this dataset or under none (see the class's note).
+     */
+    private imageOf;
+    private sync;
+}

package/lib/visualizer.component.d.ts

@@ -122,6 +122,11 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     private readonly consumedSliceHints;
     protected zIndex: number;
     protected maxIndex: number;
+    /**
+     * Planes of the spatial dataset's region set slicing the image, an image of one plane (see
+     * `IVisualizer.getDatasetPlanes$`): the slider then runs over them. 0 without.
+     */
+    protected datasetPlanes: number;
     contextMenu: ContextMenu;
     protected contextMenuItems: MenuItem[];
     /** The armed tool mode and the toolbar's tool settings. */
@@ -285,6 +290,8 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     protected isoRange: number[];
     /** The spatial-omics dataset on offer and the gates it puts on the selector. */
     protected readonly spatial: SpatialDatasetBinder;
+    /** Attaches a spatial dataset's region set (a 3D segmentation's cells) to its image's regions. */
+    private readonly regionSetLink;
     /** Whether a spatial-omics dataset is published on `SPATIAL_DATA_PORT` — gates the
      *  spatial plot types; the toolbar offers the plot modes for an image-less one too. */
     protected get hasSpatialDataset(): boolean;
@@ -298,6 +305,13 @@ export declare class VisualizerComponent implements OnInit, OnChanges, AfterView
     /** Follow the spatial-omics dataset: a dataset appearing, switching or being cleared
      *  re-gates the selector exactly as the image stream and the test-mode toggle do. */
     private watchSpatialDataset;
+    /**
+     * The slider over the dataset's planes, on an image of one plane: its bounds are the planes'
+     * (none left: back to the image's one), the slice kept within them.
+     */
+    private layOutPlanes;
+    /** The last slice index the dataset's planes give an image of one plane (0 without). */
+    private planeMaxIndex;
     /** Recompute the selector's entries for the current image, dataset and test mode
      *  (see {@link computePlotTypeMenu}). */
     private computePlotTypeOptions;