@vitessce/neuroglancer 3.9.6 → 3.9.8

package/dist-tsc/data-hook-ng-utils.js

@@ -88,7 +88,7 @@ export function toNgLayerName(dataType, layerScope, channelScope = null) {
 /**
  * @returns [viewerState]
  */
-export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentationChannelScopesByLayer, segmentationLayerCoordination, segmentationChannelCoordination, obsSegmentationsUrls, obsSegmentationsData, pointLayerScopes, pointLayerCoordination, obsPointsUrls, obsPointsData, pointMultiIndicesData) {
+export function useNeuroglancerViewerState(theme, showAxisLines, segmentationLayerScopes, segmentationChannelScopesByLayer, segmentationLayerCoordination, segmentationChannelCoordination, obsSegmentationsUrls, obsSegmentationsData, pointLayerScopes, pointLayerCoordination, obsPointsUrls, obsPointsData, pointMultiIndicesData) {
     const viewerState = useMemoCustomComparison(() => {
         let result = cloneDeep(DEFAULT_NG_PROPS);
         // ======= SEGMENTATIONS =======
@@ -103,20 +103,32 @@ export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segme
                 channelScopes.forEach((channelScope) => {
                     const channelCoordination = segmentationChannelCoordination[0]?.[layerScope]?.[channelScope];
                     const { spatialChannelVisible, } = channelCoordination || {};
+                    const { source: ngSource, ...otherNgOptions } = layerData.neuroglancerOptions ?? {};
+                    // Build source: if neuroglancerOptions has subsources
+                    const hasNgSourceOptions = layerData.neuroglancerOptions?.subsources
+                        || layerData.neuroglancerOptions?.enableDefaultSubsources !== undefined;
+                    const source = hasNgSourceOptions
+                        ? {
+                            url: toPrecomputedSource(layerUrl),
+                            subsources: layerData.neuroglancerOptions.subsources,
+                            enableDefaultSubsources: layerData.neuroglancerOptions.enableDefaultSubsources
+                                ?? false,
+                        }
+                        : toPrecomputedSource(layerUrl);
                     result = {
                         ...result,
                         layers: [
                             ...result.layers,
                             {
                                 type: 'segmentation',
-                                source: toPrecomputedSource(layerUrl),
+                                source,
                                 segments: [],
                                 name: toNgLayerName(DataType.OBS_SEGMENTATIONS, layerScope, channelScope),
                                 visible: spatialLayerVisible && spatialChannelVisible, // Both layer and channel
                                 // visibility must be true for the layer to be visible.
                                 // TODO: update this to extract specific properties from
                                 // neuroglancerOptions as needed.
-                                ...(layerData.neuroglancerOptions ?? {}),
+                                ...otherNgOptions,
                             },
                         ],
                     };
@@ -131,7 +143,7 @@ export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segme
             const layerUrl = obsPointsUrls[layerScope]?.[0]?.url;
             const featureIndex = pointMultiIndicesData[layerScope]?.featureIndex;
             if (layerUrl && layerData) {
-                const { spatialLayerVisible, spatialLayerOpacity, obsColorEncoding, spatialLayerColor, featureSelection, featureFilterMode, featureColor, } = layerCoordination || {};
+                const { spatialLayerVisible, spatialLayerOpacity, obsColorEncoding, spatialLayerColor, featureSelection, featureFilterMode, featureColor, spatialPointStrokeWidth, } = layerCoordination || {};
                 // Dynamically construct the shader based on the color encoding
                 // and other coordination values.
                 const shader = getPointsShader({
@@ -145,6 +157,7 @@ export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segme
                     featureColor,
                     featureIndexProp: layerData.neuroglancerOptions?.featureIndexProp,
                     pointIndexProp: layerData.neuroglancerOptions?.pointIndexProp,
+                    pointMarkerBorderWidth: spatialPointStrokeWidth ?? 0.0,
                 });
                 result = {
                     ...result,
@@ -182,6 +195,7 @@ export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segme
         return result;
     }, {
         theme,
+        showAxisLines,
         segmentationLayerScopes,
         segmentationChannelScopesByLayer,
         segmentationLayerCoordination,

package/dist-tsc/shader-utils.d.ts

@@ -5,7 +5,7 @@
  * @param {number} opacity Opacity (0-1).
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorShader(staticColor: [number, number, number], opacity: number): string;
+export function getSpatialLayerColorShader(staticColor: [number, number, number], opacity: number, borderWidth?: number): string;
 /**
  * Generate a shader for spatialLayerColor encoding with feature selection.
  * Selected features get the static color; unselected get the default color.
@@ -16,7 +16,7 @@ export function getSpatialLayerColorShader(staticColor: [number, number, number]
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorWithSelectionShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], defaultColor: [number, number, number], featureIndexProp: string): string;
+export function getSpatialLayerColorWithSelectionShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], defaultColor: [number, number, number], featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for spatialLayerColor encoding with feature selection
  * and featureFilterMode='featureSelection' (hide unselected points).
@@ -26,7 +26,7 @@ export function getSpatialLayerColorWithSelectionShader(staticColor: [number, nu
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorFilteredShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], featureIndexProp: string): string;
+export function getSpatialLayerColorFilteredShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for geneSelection encoding with no feature selection.
  * All points get the static color (since no features are selected to
@@ -35,7 +35,7 @@ export function getSpatialLayerColorFilteredShader(staticColor: [number, number,
  * @param {number} opacity Opacity (0-1).
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionNoSelectionShader(staticColor: [number, number, number], opacity: number): string;
+export function getGeneSelectionNoSelectionShader(staticColor: [number, number, number], opacity: number, borderWidth?: number): string;
 /**
  * Generate a shader for geneSelection encoding with feature selection.
  * Each selected feature gets its color from featureColor; unselected
@@ -51,7 +51,7 @@ export function getGeneSelectionNoSelectionShader(staticColor: [number, number,
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionWithSelectionShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], defaultColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+export function getGeneSelectionWithSelectionShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], defaultColor: [number, number, number], opacity: number, featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for geneSelection encoding with feature selection
  * and featureFilterMode='featureSelection' (hide unselected points).
@@ -63,7 +63,7 @@ export function getGeneSelectionWithSelectionShader(featureIndices: number[], fe
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionFilteredShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+export function getGeneSelectionFilteredShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], opacity: number, featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for randomByFeature encoding with no feature selection.
  * Each feature gets a deterministic color from PALETTE based on its index.
@@ -71,7 +71,7 @@ export function getGeneSelectionFilteredShader(featureIndices: number[], feature
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureShader(opacity: number, featureIndexProp: string): string;
+export function getRandomByFeatureShader(opacity: number, featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for randomByFeature encoding with feature selection.
  * Selected features get their deterministic palette color; unselected
@@ -82,7 +82,7 @@ export function getRandomByFeatureShader(opacity: number, featureIndexProp: stri
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+export function getRandomByFeatureWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for randomByFeature encoding with feature selection
  * and featureFilterMode='featureSelection' (hide unselected points).
@@ -91,7 +91,7 @@ export function getRandomByFeatureWithSelectionShader(featureIndices: number[],
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string): string;
+export function getRandomByFeatureFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for random-per-point encoding with no feature selection.
  * Each point gets a pseudo-random color based on its index.
@@ -100,7 +100,7 @@ export function getRandomByFeatureFilteredShader(featureIndices: number[], opaci
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointShader(opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+export function getRandomPerPointShader(opacity: number, featureIndexProp: string, pointIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for random-per-point encoding with feature selection.
  * Selected points get a pseudo-random color; unselected get the default color.
@@ -111,7 +111,7 @@ export function getRandomPerPointShader(opacity: number, featureIndexProp: strin
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+export function getRandomPerPointWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string, pointIndexProp: string, borderWidth?: number): string;
 /**
  * Generate a shader for random-per-point encoding with feature selection
  * and featureFilterMode='featureSelection' (hide unselected points).
@@ -121,6 +121,6 @@ export function getRandomPerPointWithSelectionShader(featureIndices: number[], d
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+export function getRandomPerPointFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string, pointIndexProp: string, borderWidth?: number): string;
 export function getPointsShader(layerCoordination: any): string;
 //# sourceMappingURL=shader-utils.d.ts.map

package/dist-tsc/shader-utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"shader-utils.d.ts","sourceRoot":"","sources":["../src/shader-utils.js"],"names":[],"mappings":"AAwCA;;;;;;GAMG;AACH,wDAJW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,GACJ,MAAM,CAUlB;AAGD;;;;;;;;;GASG;AACH,qEAPW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,kBACN,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,oBACxB,MAAM,GACJ,MAAM,CA4BlB;AAGD;;;;;;;;GAQG;AACH,gEANW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,kBACN,MAAM,EAAE,oBACR,MAAM,GACJ,MAAM,CA0BlB;AAMD;;;;;;;GAOG;AACH,+DAJW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,GACJ,MAAM,CAUlB;AAED;;;;;;;;;;;;;;GAcG;AACH,oEAXW,MAAM,EAAE,iBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,eAE1B,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,gBAExB,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WAExB,MAAM,oBACN,MAAM,GACJ,MAAM,CA+BlB;AAED;;;;;;;;;;GAUG;AACH,+DARW,MAAM,EAAE,iBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,eAE1B,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,GACJ,MAAM,CAoClB;AAMD;;;;;;GAMG;AACH,kDAJW,MAAM,oBACN,MAAM,GACJ,MAAM,CAkBlB;AAED;;;;;;;;;GASG;AACH,sEANW,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,GACJ,MAAM,CAkClB;AAED;;;;;;;GAOG;AACH,iEALW,MAAM,EAAE,WACR,MAAM,oBACN,MAAM,GACJ,MAAM,CA8BlB;AAuBD;;;;;;;GAOG;AACH,iDALW,MAAM,oBACN,MAAM,kBACN,MAAM,GACJ,MAAM,CAelB;AAED;;;;;;;;;GASG;AACH,qEAPW,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,kBACN,MAAM,GACJ,MAAM,CAgClB;AAED;;;;;;;;GAQG;AACH,gEANW,MAAM,EAAE,WACR,MAAM,oBACN,MAAM,kBACN,MAAM,GACJ,MAAM,CA8BlB;AAGD,gEAwKC"}
+{"version":3,"file":"shader-utils.d.ts","sourceRoot":"","sources":["../src/shader-utils.js"],"names":[],"mappings":"AAoDA;;;;;;GAMG;AACH,wDAJW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,yBACJ,MAAM,CAWlB;AAGD;;;;;;;;;GASG;AACH,qEAPW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,kBACN,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,oBACxB,MAAM,yBACJ,MAAM,CA8BlB;AAGD;;;;;;;;GAQG;AACH,gEANW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,kBACN,MAAM,EAAE,oBACR,MAAM,yBACJ,MAAM,CA2BlB;AAMD;;;;;;;GAOG;AACH,+DAJW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,yBACJ,MAAM,CAWlB;AAED;;;;;;;;;;;;;;GAcG;AACH,oEAXW,MAAM,EAAE,iBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,eAE1B,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,gBAExB,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WAExB,MAAM,oBACN,MAAM,yBACJ,MAAM,CAsClB;AAED;;;;;;;;;;GAUG;AACH,+DARW,MAAM,EAAE,iBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,eAE1B,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,yBACJ,MAAM,CAqClB;AAMD;;;;;;GAMG;AACH,kDAJW,MAAM,oBACN,MAAM,yBACJ,MAAM,CAmBlB;AAED;;;;;;;;;GASG;AACH,sEANW,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,yBACJ,MAAM,CAoClB;AAED;;;;;;;GAOG;AACH,iEALW,MAAM,EAAE,WACR,MAAM,oBACN,MAAM,yBACJ,MAAM,CAoClB;AAuBD;;;;;;;GAOG;AACH,iDALW,MAAM,oBACN,MAAM,kBACN,MAAM,yBACJ,MAAM,CAqBlB;AAED;;;;;;;;;GASG;AACH,qEAPW,MAAM,EAAE,gBACR,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,WACxB,MAAM,oBACN,MAAM,kBACN,MAAM,yBACJ,MAAM,CAkClB;AAED;;;;;;;;GAQG;AACH,gEANW,MAAM,EAAE,WACR,MAAM,oBACN,MAAM,kBACN,MAAM,yBACJ,MAAM,CA+BlB;AAGD,gEAkLC"}

package/dist-tsc/shader-utils.js

@@ -12,6 +12,16 @@ import { PALETTE, getDefaultColor } from '@vitessce/utils';
 function normalizeColor(rgbColor) {
     return rgbColor.map(c => c / 255);
 }
+/**
+ * GLSL call to set point marker border width.
+ * Set to 0.0 to remove the outline.
+ * @param {number} borderWidth
+ * @returns {string}
+ */
+function borderWidthGlsl(borderWidth = 0.0) {
+    // must be decimal/float value
+    return `setPointMarkerBorderWidth(${borderWidth.toFixed(1)});`;
+}
 /**
  * Format a normalized color as a GLSL vec3 literal.
  * @param {[number, number, number]} normalizedColor
@@ -39,12 +49,13 @@ function toVec4(normalizedColor, alpha) {
  * @param {number} opacity Opacity (0-1).
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorShader(staticColor, opacity) {
+export function getSpatialLayerColorShader(staticColor, opacity, borderWidth = 0.0) {
     const norm = normalizeColor(staticColor);
     // lang: glsl
     return `
         void main() {
             setColor(${toVec4(norm, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -58,7 +69,7 @@ export function getSpatialLayerColorShader(staticColor, opacity) {
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp) {
+export function getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp, borderWidth = 0.0) {
     const normStatic = normalizeColor(staticColor);
     const normDefault = normalizeColor(defaultColor);
     const numFeatures = featureIndices.length;
@@ -76,8 +87,10 @@ export function getSpatialLayerColorWithSelectionShader(staticColor, opacity, fe
             }
             if (isSelected) {
                 setColor(${toVec4(normStatic, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             } else {
                 setColor(${toVec4(normDefault, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             }
         }
     `;
@@ -91,7 +104,7 @@ export function getSpatialLayerColorWithSelectionShader(staticColor, opacity, fe
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp) {
+export function getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp, borderWidth = 0.0) {
     const normStatic = normalizeColor(staticColor);
     const numFeatures = featureIndices.length;
     const indicesArr = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(', ')});`;
@@ -110,6 +123,7 @@ export function getSpatialLayerColorFilteredShader(staticColor, opacity, feature
                 discard;
             }
             setColor(${toVec4(normStatic, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -124,12 +138,13 @@ export function getSpatialLayerColorFilteredShader(staticColor, opacity, feature
  * @param {number} opacity Opacity (0-1).
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionNoSelectionShader(staticColor, opacity) {
+export function getGeneSelectionNoSelectionShader(staticColor, opacity, borderWidth = 0.0) {
     const norm = normalizeColor(staticColor);
     // lang: glsl
     return `
         void main() {
             setColor(${toVec4(norm, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -148,7 +163,7 @@ export function getGeneSelectionNoSelectionShader(staticColor, opacity) {
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionWithSelectionShader(featureIndices, featureColors, staticColor, defaultColor, opacity, featureIndexProp) {
+export function getGeneSelectionWithSelectionShader(featureIndices, featureColors, staticColor, defaultColor, opacity, featureIndexProp, borderWidth = 0.0) {
     const numFeatures = featureIndices.length;
     const normDefault = normalizeColor(defaultColor);
     const normColors = featureColors.map(c => normalizeColor(c));
@@ -169,6 +184,7 @@ export function getGeneSelectionWithSelectionShader(featureIndices, featureColor
                 }
             }
             setColor(color);
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -183,7 +199,7 @@ export function getGeneSelectionWithSelectionShader(featureIndices, featureColor
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getGeneSelectionFilteredShader(featureIndices, featureColors, staticColor, opacity, featureIndexProp) {
+export function getGeneSelectionFilteredShader(featureIndices, featureColors, staticColor, opacity, featureIndexProp, borderWidth = 0.0) {
     const numFeatures = featureIndices.length;
     const normColors = featureColors.map(c => normalizeColor(c));
     const normStatic = normalizeColor(staticColor);
@@ -208,6 +224,7 @@ export function getGeneSelectionFilteredShader(featureIndices, featureColors, st
                 discard;
             }
             setColor(vec4(matchedColor, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -221,7 +238,7 @@ export function getGeneSelectionFilteredShader(featureIndices, featureColors, st
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureShader(opacity, featureIndexProp) {
+export function getRandomByFeatureShader(opacity, featureIndexProp, borderWidth = 0.0) {
     const paletteSize = PALETTE.length;
     const normPalette = PALETTE.map(c => normalizeColor(c));
     const paletteDecl = `vec3 palette[${paletteSize}] = vec3[${paletteSize}](${normPalette.map(c => toVec3(c)).join(', ')});`;
@@ -234,6 +251,7 @@ export function getRandomByFeatureShader(opacity, featureIndexProp) {
             if (colorIdx < 0) { colorIdx = -colorIdx; }
             vec3 color = palette[colorIdx];
             setColor(vec4(color, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -247,7 +265,7 @@ export function getRandomByFeatureShader(opacity, featureIndexProp) {
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp) {
+export function getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, borderWidth = 0.0) {
     const paletteSize = PALETTE.length;
     const normPalette = PALETTE.map(c => normalizeColor(c));
     const normDefault = normalizeColor(defaultColor);
@@ -270,8 +288,10 @@ export function getRandomByFeatureWithSelectionShader(featureIndices, defaultCol
                 int colorIdx = geneIndex - (geneIndex / ${paletteSize}) * ${paletteSize};
                 if (colorIdx < 0) { colorIdx = -colorIdx; }
                 setColor(vec4(palette[colorIdx], ${opacity}));
+                ${borderWidthGlsl(borderWidth)}
             } else {
                 setColor(${toVec4(normDefault, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             }
         }
     `;
@@ -284,7 +304,7 @@ export function getRandomByFeatureWithSelectionShader(featureIndices, defaultCol
  * @param {string} featureIndexProp The property name for the feature index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp) {
+export function getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp, borderWidth = 0.0) {
     const paletteSize = PALETTE.length;
     const normPalette = PALETTE.map(c => normalizeColor(c));
     const numFeatures = featureIndices.length;
@@ -308,6 +328,7 @@ export function getRandomByFeatureFilteredShader(featureIndices, opacity, featur
             int colorIdx = geneIndex - (geneIndex / ${paletteSize}) * ${paletteSize};
             if (colorIdx < 0) { colorIdx = -colorIdx; }
             setColor(vec4(palette[colorIdx], ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -338,7 +359,7 @@ function hashToFloatGlsl() {
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp) {
+export function getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp, borderWidth = 0.0) {
     // lang: glsl
     return `
         ${hashToFloatGlsl()}
@@ -349,6 +370,7 @@ export function getRandomPerPointShader(opacity, featureIndexProp, pointIndexPro
             float g = hashToFloat(pointIndex, 1);
             float b = hashToFloat(pointIndex, 2);
             setColor(vec4(r, g, b, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -362,7 +384,7 @@ export function getRandomPerPointShader(opacity, featureIndexProp, pointIndexPro
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp) {
+export function getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp, borderWidth = 0.0) {
     const normDefault = normalizeColor(defaultColor);
     const numFeatures = featureIndices.length;
     const indicesDecl = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(', ')});`;
@@ -384,8 +406,10 @@ export function getRandomPerPointWithSelectionShader(featureIndices, defaultColo
                 float g = hashToFloat(pointIndex, 1);
                 float b = hashToFloat(pointIndex, 2);
                 setColor(vec4(r, g, b, ${opacity}));
+                ${borderWidthGlsl(borderWidth)}
             } else {
                 setColor(${toVec4(normDefault, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             }
         }
     `;
@@ -399,7 +423,7 @@ export function getRandomPerPointWithSelectionShader(featureIndices, defaultColo
  * @param {string} pointIndexProp The property name for the point index in the shader.
  * @returns {string} A GLSL shader string.
  */
-export function getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp) {
+export function getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp, borderWidth = 0.0) {
     const numFeatures = featureIndices.length;
     const indicesDecl = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(', ')});`;
     // lang: glsl
@@ -422,11 +446,12 @@ export function getRandomPerPointFilteredShader(featureIndices, opacity, feature
             float g = hashToFloat(pointIndex, 1);
             float b = hashToFloat(pointIndex, 2);
             setColor(vec4(r, g, b, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
 export function getPointsShader(layerCoordination) {
-    const { theme, featureIndex, spatialLayerOpacity, obsColorEncoding, spatialLayerColor, featureSelection, featureFilterMode, featureColor, featureIndexProp, pointIndexProp, } = layerCoordination;
+    const { theme, featureIndex, spatialLayerOpacity, obsColorEncoding, spatialLayerColor, featureSelection, featureFilterMode, featureColor, pointMarkerBorderWidth = 0.0, featureIndexProp, pointIndexProp, } = layerCoordination;
     const defaultColor = getDefaultColor(theme);
     const opacity = spatialLayerOpacity ?? 1.0;
     const staticColor = (Array.isArray(spatialLayerColor) && spatialLayerColor.length === 3
@@ -496,12 +521,12 @@ export function getPointsShader(layerCoordination) {
     // ---- spatialLayerColor ----
     if (obsColorEncoding === 'spatialLayerColor') {
         if (!hasFeatureSelection || !hasResolvedIndices) {
-            return getSpatialLayerColorShader(staticColor, opacity);
+            return getSpatialLayerColorShader(staticColor, opacity, pointMarkerBorderWidth);
         }
         if (isFiltered) {
-            return getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp);
+            return getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp, pointMarkerBorderWidth);
         }
-        return getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp);
+        return getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp, pointMarkerBorderWidth);
     }
     // ---- geneSelection ----
     if (obsColorEncoding === 'geneSelection') {
@@ -509,12 +534,12 @@ export function getPointsShader(layerCoordination) {
             throw new Error('In order to use gene-based color encoding for Neuroglancer Points, options.featureIndexProp must be specified for the obsPoints.ng-annotations fileType in the Vitessce configuration.');
         }
         if (!hasFeatureSelection || !hasResolvedIndices) {
-            return getGeneSelectionNoSelectionShader(staticColor, opacity);
+            return getGeneSelectionNoSelectionShader(staticColor, opacity, pointMarkerBorderWidth);
         }
         if (isFiltered) {
-            return getGeneSelectionFilteredShader(featureIndices, resolvedFeatureColors, staticColor, opacity, featureIndexProp);
+            return getGeneSelectionFilteredShader(featureIndices, resolvedFeatureColors, staticColor, opacity, featureIndexProp, pointMarkerBorderWidth);
         }
-        return getGeneSelectionWithSelectionShader(featureIndices, resolvedFeatureColors, staticColor, defaultColor, opacity, featureIndexProp);
+        return getGeneSelectionWithSelectionShader(featureIndices, resolvedFeatureColors, staticColor, defaultColor, opacity, featureIndexProp, pointMarkerBorderWidth);
     }
     // ---- randomByFeature ----
     if (obsColorEncoding === 'randomByFeature') {
@@ -522,12 +547,12 @@ export function getPointsShader(layerCoordination) {
             throw new Error('In order to use gene-based color encoding for Neuroglancer Points, options.featureIndexProp must be specified for the obsPoints.ng-annotations fileType in the Vitessce configuration.');
         }
         if (!hasFeatureSelection || !hasResolvedIndices) {
-            return getRandomByFeatureShader(opacity, featureIndexProp);
+            return getRandomByFeatureShader(opacity, featureIndexProp, pointMarkerBorderWidth);
         }
         if (isFiltered) {
-            return getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp);
+            return getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp, pointMarkerBorderWidth);
         }
-        return getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp);
+        return getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointMarkerBorderWidth);
     }
     // ---- random (per point) ----
     if (obsColorEncoding === 'random') {
@@ -535,13 +560,13 @@ export function getPointsShader(layerCoordination) {
             throw new Error('In order to use per-point color encoding for Neuroglancer Points, options.pointIndexProp must be specified for the obsPoints.ng-annotations fileType in the Vitessce configuration.');
         }
         if (!hasFeatureSelection || !hasResolvedIndices) {
-            return getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp);
+            return getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp, pointMarkerBorderWidth);
         }
         if (isFiltered) {
-            return getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp);
+            return getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp, pointMarkerBorderWidth);
         }
-        return getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp);
+        return getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp, pointMarkerBorderWidth);
     }
     // Fallback: static color.
-    return getSpatialLayerColorShader(staticColor, opacity);
+    return getSpatialLayerColorShader(staticColor, opacity, pointMarkerBorderWidth);
 }

package/dist-tsc/shader-utils.test.js

@@ -29,6 +29,7 @@ describe('getSpatialLayerColorShader', () => {
         const expected = `
 void main() {
     setColor(vec4(1, 0.5019607843137255, 0, 0.8));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -38,6 +39,7 @@ void main() {
         const expected = `
 void main() {
     setColor(vec4(0, 0, 0, 0));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -47,6 +49,7 @@ void main() {
         const expected = `
 void main() {
     setColor(vec4(1, 1, 1, 1));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -67,8 +70,10 @@ void main() {
     }
     if (isSelected) {
         setColor(vec4(1, 0, 0, 0.5));
+        setPointMarkerBorderWidth(0.0);
     } else {
         setColor(vec4(0.5019607843137255, 0.5019607843137255, 0.5019607843137255, 0.5));
+        setPointMarkerBorderWidth(0.0);
     }
 }
 `;
@@ -88,8 +93,10 @@ void main() {
     }
     if (isSelected) {
         setColor(vec4(0, 1, 0, 1));
+        setPointMarkerBorderWidth(0.0);
     } else {
         setColor(vec4(0, 0, 0, 1));
+        setPointMarkerBorderWidth(0.0);
     }
 }
 `;
@@ -113,6 +120,7 @@ void main() {
         discard;
     }
     setColor(vec4(0, 0, 1, 0.9));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -127,6 +135,7 @@ describe('getGeneSelectionNoSelectionShader', () => {
         const expected = `
 void main() {
     setColor(vec4(0.39215686274509803, 0.7843137254901961, 0.19607843137254902, 0.7));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -147,6 +156,7 @@ void main() {
         }
     }
     setColor(color);
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -169,6 +179,7 @@ void main() {
         }
     }
     setColor(color);
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -194,6 +205,7 @@ void main() {
         discard;
     }
     setColor(vec4(matchedColor, 0.75));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -213,6 +225,7 @@ void main() {
     if (colorIdx < 0) { colorIdx = -colorIdx; }
     vec3 color = palette[colorIdx];
     setColor(vec4(color, 0.5));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -236,8 +249,10 @@ void main() {
         int colorIdx = geneIndex - (geneIndex / 3) * 3;
         if (colorIdx < 0) { colorIdx = -colorIdx; }
         setColor(vec4(palette[colorIdx], 0.8));
+        setPointMarkerBorderWidth(0.0);
     } else {
         setColor(vec4(0.19607843137254902, 0.19607843137254902, 0.19607843137254902, 0.8));
+        setPointMarkerBorderWidth(0.0);
     }
 }
 `;
@@ -264,6 +279,7 @@ void main() {
     int colorIdx = geneIndex - (geneIndex / 3) * 3;
     if (colorIdx < 0) { colorIdx = -colorIdx; }
     setColor(vec4(palette[colorIdx], 1));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -290,6 +306,7 @@ void main() {
     float g = hashToFloat(pointIndex, 1);
     float b = hashToFloat(pointIndex, 2);
     setColor(vec4(r, g, b, 0.9));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);
@@ -321,8 +338,10 @@ void main() {
         float g = hashToFloat(pointIndex, 1);
         float b = hashToFloat(pointIndex, 2);
         setColor(vec4(r, g, b, 0.5));
+        setPointMarkerBorderWidth(0.0);
     } else {
         setColor(vec4(0.39215686274509803, 0.39215686274509803, 0.39215686274509803, 0.5));
+        setPointMarkerBorderWidth(0.0);
     }
 }
 `;
@@ -357,6 +376,7 @@ void main() {
     float g = hashToFloat(pointIndex, 1);
     float b = hashToFloat(pointIndex, 2);
     setColor(vec4(r, g, b, 1));
+    setPointMarkerBorderWidth(0.0);
 }
 `;
         expectShaderEqual(result, expected);

package/dist-tsc/use-memo-custom-comparison.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"use-memo-custom-comparison.d.ts","sourceRoot":"","sources":["../src/use-memo-custom-comparison.js"],"names":[],"mappings":"AAIA;;;;;;;;;GASG;AACH,wCAPa,CAAC,WACH,MAAM,CAAC,gBACP,GAAG,iBACH,CAAC,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,KAAK,OAAO,GAEvC,CAAC,CAUb;AA6CD,kFA8CC;AAED,0FAyEC"}
+{"version":3,"file":"use-memo-custom-comparison.d.ts","sourceRoot":"","sources":["../src/use-memo-custom-comparison.js"],"names":[],"mappings":"AAIA;;;;;;;;;GASG;AACH,wCAPa,CAAC,WACH,MAAM,CAAC,gBACP,GAAG,iBACH,CAAC,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,KAAK,OAAO,GAEvC,CAAC,CAUb;AA6CD,kFAgDC;AAED,0FA8EC"}

package/dist-tsc/use-memo-custom-comparison.js

@@ -73,6 +73,8 @@ export function customIsEqualForCellColors(prevDeps, nextDeps) {
                         'obsColorEncoding',
                         'obsSetSelection',
                         'additionalObsSets',
+                        'spatialChannelColor',
+                        'spatialChannelOpacity',
                     ])) {
                     forceUpdate = true;
                 }
@@ -95,6 +97,9 @@ export function customIsEqualForInitialViewerState(prevDeps, nextDeps) {
     const curriedShallowDiffByLayerCoordinationWithKeys = (depName, layerScope, keys) => shallowDiffByLayerCoordinationWithKeys(prevDeps, nextDeps, depName, layerScope, keys);
     const curriedShallowDiffByChannelCoordination = (depName, layerScope, channelScope) => shallowDiffByChannelCoordination(prevDeps, nextDeps, depName, layerScope, channelScope);
     const curriedShallowDiffByChannelCoordinationWithKeys = (depName, layerScope, channelScope, keys) => shallowDiffByChannelCoordinationWithKeys(prevDeps, nextDeps, depName, layerScope, channelScope, keys);
+    if (['theme', 'showAxisLines'].some(curriedShallowDiff)) {
+        forceUpdate = true;
+    }
     // Segmentation layers/channels.
     if (['segmentationLayerScopes', 'segmentationChannelScopesByLayer'].some(curriedShallowDiff)) {
         // Force update for all layers since the layerScopes array changed.
@@ -135,6 +140,7 @@ export function customIsEqualForInitialViewerState(prevDeps, nextDeps) {
                     'featureSelection',
                     'featureFilterMode',
                     'featureColor',
+                    'spatialPointStrokeWidth',
                 ])
                 // For opacity, use an epsilon comparison to avoid too many re-renders, as it affects performance.
                 || (Math.abs(prevDeps?.pointLayerCoordination?.[0]?.[layerScope]?.spatialLayerOpacity - nextDeps?.pointLayerCoordination?.[0]?.[layerScope]?.spatialLayerOpacity)