@vitessce/neuroglancer 3.9.7 → 3.9.9

package/dist/{index-BEPd2Tds.js → index-anGvS-pL.js}

@@ -296,6 +296,7 @@ const CoordinationType$1 = {
   SPATIAL_LAYER_MODEL_MATRIX: "spatialLayerModelMatrix",
   SPATIAL_SEGMENTATION_FILLED: "spatialSegmentationFilled",
   SPATIAL_SEGMENTATION_STROKE_WIDTH: "spatialSegmentationStrokeWidth",
+  SPATIAL_POINT_STROKE_WIDTH: "spatialPointStrokeWidth",
   SPATIAL_CHANNEL_COLOR: "spatialChannelColor",
   SPATIAL_CHANNEL_VISIBLE: "spatialChannelVisible",
   SPATIAL_CHANNEL_OPACITY: "spatialChannelOpacity",
@@ -664,7 +665,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_CHANNEL_COLOR,
     CoordinationType$1.SPATIAL_CHANNEL_OPACITY,
     CoordinationType$1.SPATIAL_CHANNEL_VISIBLE,
-    CoordinationType$1.LEGEND_VISIBLE
+    CoordinationType$1.LEGEND_VISIBLE,
+    CoordinationType$1.SPATIAL_POINT_STROKE_WIDTH
   ],
   [ViewType$1.SCATTERPLOT]: [
     CoordinationType$1.DATASET,
@@ -1048,6 +1050,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_CHANNEL_COLOR,
     CoordinationType$1.SPATIAL_SEGMENTATION_FILLED,
     CoordinationType$1.SPATIAL_SEGMENTATION_STROKE_WIDTH,
+    CoordinationType$1.SPATIAL_POINT_STROKE_WIDTH,
     CoordinationType$1.IMAGE_CHANNEL,
     CoordinationType$1.IMAGE_LAYER,
     CoordinationType$1.SEGMENTATION_CHANNEL,
@@ -10630,6 +10633,8 @@ z.object({
   // projectionScale: z.number(),
   // position: z.array(z.number()).length(3),
   // projectionOrientation: z.array(z.number()).length(4),
+  subsources: z.record(z.boolean()).describe("Subsources are the individual data components of a source (e.g. meshes, skeletons, etc.). Each entry explicitly enables or disables a subsource.").optional(),
+  enableDefaultSubsources: z.boolean().describe("When true (default), automatically loads all subsources (defined in mesh metadata), when false loads what is explicitly enabled in `subsources`.").optional()
 }).partial().nullable();
 z.object({
   projectionAnnotationSpacing: z.number(),
@@ -31842,7 +31847,9 @@ function Legend(props) {
     isStaticColor,
     missing,
     showObsLabel,
-    staticColor
+    staticColor,
+    featureColor,
+    pointsLegendElements
   ]);
   const showInteractiveSlider = !isPointsLayer && setFeatureValueColormapRange && ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && pointsVisible && featureValueColormap;
   const globalExtent = useMemo(() => {
@@ -34680,7 +34687,7 @@ function NeuroglancerGlobalStyles(props) {
     }
   ));
 }
-const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-pv4bM8Yp.js"));
+const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-Bxe4YcLF.js"));
 function createWorker() {
   const worker = new WorkerFactory$1();
   worker.AsyncComputationWorker = WorkerFactory;
@@ -34752,13 +34759,14 @@ class NeuroglancerComp extends PureComponent {
     }
   }
   render() {
-    const { classes, viewerState, cellColorMapping } = this.props;
+    const { classes, viewerState, cellColorMapping, onLayerLoadingChange } = this.props;
     return /* @__PURE__ */ React__default.createElement(React__default.Fragment, null, /* @__PURE__ */ React__default.createElement(NeuroglancerGlobalStyles, { classes }), /* @__PURE__ */ React__default.createElement("div", { className: classes.neuroglancerWrapper }, /* @__PURE__ */ React__default.createElement(Suspense, { fallback: /* @__PURE__ */ React__default.createElement("div", null, "Loading...") }, /* @__PURE__ */ React__default.createElement(
       LazyReactNeuroglancer,
       {
         brainMapsClientId: "NOT_A_VALID_ID",
         viewerState,
         onViewerStateChanged: this.onViewerStateChanged,
+        onLayerLoadingChange,
         bundleRoot: this.bundleRoot,
         cellColorMapping,
         ref: this.onRef
@@ -34822,7 +34830,8 @@ function customIsEqualForCellColors(prevDeps, nextDeps) {
           "obsColorEncoding",
           "obsSetSelection",
           "additionalObsSets",
-          "spatialChannelColor"
+          "spatialChannelColor",
+          "spatialChannelOpacity"
         ])) {
           forceUpdate = true;
         }
@@ -34838,6 +34847,9 @@ function customIsEqualForInitialViewerState(prevDeps, nextDeps) {
   const curriedShallowDiffByLayer = (depName, scopeName) => shallowDiffByLayer(prevDeps, nextDeps, depName, scopeName);
   const curriedShallowDiffByLayerCoordinationWithKeys = (depName, layerScope, keys2) => shallowDiffByLayerCoordinationWithKeys(prevDeps, nextDeps, depName, layerScope, keys2);
   const curriedShallowDiffByChannelCoordinationWithKeys = (depName, layerScope, channelScope, keys2) => shallowDiffByChannelCoordinationWithKeys(prevDeps, nextDeps, depName, layerScope, channelScope, keys2);
+  if (["theme", "showAxisLines"].some(curriedShallowDiff)) {
+    forceUpdate = true;
+  }
   if (["segmentationLayerScopes", "segmentationChannelScopesByLayer"].some(curriedShallowDiff)) {
     forceUpdate = true;
   } else {
@@ -34868,7 +34880,8 @@ function customIsEqualForInitialViewerState(prevDeps, nextDeps) {
         "spatialLayerColor",
         "featureSelection",
         "featureFilterMode",
-        "featureColor"
+        "featureColor",
+        "spatialPointStrokeWidth"
       ]) || Math.abs(((_c = (_b2 = (_a2 = prevDeps == null ? void 0 : prevDeps.pointLayerCoordination) == null ? void 0 : _a2[0]) == null ? void 0 : _b2[layerScope]) == null ? void 0 : _c.spatialLayerOpacity) - ((_f = (_e = (_d = nextDeps == null ? void 0 : nextDeps.pointLayerCoordination) == null ? void 0 : _d[0]) == null ? void 0 : _e[layerScope]) == null ? void 0 : _f.spatialLayerOpacity)) >= 0.05) {
         forceUpdate = true;
       }
@@ -34879,21 +34892,25 @@ function customIsEqualForInitialViewerState(prevDeps, nextDeps) {
 function normalizeColor(rgbColor) {
   return rgbColor.map((c) => c / 255);
 }
+function borderWidthGlsl(borderWidth = 0) {
+  return `setPointMarkerBorderWidth(${borderWidth.toFixed(1)});`;
+}
 function toVec3(normalizedColor) {
   return `vec3(${normalizedColor.join(", ")})`;
 }
 function toVec4(normalizedColor, alpha2) {
   return `vec4(${normalizedColor.join(", ")}, ${alpha2})`;
 }
-function getSpatialLayerColorShader(staticColor, opacity) {
+function getSpatialLayerColorShader(staticColor, opacity, borderWidth = 0) {
   const norm = normalizeColor(staticColor);
   return `
         void main() {
             setColor(${toVec4(norm, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp) {
+function getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIndices, defaultColor, featureIndexProp, borderWidth = 0) {
   const normStatic = normalizeColor(staticColor);
   const normDefault = normalizeColor(defaultColor);
   const numFeatures = featureIndices.length;
@@ -34910,13 +34927,15 @@ function getSpatialLayerColorWithSelectionShader(staticColor, opacity, featureIn
             }
             if (isSelected) {
                 setColor(${toVec4(normStatic, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             } else {
                 setColor(${toVec4(normDefault, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             }
         }
     `;
 }
-function getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp) {
+function getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices, featureIndexProp, borderWidth = 0) {
   const normStatic = normalizeColor(staticColor);
   const numFeatures = featureIndices.length;
   const indicesArr = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(", ")});`;
@@ -34934,18 +34953,20 @@ function getSpatialLayerColorFilteredShader(staticColor, opacity, featureIndices
                 discard;
             }
             setColor(${toVec4(normStatic, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getGeneSelectionNoSelectionShader(staticColor, opacity) {
+function getGeneSelectionNoSelectionShader(staticColor, opacity, borderWidth = 0) {
   const norm = normalizeColor(staticColor);
   return `
         void main() {
             setColor(${toVec4(norm, opacity)});
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getGeneSelectionWithSelectionShader(featureIndices, featureColors, staticColor, defaultColor, opacity, featureIndexProp) {
+function getGeneSelectionWithSelectionShader(featureIndices, featureColors, staticColor, defaultColor, opacity, featureIndexProp, borderWidth = 0) {
   const numFeatures = featureIndices.length;
   const normDefault = normalizeColor(defaultColor);
   const normColors = featureColors.map((c) => normalizeColor(c));
@@ -34967,10 +34988,11 @@ function getGeneSelectionWithSelectionShader(featureIndices, featureColors, stat
                 }
             }
             setColor(color);
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getGeneSelectionFilteredShader(featureIndices, featureColors, staticColor, opacity, featureIndexProp) {
+function getGeneSelectionFilteredShader(featureIndices, featureColors, staticColor, opacity, featureIndexProp, borderWidth = 0) {
   const numFeatures = featureIndices.length;
   const normColors = featureColors.map((c) => normalizeColor(c));
   const normStatic = normalizeColor(staticColor);
@@ -34996,10 +35018,11 @@ function getGeneSelectionFilteredShader(featureIndices, featureColors, staticCol
                 discard;
             }
             setColor(vec4(matchedColor, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getRandomByFeatureShader(opacity, featureIndexProp) {
+function getRandomByFeatureShader(opacity, featureIndexProp, borderWidth = 0) {
   const paletteSize = PALETTE.length;
   const normPalette = PALETTE.map((c) => normalizeColor(c));
   const paletteDecl = `vec3 palette[${paletteSize}] = vec3[${paletteSize}](${normPalette.map((c) => toVec3(c)).join(", ")});`;
@@ -35011,10 +35034,11 @@ function getRandomByFeatureShader(opacity, featureIndexProp) {
             if (colorIdx < 0) { colorIdx = -colorIdx; }
             vec3 color = palette[colorIdx];
             setColor(vec4(color, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp) {
+function getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, borderWidth = 0) {
   const paletteSize = PALETTE.length;
   const normPalette = PALETTE.map((c) => normalizeColor(c));
   const normDefault = normalizeColor(defaultColor);
@@ -35036,13 +35060,15 @@ function getRandomByFeatureWithSelectionShader(featureIndices, defaultColor, opa
                 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)}
             }
         }
     `;
 }
-function getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp) {
+function getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexProp, borderWidth = 0) {
   const paletteSize = PALETTE.length;
   const normPalette = PALETTE.map((c) => normalizeColor(c));
   const numFeatures = featureIndices.length;
@@ -35065,6 +35091,7 @@ function getRandomByFeatureFilteredShader(featureIndices, opacity, featureIndexP
             int colorIdx = geneIndex - (geneIndex / ${paletteSize}) * ${paletteSize};
             if (colorIdx < 0) { colorIdx = -colorIdx; }
             setColor(vec4(palette[colorIdx], ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -35079,7 +35106,7 @@ function hashToFloatGlsl() {
         }
     `;
 }
-function getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp) {
+function getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp, borderWidth = 0) {
   return `
         ${hashToFloatGlsl()}
         void main() {
@@ -35089,10 +35116,11 @@ function getRandomPerPointShader(opacity, featureIndexProp, pointIndexProp) {
             float g = hashToFloat(pointIndex, 1);
             float b = hashToFloat(pointIndex, 2);
             setColor(vec4(r, g, b, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
-function getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp) {
+function getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opacity, featureIndexProp, pointIndexProp, borderWidth = 0) {
   const normDefault = normalizeColor(defaultColor);
   const numFeatures = featureIndices.length;
   const indicesDecl = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(", ")});`;
@@ -35113,13 +35141,15 @@ function getRandomPerPointWithSelectionShader(featureIndices, defaultColor, opac
                 float g = hashToFloat(pointIndex, 1);
                 float b = hashToFloat(pointIndex, 2);
                 setColor(vec4(r, g, b, ${opacity}));
+                ${borderWidthGlsl(borderWidth)}
             } else {
                 setColor(${toVec4(normDefault, opacity)});
+                ${borderWidthGlsl(borderWidth)}
             }
         }
     `;
 }
-function getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp) {
+function getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexProp, pointIndexProp, borderWidth = 0) {
   const numFeatures = featureIndices.length;
   const indicesDecl = `int selectedIndices[${numFeatures}] = int[${numFeatures}](${featureIndices.join(", ")});`;
   return `
@@ -35141,6 +35171,7 @@ function getRandomPerPointFilteredShader(featureIndices, opacity, featureIndexPr
             float g = hashToFloat(pointIndex, 1);
             float b = hashToFloat(pointIndex, 2);
             setColor(vec4(r, g, b, ${opacity}));
+            ${borderWidthGlsl(borderWidth)}
         }
     `;
 }
@@ -35154,6 +35185,7 @@ function getPointsShader(layerCoordination) {
     featureSelection,
     featureFilterMode,
     featureColor,
+    pointMarkerBorderWidth = 0,
     featureIndexProp,
     pointIndexProp
   } = layerCoordination;
@@ -35174,14 +35206,15 @@ function getPointsShader(layerCoordination) {
   }) : [];
   if (obsColorEncoding === "spatialLayerColor") {
     if (!hasFeatureSelection || !hasResolvedIndices) {
-      return getSpatialLayerColorShader(staticColor, opacity);
+      return getSpatialLayerColorShader(staticColor, opacity, pointMarkerBorderWidth);
     }
     if (isFiltered) {
       return getSpatialLayerColorFilteredShader(
         staticColor,
         opacity,
         featureIndices,
-        featureIndexProp
+        featureIndexProp,
+        pointMarkerBorderWidth
       );
     }
     return getSpatialLayerColorWithSelectionShader(
@@ -35189,7 +35222,8 @@ function getPointsShader(layerCoordination) {
       opacity,
       featureIndices,
       defaultColor,
-      featureIndexProp
+      featureIndexProp,
+      pointMarkerBorderWidth
     );
   }
   if (obsColorEncoding === "geneSelection") {
@@ -35197,7 +35231,7 @@ 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(
@@ -35205,7 +35239,8 @@ function getPointsShader(layerCoordination) {
         resolvedFeatureColors,
         staticColor,
         opacity,
-        featureIndexProp
+        featureIndexProp,
+        pointMarkerBorderWidth
       );
     }
     return getGeneSelectionWithSelectionShader(
@@ -35214,7 +35249,8 @@ function getPointsShader(layerCoordination) {
       staticColor,
       defaultColor,
       opacity,
-      featureIndexProp
+      featureIndexProp,
+      pointMarkerBorderWidth
     );
   }
   if (obsColorEncoding === "randomByFeature") {
@@ -35222,20 +35258,22 @@ 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
+        featureIndexProp,
+        pointMarkerBorderWidth
       );
     }
     return getRandomByFeatureWithSelectionShader(
       featureIndices,
       defaultColor,
       opacity,
-      featureIndexProp
+      featureIndexProp,
+      pointMarkerBorderWidth
     );
   }
   if (obsColorEncoding === "random") {
@@ -35243,14 +35281,20 @@ 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
+        pointIndexProp,
+        pointMarkerBorderWidth
       );
     }
     return getRandomPerPointWithSelectionShader(
@@ -35258,10 +35302,11 @@ function getPointsShader(layerCoordination) {
       defaultColor,
       opacity,
       featureIndexProp,
-      pointIndexProp
+      pointIndexProp,
+      pointMarkerBorderWidth
     );
   }
-  return getSpatialLayerColorShader(staticColor, opacity);
+  return getSpatialLayerColorShader(staticColor, opacity, pointMarkerBorderWidth);
 }
 const DEFAULT_NG_PROPS = {
   layout: "3d",
@@ -35291,7 +35336,7 @@ function toNgLayerName(dataType, layerScope, channelScope = null) {
   }
   throw new Error(`Unsupported data type: ${dataType}`);
 }
-function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentationChannelScopesByLayer, segmentationLayerCoordination, segmentationChannelCoordination, obsSegmentationsUrls, obsSegmentationsData, pointLayerScopes, pointLayerCoordination, obsPointsUrls, obsPointsData, pointMultiIndicesData) {
+function useNeuroglancerViewerState(theme, showAxisLines, segmentationLayerScopes, segmentationChannelScopesByLayer, segmentationLayerCoordination, segmentationChannelCoordination, obsSegmentationsUrls, obsSegmentationsData, pointLayerScopes, pointLayerCoordination, obsPointsUrls, obsPointsData, pointMultiIndicesData) {
   const viewerState = useMemoCustomComparison(() => {
     let result = cloneDeep(DEFAULT_NG_PROPS);
     segmentationLayerScopes.forEach((layerScope) => {
@@ -35305,18 +35350,25 @@ function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentation
           spatialLayerVisible
         } = layerCoordination || {};
         channelScopes.forEach((channelScope) => {
-          var _a2, _b2;
+          var _a2, _b2, _c, _d;
           const channelCoordination = (_b2 = (_a2 = segmentationChannelCoordination[0]) == null ? void 0 : _a2[layerScope]) == null ? void 0 : _b2[channelScope];
           const {
             spatialChannelVisible
           } = channelCoordination || {};
+          const { source: ngSource, ...otherNgOptions } = layerData.neuroglancerOptions ?? {};
+          const hasNgSourceOptions = ((_c = layerData.neuroglancerOptions) == null ? void 0 : _c.subsources) || ((_d = layerData.neuroglancerOptions) == null ? void 0 : _d.enableDefaultSubsources) !== void 0;
+          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$1.OBS_SEGMENTATIONS, layerScope, channelScope),
                 visible: spatialLayerVisible && spatialChannelVisible,
@@ -35324,7 +35376,7 @@ function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentation
                 // visibility must be true for the layer to be visible.
                 // TODO: update this to extract specific properties from
                 // neuroglancerOptions as needed.
-                ...layerData.neuroglancerOptions ?? {}
+                ...otherNgOptions
               }
             ]
           };
@@ -35345,7 +35397,8 @@ function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentation
           spatialLayerColor,
           featureSelection,
           featureFilterMode,
-          featureColor
+          featureColor,
+          spatialPointStrokeWidth
         } = layerCoordination || {};
         const shader = getPointsShader({
           theme,
@@ -35357,7 +35410,8 @@ function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentation
           featureFilterMode,
           featureColor,
           featureIndexProp: (_d = layerData.neuroglancerOptions) == null ? void 0 : _d.featureIndexProp,
-          pointIndexProp: (_e = layerData.neuroglancerOptions) == null ? void 0 : _e.pointIndexProp
+          pointIndexProp: (_e = layerData.neuroglancerOptions) == null ? void 0 : _e.pointIndexProp,
+          pointMarkerBorderWidth: spatialPointStrokeWidth ?? 0
         });
         result = {
           ...result,
@@ -35394,6 +35448,7 @@ function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentation
     return result;
   }, {
     theme,
+    showAxisLines,
     segmentationLayerScopes,
     segmentationChannelScopesByLayer,
     segmentationLayerCoordination,
@@ -37281,6 +37336,7 @@ function NeuroglancerSubscriber(props) {
     downloadButtonVisible,
     removeGridComponent,
     theme,
+    showAxisLines = false,
     title = "Spatial",
     subtitle = "Powered by Neuroglancer",
     helpText = ViewHelpMapping.NEUROGLANCER,
@@ -37395,7 +37451,8 @@ function NeuroglancerSubscriber(props) {
       CoordinationType$1.OBS_HIGHLIGHT,
       CoordinationType$1.TOOLTIPS_VISIBLE,
       CoordinationType$1.TOOLTIP_CROSSHAIRS_VISIBLE,
-      CoordinationType$1.LEGEND_VISIBLE
+      CoordinationType$1.LEGEND_VISIBLE,
+      CoordinationType$1.SPATIAL_POINT_STROKE_WIDTH
     ],
     coordinationScopes,
     coordinationScopesBy,
@@ -37480,7 +37537,8 @@ function NeuroglancerSubscriber(props) {
           obsColorEncoding,
           obsSetSelection,
           additionalObsSets,
-          spatialChannelColor
+          spatialChannelColor,
+          spatialChannelOpacity
         } = segmentationChannelCoordination[0][layerScope][channelScope];
         if (obsColorEncoding === "spatialChannelColor") {
           if (layerIndex && spatialChannelColor) {
@@ -37502,6 +37560,7 @@ function NeuroglancerSubscriber(props) {
               });
             }
             result[layerScope][channelScope] = ngCellColors;
+            result[layerScope].opacity = spatialChannelOpacity ?? 1;
           }
         } else if (layerSets && layerIndex) {
           const mergedCellSets = mergeObsSets(layerSets, additionalObsSets);
@@ -37517,6 +37576,7 @@ function NeuroglancerSubscriber(props) {
             ngCellColors[i] = rgbToHex(color2);
           });
           result[layerScope][channelScope] = ngCellColors;
+          result[layerScope].opacity = spatialChannelOpacity ?? 1;
         }
       });
     });
@@ -37532,6 +37592,7 @@ function NeuroglancerSubscriber(props) {
   }, customIsEqualForCellColors);
   const initalViewerState = useNeuroglancerViewerState(
     theme,
+    showAxisLines,
     segmentationLayerScopes,
     segmentationChannelScopesByLayer,
     segmentationLayerCoordination,
@@ -37577,6 +37638,7 @@ function NeuroglancerSubscriber(props) {
     z: spatialRotationZ,
     orbit: spatialRotationOrbit
   });
+  const [isLayersLoaded, setIsLayersLoaded] = useState(false);
   const prevCoordsRef = useRef({
     zoom: spatialZoom,
     rx: spatialRotationX,
@@ -37690,9 +37752,12 @@ function NeuroglancerSubscriber(props) {
   const cellColorMappingByLayer = useMemo(() => {
     const result = {};
     segmentationLayerScopes == null ? void 0 : segmentationLayerScopes.forEach((layerScope) => {
-      var _a2, _b;
+      var _a2, _b, _c;
       const channelScope = (_a2 = segmentationChannelScopesByLayer == null ? void 0 : segmentationChannelScopesByLayer[layerScope]) == null ? void 0 : _a2[0];
-      result[layerScope] = ((_b = segmentationColorMapping == null ? void 0 : segmentationColorMapping[layerScope]) == null ? void 0 : _b[channelScope]) ?? {};
+      result[layerScope] = {
+        colors: ((_b = segmentationColorMapping == null ? void 0 : segmentationColorMapping[layerScope]) == null ? void 0 : _b[channelScope]) ?? {},
+        opacity: ((_c = segmentationColorMapping == null ? void 0 : segmentationColorMapping[layerScope]) == null ? void 0 : _c.opacity) ?? 1
+      };
     });
     return result;
   }, [segmentationColorMapping, segmentationLayerScopes, segmentationChannelScopesByLayer]);
@@ -37767,13 +37832,15 @@ function NeuroglancerSubscriber(props) {
       lastInteractionSource.current = null;
     }
     const updatedLayers = ((_c = current == null ? void 0 : current.layers) == null ? void 0 : _c.map((layer, idx) => {
+      var _a3, _b2;
       const layerScope = segmentationLayerScopes == null ? void 0 : segmentationLayerScopes[idx];
-      const layerColorMapping = (cellColorMappingByLayer == null ? void 0 : cellColorMappingByLayer[layerScope]) ?? {};
+      const layerColorMapping = ((_a3 = cellColorMappingByLayer == null ? void 0 : cellColorMappingByLayer[layerScope]) == null ? void 0 : _a3.colors) ?? {};
       const layerSegments = Object.keys(layerColorMapping);
       return {
         ...layer,
         segments: layerSegments,
-        segmentColors: layerColorMapping
+        segmentColors: layerColorMapping,
+        objectAlpha: ((_b2 = cellColorMappingByLayer == null ? void 0 : cellColorMappingByLayer[layerScope]) == null ? void 0 : _b2.opacity) ?? 1
       };
     })) ?? [];
     const updated = {
@@ -37808,6 +37875,9 @@ function NeuroglancerSubscriber(props) {
   const onSegmentHighlight = useCallback((obsId) => {
     setCellHighlight(String(obsId));
   }, [setCellHighlight]);
+  const handleLayerLoadingChange = useCallback((isLoaded) => {
+    setIsLayersLoaded(isLoaded);
+  }, []);
   const hasLayers = ((_a = derivedViewerState == null ? void 0 : derivedViewerState.layers) == null ? void 0 : _a.length) > 0;
   return /* @__PURE__ */ React__default.createElement(
     TitleInfo,
@@ -37820,7 +37890,7 @@ function NeuroglancerSubscriber(props) {
       closeButtonVisible,
       downloadButtonVisible,
       removeGridComponent,
-      isReady,
+      isReady: isReady && isLayersLoaded,
       errors,
       withPadding: false,
       guideUrl: GUIDE_URL
@@ -37833,7 +37903,10 @@ function NeuroglancerSubscriber(props) {
         segmentationLayerScopes,
         segmentationLayerCoordination,
         segmentationChannelScopesByLayer,
-        segmentationChannelCoordination
+        segmentationChannelCoordination,
+        pointLayerScopes,
+        pointLayerCoordination,
+        pointMultiIndicesData
       }
     )), /* @__PURE__ */ React__default.createElement(
       NeuroglancerComp,
@@ -37843,7 +37916,8 @@ function NeuroglancerSubscriber(props) {
         onSelectHoveredCoords: onSegmentHighlight,
         viewerState: derivedViewerState,
         cellColorMapping: cellColorMappingByLayer,
-        setViewerState: handleStateUpdate
+        setViewerState: handleStateUpdate,
+        onLayerLoadingChange: handleLayerLoadingChange
       }
     )) : null
   );

package/dist/index.js

@@ -1,4 +1,4 @@
-import { N } from "./index-BEPd2Tds.js";
+import { N } from "./index-anGvS-pL.js";
 export {
   N as NeuroglancerSubscriber
 };

package/dist-tsc/Neuroglancer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"Neuroglancer.d.ts","sourceRoot":"","sources":["../src/Neuroglancer.js"],"names":[],"mappings":"AAYA;IACE,wBAYC;IAVC,gBAAgC;IAChC,sBAA8C;IAC9C,oCAAuC;IACvC,2BAAiC;IACjC,sCAA4B;IA8D9B,2CAGC;IAzDD,4BAoDC;IAxDC,0BAAgD;IAChD,iCAA8D;IA8DhE,yCAKC;IAED,sBAoBC;CACF"}
+{"version":3,"file":"Neuroglancer.d.ts","sourceRoot":"","sources":["../src/Neuroglancer.js"],"names":[],"mappings":"AAYA;IACE,wBAYC;IAVC,gBAAgC;IAChC,sBAA8C;IAC9C,oCAAuC;IACvC,2BAAiC;IACjC,sCAA4B;IA8D9B,2CAGC;IAzDD,4BAoDC;IAxDC,0BAAgD;IAChD,iCAA8D;IA8DhE,yCAKC;IAED,sBAqBC;CACF"}

package/dist-tsc/Neuroglancer.js

@@ -82,7 +82,7 @@ export class NeuroglancerComp extends PureComponent {
         }
     }
     render() {
-        const { classes, viewerState, cellColorMapping } = this.props;
-        return (_jsxs(_Fragment, { children: [_jsx(NeuroglancerGlobalStyles, { classes: classes }), _jsx("div", { className: classes.neuroglancerWrapper, children: _jsx(Suspense, { fallback: _jsx("div", { children: "Loading..." }), children: _jsx(LazyReactNeuroglancer, { brainMapsClientId: "NOT_A_VALID_ID", viewerState: viewerState, onViewerStateChanged: this.onViewerStateChanged, bundleRoot: this.bundleRoot, cellColorMapping: cellColorMapping, ref: this.onRef }) }) })] }));
+        const { classes, viewerState, cellColorMapping, onLayerLoadingChange } = this.props;
+        return (_jsxs(_Fragment, { children: [_jsx(NeuroglancerGlobalStyles, { classes: classes }), _jsx("div", { className: classes.neuroglancerWrapper, children: _jsx(Suspense, { fallback: _jsx("div", { children: "Loading..." }), children: _jsx(LazyReactNeuroglancer, { brainMapsClientId: "NOT_A_VALID_ID", viewerState: viewerState, onViewerStateChanged: this.onViewerStateChanged, onLayerLoadingChange: onLayerLoadingChange, bundleRoot: this.bundleRoot, cellColorMapping: cellColorMapping, ref: this.onRef }) }) })] }));
     }
 }

package/dist-tsc/NeuroglancerSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"NeuroglancerSubscriber.d.ts","sourceRoot":"","sources":["../src/NeuroglancerSubscriber.js"],"names":[],"mappings":"AAwEA,gEAkuBC"}
+{"version":3,"file":"NeuroglancerSubscriber.d.ts","sourceRoot":"","sources":["../src/NeuroglancerSubscriber.js"],"names":[],"mappings":"AAwEA,gEA0vBC"}