@vitessce/all 3.9.1 → 3.9.2

package/dist/{OrbitControls-BpeUSyh9.js → OrbitControls-DcLq7d8o.js}

@@ -1,4 +1,4 @@
-import { aG as getDefaultExportFromCjs, aH as Raycaster, W as OrthographicCamera, K as PerspectiveCamera, av as Scene, aI as PCFSoftShadowMap, aJ as VSMShadowMap, aK as PCFShadowMap, aL as BasicShadowMap, aM as NoToneMapping, aN as ACESFilmicToneMapping, e as Vector3, V as Vector2, aO as Clock, aP as WebGLRenderer, aQ as Camera, x as BufferGeometry, r as Material, aR as Layers, a1 as Texture, aC as RGBAFormat, ay as UnsignedByteType, C as Color, aj as _extends, aS as THREE, aT as EventDispatcher, aU as MOUSE, aV as TOUCH, aW as Spherical, Q as Quaternion, an as Ray, ak as Plane } from "./index-B-aCUFst.js";
+import { aG as getDefaultExportFromCjs, aH as Raycaster, W as OrthographicCamera, K as PerspectiveCamera, av as Scene, aI as PCFSoftShadowMap, aJ as VSMShadowMap, aK as PCFShadowMap, aL as BasicShadowMap, aM as NoToneMapping, aN as ACESFilmicToneMapping, e as Vector3, V as Vector2, aO as Clock, aP as WebGLRenderer, aQ as Camera, x as BufferGeometry, r as Material, aR as Layers, a1 as Texture, aC as RGBAFormat, ay as UnsignedByteType, C as Color, aj as _extends, aS as THREE, aT as EventDispatcher, aU as MOUSE, aV as TOUCH, aW as Spherical, Q as Quaternion, an as Ray, ak as Plane } from "./index-DKpg3n-y.js";
 import * as React from "react";
 import React__default, { useReducer, useRef, useEffect, useLayoutEffect, useDebugValue, useState, useMemo } from "react";
 var constants = { exports: {} };

package/dist/{ReactNeuroglancer-CGvAuFr6.js → ReactNeuroglancer-DmKC4Wha.js}

@@ -1,4 +1,4 @@
-import { aG as getDefaultExportFromCjs, b1 as requireAssign, b2 as require_export, b3 as require_core, b4 as require_fails, b5 as require_toObject, b6 as require_objectKeys, b7 as require_cof, b8 as require_wks, b9 as require_iterators, ba as requireWeb_dom_iterable, bb as requireEs6_string_iterator, bc as require_anObject, bd as require_hide, be as require_ctx, bf as require_toLength, bg as require_global, bh as require_objectDp, bi as require_descriptors, bj as require_isObject, bk as require_objectCreate, bl as require_iterDefine, bm as require_iterStep, bn as require_meta, bo as require_isArray, bp as require_iobject, bq as require_setToStringTag, br as require_aFunction, bs as requireIterator, bt as require_propertyDesc, a_ as commonjsGlobal, bu as requireEs6_symbol, bv as requireDefineProperty, bw as require_toIobject, bx as require_objectGopd, by as require_html, bz as require_domCreate, bA as require_library, bB as requireSymbol, bC as require_objectPie, bD as require_has, bE as require_redefine, bF as require_objectAssign, bG as diffCameraState, ao as jsxRuntimeExports } from "./index-B-aCUFst.js";
+import { aG as getDefaultExportFromCjs, b1 as requireAssign, b2 as require_export, b3 as require_core, b4 as require_fails, b5 as require_toObject, b6 as require_objectKeys, b7 as require_cof, b8 as require_wks, b9 as require_iterators, ba as requireWeb_dom_iterable, bb as requireEs6_string_iterator, bc as require_anObject, bd as require_hide, be as require_ctx, bf as require_toLength, bg as require_global, bh as require_objectDp, bi as require_descriptors, bj as require_isObject, bk as require_objectCreate, bl as require_iterDefine, bm as require_iterStep, bn as require_meta, bo as require_isArray, bp as require_iobject, bq as require_setToStringTag, br as require_aFunction, bs as requireIterator, bt as require_propertyDesc, a_ as commonjsGlobal, bu as requireEs6_symbol, bv as requireDefineProperty, bw as require_toIobject, bx as require_objectGopd, by as require_html, bz as require_domCreate, bA as require_library, bB as requireSymbol, bC as require_objectPie, bD as require_has, bE as require_redefine, bF as require_objectAssign, bG as diffCameraState, ao as jsxRuntimeExports } from "./index-DKpg3n-y.js";
 import React__default from "react";
 var assignExports = requireAssign();
 const _Object$assign = /* @__PURE__ */ getDefaultExportFromCjs(assignExports);

package/dist/{deflate-C63ycJxP.js → deflate-CmVftsf2.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{higlass-Dsba4gSg.js → higlass-BE5OHbDt.js}

@@ -1,7 +1,7 @@
 import * as React$7 from "react";
 import React__default, { isValidElement, PureComponent, Component, createElement, createContext, createRef } from "react";
 import ReactDOM__default, { findDOMNode as findDOMNode$1 } from "react-dom";
-import { a_ as commonjsGlobal$1, a$ as requireObjectAssign, aG as getDefaultExportFromCjs$1, b0 as earcut } from "./index-B-aCUFst.js";
+import { a_ as commonjsGlobal$1, a$ as requireObjectAssign, aG as getDefaultExportFromCjs$1, b0 as earcut } from "./index-DKpg3n-y.js";
 var promise = {};
 var hasRequiredPromise;
 function requirePromise() {

package/dist/{index-DBnzUqAs.js → index-4Tuk9eGd.js}

@@ -1,7 +1,7 @@
-import { G as Group, M as Matrix4, T as TrianglesDrawMode, a as TriangleFanDrawMode, b as TriangleStripDrawMode, R as REVISION, L as Loader, c as LoaderUtils, F as FileLoader, d as MeshPhysicalMaterial, V as Vector2, C as Color, S as SpotLight, P as PointLight, D as DirectionalLight, e as Vector3, I as InstancedMesh, Q as Quaternion, O as Object3D, f as TextureLoader, g as ImageBitmapLoader, B as BufferAttribute, h as InterleavedBuffer, i as LinearMipmapLinearFilter, N as NearestMipmapLinearFilter, j as LinearMipmapNearestFilter, k as NearestMipmapNearestFilter, l as LinearFilter, m as NearestFilter, n as RepeatWrapping, o as MirroredRepeatWrapping, p as ClampToEdgeWrapping, q as PointsMaterial, r as Material, s as LineBasicMaterial, t as MeshStandardMaterial, u as DoubleSide, v as MeshBasicMaterial, w as PropertyBinding, x as BufferGeometry, y as SkinnedMesh, z as Mesh, A as LineSegments, E as Line$1, H as LineLoop, J as Points, K as PerspectiveCamera, U as MathUtils, W as OrthographicCamera, X as Skeleton, Y as InterpolateDiscrete, Z as InterpolateLinear, _ as AnimationClip, $ as Bone, a0 as InterleavedBufferAttribute, a1 as Texture, a2 as VectorKeyframeTrack, a3 as QuaternionKeyframeTrack, a4 as NumberKeyframeTrack, a5 as FrontSide, a6 as Interpolant, a7 as Box3, a8 as Sphere, a9 as InstancedBufferGeometry, aa as Float32BufferAttribute, ab as InstancedInterleavedBuffer, ac as WireframeGeometry, ad as ShaderMaterial, ae as UniformsUtils, af as UniformsLib, ag as Vector4, ah as Line3, ai as SphereGeometry, aj as _extends, ak as Plane, al as Triangle, am as BackSide, an as Ray$1, ao as jsxRuntimeExports, ap as Matrix3, aq as CoordinationType, ar as Data3DTexture, as as RedFormat, at as FloatType, au as getImageSize, av as Scene } from "./index-B-aCUFst.js";
+import { G as Group, M as Matrix4, T as TrianglesDrawMode, a as TriangleFanDrawMode, b as TriangleStripDrawMode, R as REVISION, L as Loader, c as LoaderUtils, F as FileLoader, d as MeshPhysicalMaterial, V as Vector2, C as Color, S as SpotLight, P as PointLight, D as DirectionalLight, e as Vector3, I as InstancedMesh, Q as Quaternion, O as Object3D, f as TextureLoader, g as ImageBitmapLoader, B as BufferAttribute, h as InterleavedBuffer, i as LinearMipmapLinearFilter, N as NearestMipmapLinearFilter, j as LinearMipmapNearestFilter, k as NearestMipmapNearestFilter, l as LinearFilter, m as NearestFilter, n as RepeatWrapping, o as MirroredRepeatWrapping, p as ClampToEdgeWrapping, q as PointsMaterial, r as Material, s as LineBasicMaterial, t as MeshStandardMaterial, u as DoubleSide, v as MeshBasicMaterial, w as PropertyBinding, x as BufferGeometry, y as SkinnedMesh, z as Mesh, A as LineSegments, E as Line$1, H as LineLoop, J as Points, K as PerspectiveCamera, U as MathUtils, W as OrthographicCamera, X as Skeleton, Y as InterpolateDiscrete, Z as InterpolateLinear, _ as AnimationClip, $ as Bone, a0 as InterleavedBufferAttribute, a1 as Texture, a2 as VectorKeyframeTrack, a3 as QuaternionKeyframeTrack, a4 as NumberKeyframeTrack, a5 as FrontSide, a6 as Interpolant, a7 as Box3, a8 as Sphere, a9 as InstancedBufferGeometry, aa as Float32BufferAttribute, ab as InstancedInterleavedBuffer, ac as WireframeGeometry, ad as ShaderMaterial, ae as UniformsUtils, af as UniformsLib, ag as Vector4, ah as Line3, ai as SphereGeometry, aj as _extends, ak as Plane, al as Triangle, am as BackSide, an as Ray$1, ao as jsxRuntimeExports, ap as Matrix3, aq as CoordinationType, ar as Data3DTexture, as as RedFormat, at as FloatType, au as getImageSize, av as Scene } from "./index-DKpg3n-y.js";
 import * as React from "react";
 import { useRef, useEffect, useState, forwardRef } from "react";
-import { u as useThree, a as useFrame, c as create, e as extend, b as createPortal, O as OrbitControls, C as Canvas } from "./OrbitControls-BpeUSyh9.js";
+import { u as useThree, a as useFrame, c as create, e as extend, b as createPortal, O as OrbitControls, C as Canvas } from "./OrbitControls-DcLq7d8o.js";
 const isPromise = (promise) => typeof promise === "object" && typeof promise.then === "function";
 const globalCache = [];
 function shallowEqualArrays(arrA, arrB, equal = (a, b) => a === b) {
@@ -5027,7 +5027,7 @@ const Text = /* @__PURE__ */ React.forwardRef(({
   const {
     Text: TextMeshImpl,
     preloadFont
-  } = suspend(async () => import("./troika-three-text.esm-Cf8otk5M.js"), []);
+  } = suspend(async () => import("./troika-three-text.esm-1SLW0Iby.js"), []);
   const invalidate = useThree(({
     invalidate: invalidate2
   }) => invalidate2);

package/dist/{index-B-aCUFst.js → index-DKpg3n-y.js}

@@ -72922,21 +72922,20 @@ Popper$1.Utils = (typeof window !== "undefined" ? window : global).PopperUtils;
 Popper$1.placements = placements$1;
 Popper$1.Defaults = Defaults;
 function createChainedFunction(...funcs) {
-  return funcs.reduce((acc, func) => {
-    if (func == null) {
-      return acc;
-    }
-    {
-      if (typeof func !== "function") {
-        console.error("Material-UI: Invalid Argument Type, must only provide functions, undefined, or null.");
+  return funcs.reduce(
+    (acc, func) => {
+      if (func == null) {
+        return acc;
       }
+      return function chainedFunction(...args) {
+        acc.apply(this, args);
+        func.apply(this, args);
+      };
+    },
+    // eslint-disable-next-line @typescript-eslint/no-empty-function
+    () => {
     }
-    return function chainedFunction(...args) {
-      acc.apply(this, args);
-      func.apply(this, args);
-    };
-  }, () => {
-  });
+  );
 }
 function setRef(ref2, value2) {
   if (typeof ref2 === "function") {
@@ -72975,7 +72974,7 @@ function flipPlacement(placement, theme) {
   }
 }
 function getAnchorEl(anchorEl) {
-  return typeof anchorEl === "function" ? anchorEl() : anchorEl;
+  return typeof anchorEl === "function" ? anchorEl(document.body) : anchorEl;
 }
 const useEnhancedEffect = typeof window !== "undefined" ? React.useLayoutEffect : React.useEffect;
 const defaultPopperOptions = {};
@@ -73005,25 +73004,18 @@ const Popper = React.forwardRef((props, ref2) => {
     }
     if (popperRef.current) {
       popperRef.current.destroy();
-      handlePopperRefRef.current(null);
+      if (handlePopperRefRef.current) {
+        setRef(handlePopperRefRef.current, null);
+      }
     }
     const handlePopperUpdate = (data2) => {
       setPlacement(data2.placement);
     };
-    const resolvedAnchorEl = getAnchorEl(anchorEl);
-    {
-      if (resolvedAnchorEl && resolvedAnchorEl.nodeType === 1) {
-        const box = resolvedAnchorEl.getBoundingClientRect();
-        if (box.top === 0 && box.left === 0 && box.right === 0 && box.bottom === 0) {
-          console.warn([
-            "Material-UI: The `anchorEl` prop provided to the component is invalid.",
-            "The anchor element should be part of the document layout.",
-            "Make sure the element is present in the document or that it's not display none."
-          ].join("\n"));
-        }
-      }
+    const anchorElement = getAnchorEl(anchorEl);
+    if (!anchorElement) {
+      return;
     }
-    const popper2 = new Popper$1(getAnchorEl(anchorEl), tooltipRef.current, {
+    const popper2 = new Popper$1(anchorElement, tooltipRef.current, {
       placement: rtlPlacement,
       ...popperOptions,
       modifiers: {
@@ -73041,7 +73033,9 @@ const Popper = React.forwardRef((props, ref2) => {
       onCreate: createChainedFunction(handlePopperUpdate, popperOptions.onCreate),
       onUpdate: createChainedFunction(handlePopperUpdate, popperOptions.onUpdate)
     });
-    handlePopperRefRef.current(popper2);
+    if (handlePopperRefRef.current) {
+      setRef(handlePopperRefRef.current, popper2);
+    }
   }, [anchorEl, disablePortal, modifiers2, open2, rtlPlacement, popperOptions]);
   const handleRef = React.useCallback((node2) => {
     setRef(ownRef, node2);
@@ -73055,7 +73049,9 @@ const Popper = React.forwardRef((props, ref2) => {
       return;
     }
     popperRef.current.destroy();
-    handlePopperRefRef.current(null);
+    if (handlePopperRefRef.current) {
+      setRef(handlePopperRefRef.current, null);
+    }
   };
   const handleExited = () => {
     setExited(true);
@@ -73086,7 +73082,7 @@ const Popper = React.forwardRef((props, ref2) => {
     // Fix Popper.js display issue
     top: 0,
     left: 0,
-    display: !open2 && keepMounted && !transition3 ? "none" : null,
+    display: !open2 && keepMounted && !transition3 ? "none" : void 0,
     ...style2
   }, children: typeof children3 === "function" ? children3(childProps) : children3 }) });
 });
@@ -73101,7 +73097,7 @@ function ScopedGlobalStyles(props) {
   const component = useMemo$1(() => {
     const computedStyles = prependParentClassName(styles2, parentClassName);
     return jsxRuntimeExports.jsx(GlobalStyles$3, { styles: computedStyles });
-  }, [parentClassName]);
+  }, [parentClassName, styles2]);
   return component;
 }
 function ok$1() {
@@ -209142,22 +209138,22 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-fm6sEfJs.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-fa9yKTSy.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-QxVylWDO.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-CMvKxrGF.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-BZSLq5O3.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-C63ycJxP.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-8C0e8lDT.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-DeFocpVz.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-CmVftsf2.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-Crf3i8qg.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-BZk5g5T2.js").then(async (m2) => {
+  () => import("./lerc-BCstSar4.js").then(async (m2) => {
     await m2.zstd.init();
     return m2;
   }).then((m2) => m2.default)
 );
-addDecoder(50001, () => import("./webimage-CyRSWQVR.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-DJBIWr5d.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -252456,21 +252452,18 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
         };
       }
     }
-    const isStaticColor = obsColorEncoding === "spatialLayerColor";
-    const getMoleculeColor = (object2, { data: data2, index: index2, target: target2 }) => {
-      const obsId = data2.src.obsIndex[index2];
-      if (data2.src.obsLabelsMap && data2.src.uniqueObsLabels && data2.src.PALETTE) {
-        const obsLabel = data2.src.obsLabelsMap.get(obsId);
-        const labelIndex = data2.src.uniqueObsLabels.indexOf(obsLabel);
-        target2[0] = data2.src.PALETTE[labelIndex % data2.src.PALETTE.length]?.[0];
-        target2[1] = data2.src.PALETTE[labelIndex % data2.src.PALETTE.length]?.[1];
-        target2[2] = data2.src.PALETTE[labelIndex % data2.src.PALETTE.length]?.[2];
-      }
-      return target2;
-    };
-    const { obsPointsModelMatrix, obsPoints, obsPointsTilingType, loadPointsInRect } = this.obsPointsData?.[layerScope]?.src ?? {};
+    const {
+      obsPointsModelMatrix,
+      obsPoints,
+      // featureIndices: obsPointsFeatureIndices,
+      obsPointsTilingType,
+      loadPointsInRect
+    } = this.obsPointsData?.[layerScope]?.src ?? {};
     obsPoints?.shape?.[0] === 3;
     const modelMatrix2 = obsPointsModelMatrix?.clone();
+    const hasFeatureIndicesMinMax = !showUnselected && Array.isArray(featureIndices) && featureIndices.length === 1;
+    const FILTER_PLACEHOLDER = 0;
+    const featureIndicesMinMax = hasFeatureIndicesMinMax ? [featureIndices[0], featureIndices[0]] : [FILTER_PLACEHOLDER, FILTER_PLACEHOLDER];
     if (obsPointsTilingType === "tiled") {
       return new TileLayer({
         id: `Tiled-${POINT_LAYER_PREFIX}${layerScope}`,
@@ -252521,9 +252514,6 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
         renderSubLayers: (subLayerProps) => {
           const { bbox: bbox2, content: tileData } = subLayerProps.tile;
           const { left: left2, top: top2, right: right2, bottom: bottom2 } = bbox2;
-          const hasFeatureIndicesMinMax = !showUnselected && Array.isArray(featureIndices) && featureIndices.length === 1;
-          const FILTER_PLACEHOLDER = 0;
-          const featureIndicesMinMax = hasFeatureIndicesMinMax ? [featureIndices[0], featureIndices[0]] : [FILTER_PLACEHOLDER, FILTER_PLACEHOLDER];
           return new ScatterplotLayer(subLayerProps, {
             bounds: [left2, top2, right2, bottom2],
             data: tileData,
@@ -252600,26 +252590,44 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       pickable: true,
       autoHighlight: AUTO_HIGHLIGHT,
-      radiusMaxPixels: 3,
       opacity: spatialLayerOpacity,
       visible: spatialLayerVisible,
       modelMatrix: modelMatrix2,
-      getRadius: 300,
+      getRadius: 5,
+      radiusMaxPixels: 3,
       getPosition: (object2, { data: data2, index: index2, target: target2 }) => {
         target2[0] = data2.src.obsPoints.data[0][index2];
         target2[1] = data2.src.obsPoints.data[1][index2];
         target2[2] = 0;
         return target2;
       },
-      getLineColor: isStaticColor ? staticColor : getMoleculeColor,
-      getFillColor: isStaticColor ? staticColor : getMoleculeColor,
+      getFillColor,
       onHover: (info2) => delegateHover(info2, "point", layerScope),
+      // Use GPU filtering to filter to only the points in the tile bounding box,
+      // since the row groups may contain points from other tiles.
+      // Note: this can be improved using filterCategories,
+      // but it is not available until post-v9 deck.gl/extensions.
+      filterRange: [featureIndicesMinMax],
+      getFilterValue: hasFeatureIndicesMinMax ? (object2, { data: data2, index: index2 }) => [
+        data2.src.featureIndices[index2]
+      ] : (object2, { data: data2, index: index2 }) => [
+        FILTER_PLACEHOLDER
+      ],
+      extensions: [
+        new DataFilterExtension({ filterSize: 1 })
+      ],
       updateTriggers: {
-        getRadius: [],
-        getFillColor: [obsColorEncoding, staticColor],
-        getLineColor: [obsColorEncoding, staticColor]
-      },
-      ...{}
+        getFillColor: [
+          showUnselected,
+          featureColor,
+          obsColorEncoding,
+          spatialLayerColor,
+          featureSelection,
+          hasMultipleFeaturesSelected
+        ],
+        getFilterValue: [hasFeatureIndicesMinMax, showUnselected, featureSelection],
+        filterRange: [hasFeatureIndicesMinMax, showUnselected, featureSelection]
+      }
     });
   }
   createSelectionLayer() {
@@ -253158,8 +253166,8 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
     this.obsSegmentationsLayers = this.createSegmentationLayers();
   }
   onUpdatePointsData(layerScope) {
-    const { obsPoints, pointMultiObsLabels } = this.props;
-    const { obsIndex, obsPoints: layerObsPoints, obsPointsModelMatrix, loadPointsInRect, obsPointsTilingType } = obsPoints?.[layerScope] || {};
+    const { obsPoints, pointMultiObsLabels, pointMatrixIndices } = this.props;
+    const { obsIndex, obsPoints: layerObsPoints, featureIds: layerObsPointsFeatureIds, obsPointsModelMatrix, loadPointsInRect, obsPointsTilingType } = obsPoints?.[layerScope] || {};
     const { obsIndex: obsLabelsIndex, obsLabels } = pointMultiObsLabels?.[layerScope] || {};
     if (obsPointsTilingType === "tiled") {
       this.obsPointsData[layerScope] = {
@@ -253167,6 +253175,7 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
           obsPointsTilingType,
           obsIndex: null,
           obsPoints: null,
+          featureIndices: null,
           obsPointsModelMatrix,
           obsLabelsMap: null,
           uniqueObsLabels: null,
@@ -253179,11 +253188,17 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
       if (layerObsPoints) {
         const getCellCoords = makeDefaultGetObsCoords(layerObsPoints);
         this.obsPointsQuadTree[layerScope] = createQuadTree(layerObsPoints, getCellCoords);
+        let pointFeatureIndex = pointMatrixIndices?.[layerScope]?.featureIndex;
+        if (!pointFeatureIndex) {
+          pointFeatureIndex = Array.from(new Set(layerObsPointsFeatureIds));
+        }
+        const featureIndices = layerObsPointsFeatureIds.map((featureId2) => pointFeatureIndex?.indexOf(featureId2));
         this.obsPointsData[layerScope] = {
           src: {
             obsPointsTilingType,
             obsIndex,
             obsPoints: layerObsPoints,
+            featureIndices,
             obsPointsModelMatrix,
             obsLabelsMap: null,
             uniqueObsLabels: null,
@@ -253396,7 +253411,7 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
       forceUpdate = true;
     } else {
       this.props.pointLayerScopes.forEach((layerScope) => {
-        if (shallowDiffByLayer("obsPoints", layerScope) || shallowDiffByLayer("pointMultiObsLabels", layerScope)) {
+        if (shallowDiffByLayer("obsPoints", layerScope) || shallowDiffByLayer("pointMultiObsLabels", layerScope) || shallowDiffByLayer("pointMatrixIndices", layerScope)) {
           this.onUpdatePointsData(layerScope);
           forceUpdate = true;
         }
@@ -253561,12 +253576,12 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-DBnzUqAs.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-4Tuk9eGd.js");
   return { default: SpatialWrapper2 };
 });
 const SpatialThreeAdapter = React__default.forwardRef((props, ref2) => jsxRuntimeExports.jsx("div", { ref: ref2, style: { width: "100%", height: "100%" }, children: jsxRuntimeExports.jsx(ErrorBoundary, { children: jsxRuntimeExports.jsx(Suspense, { fallback: jsxRuntimeExports.jsx("div", { children: "Loading..." }), children: jsxRuntimeExports.jsx(LazySpatialThree, { ...props }) }) }) }));
 const LazySpatialAccelerated = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-Do4xvqoi.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-txFb0D-X.js");
   return { default: SpatialWrapper2 };
 });
 const SpatialAcceleratedAdapter = React__default.forwardRef((props, ref2) => jsxRuntimeExports.jsx("div", { ref: ref2, style: { width: "100%", height: "100%" }, children: jsxRuntimeExports.jsx(ErrorBoundary, { children: jsxRuntimeExports.jsx(Suspense, { fallback: jsxRuntimeExports.jsx("div", { children: "Loading..." }), children: jsxRuntimeExports.jsx(LazySpatialAccelerated, { ...props }) }) }) }));
@@ -267044,7 +267059,7 @@ function HiglassGlobalStyles(props) {
 }
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-Dsba4gSg.js");
+  const { HiGlassComponent } = await import("./higlass-BE5OHbDt.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -269991,7 +270006,7 @@ function NeuroglancerGlobalStyles(props) {
   const { classes: classes2 } = props;
   return jsxRuntimeExports.jsxs(jsxRuntimeExports.Fragment, { children: [jsxRuntimeExports.jsx(GlobalStyles$3, { styles: globalNeuroglancerCss }), jsxRuntimeExports.jsx(ScopedGlobalStyles, { styles: globalNeuroglancerStyles, parentClassName: classes2.neuroglancerWrapper })] });
 }
-const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-CGvAuFr6.js"));
+const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-DmKC4Wha.js"));
 function createWorker() {
   return new WorkerFactory();
 }
@@ -356077,6 +356092,9 @@ class AnnDataSource extends ZarrDataSource {
   async getFlatArrDecompressed(path2) {
     const { storeRoot } = this;
     const arr = await open$1(storeRoot.resolve(path2), { kind: "array" });
+    if (arr.shape[0] === 0) {
+      return [];
+    }
     const data2 = await get$c(arr);
     if (data2.data?.[Symbol.iterator]) {
       return (
@@ -358391,20 +358409,39 @@ class SpatialDataObsPointsLoader extends AbstractTwoStepLoader {
      * @returns {Promise} A promise for an array of columns.
      */
   async loadPoints() {
-    const { path: path2, featureIndexColumn } = this.options;
+    const { path: path2 } = this.options;
     if (this.locations) {
       return this.locations;
     }
     let locations;
     const formatVersion = await this.dataSource.getPointsFormatVersion(path2);
     if (formatVersion === "0.1") {
-      locations = await this.dataSource.loadPoints(path2, featureIndexColumn);
+      locations = await this.dataSource.loadPoints(path2);
     } else {
       throw new UnknownSpatialDataFormatError("Only points format version 0.1 is supported.");
     }
     this.locations = locations;
     return this.locations;
   }
+  /**
+     * Class method for loading the feature index column for points.
+     * @returns {Promise} A promise for a column array of integers.
+     */
+  async loadPointsFeatureIds() {
+    const { path: path2 } = this.options;
+    if (this.locationsFeatureIndex) {
+      return this.locationsFeatureIndex;
+    }
+    let locationsFeatureIndex;
+    const formatVersion = await this.dataSource.getPointsFormatVersion(path2);
+    if (formatVersion === "0.1") {
+      locationsFeatureIndex = await this.dataSource.loadPointsFeatureIds(path2);
+    } else {
+      throw new UnknownSpatialDataFormatError("Only points format version 0.1 is supported.");
+    }
+    this.locationsFeatureIndex = locationsFeatureIndex;
+    return this.locationsFeatureIndex;
+  }
   async loadPointsInRect(bounds2, signal) {
     const { path: path2, featureIndexColumn, mortonCodeColumn } = this.options;
     let locations;
@@ -358467,23 +358504,19 @@ class SpatialDataObsPointsLoader extends AbstractTwoStepLoader {
     };
     let obsIndex = null;
     let obsPoints = null;
-    const featureIndices = null;
+    let featureIds = null;
     if (!supportsTiling) {
-      [obsIndex, obsPoints] = await Promise.all([
+      [obsIndex, obsPoints, featureIds] = await Promise.all([
         this.loadObsIndex(),
-        this.loadPoints()
+        this.loadPoints(),
+        this.loadPointsFeatureIds()
       ]);
     }
     return new LoaderResult({
-      /* obsIndex: ["1"], // TEMP
-      obsPoints: { // TEMP
-        shape: [2, 1],
-        data: [[0], [0]],
-      }, */
       // These will be null if tiling is supported.
       obsIndex,
       obsPoints,
-      featureIndices,
+      featureIds,
       obsPointsModelMatrix: modelMatrix2,
       // Return 'tiled' if the morton_code_2d column
       // and bounding_box metadata are present,
@@ -374884,14 +374917,13 @@ class SpatialDataPointsSource extends SpatialDataTableSource {
    *  shape: [number, number],
    * }>} A promise for a zarr array containing the data.
    */
-  async loadPoints(elementPath, featureIndexColumnNameFromOptions) {
+  async loadPoints(elementPath) {
     const parquetPath = getParquetPath(elementPath);
     const zattrs = await this.loadSpatialDataElementAttrs(elementPath);
-    const { axes, spatialdata_attrs: spatialDataAttrs } = zattrs;
+    const { axes } = zattrs;
     const normAxes = normalizeAxes(axes);
     const axisNames = normAxes.map((axis2) => axis2.name);
-    const { feature_key: featureKey } = spatialDataAttrs;
-    const columnNames = [...axisNames, featureKey].filter(Boolean);
+    const columnNames = axisNames.filter(Boolean);
     const arrowTable = await this.loadParquetTable(parquetPath, columnNames);
     const axisColumnArrs = axisNames.map((name2) => {
       const column2 = arrowTable.getChild(name2);
@@ -374905,6 +374937,30 @@ class SpatialDataPointsSource extends SpatialDataTableSource {
       data: axisColumnArrs
     };
   }
+  /**
+   *
+   * @param {string} elementPath The path to the points element,
+   * like "points/element_name".
+   * @param {string|undefined} featureIndexColumnNameFromOptions The name
+   * of the feature index column specified in the file definition options, if any.
+   * @returns {Promise<number[]>} A promise for a zarr array containing the data.
+   */
+  async loadPointsFeatureIds(elementPath) {
+    const parquetPath = getParquetPath(elementPath);
+    const zattrs = await this.loadSpatialDataElementAttrs(elementPath);
+    const { spatialdata_attrs: spatialDataAttrs } = zattrs;
+    const { feature_key: featureKey } = spatialDataAttrs;
+    const columnNames = [featureKey];
+    const arrowTable = await this.loadParquetTable(parquetPath, columnNames);
+    const axisColumnArrs = columnNames.map((name2) => {
+      const column2 = arrowTable.getChild(name2);
+      if (!column2) {
+        throw new Error(`Column "${name2}" not found in the arrow table.`);
+      }
+      return column2.toArray();
+    });
+    return axisColumnArrs[0];
+  }
   /**
    *
    * @param {string} elementPath

package/dist/{index-Do4xvqoi.js → index-txFb0D-X.js}

@@ -1,6 +1,6 @@
-import { aw as log, ax as isEqual, ar as Data3DTexture, as as RedFormat, ay as UnsignedByteType, l as LinearFilter, az as RedIntegerFormat, aA as UnsignedIntType, m as NearestFilter, e as Vector3, V as Vector2, ag as Vector4, ae as UniformsUtils, aq as CoordinationType, aB as WebGLMultipleRenderTargets, aC as RGBAFormat, av as Scene, W as OrthographicCamera, ad as ShaderMaterial, z as Mesh, aD as PlaneGeometry, aE as useEventCallback, ao as jsxRuntimeExports, aF as GLSL3, am as BackSide } from "./index-B-aCUFst.js";
+import { aw as log, ax as isEqual, ar as Data3DTexture, as as RedFormat, ay as UnsignedByteType, l as LinearFilter, az as RedIntegerFormat, aA as UnsignedIntType, m as NearestFilter, e as Vector3, V as Vector2, ag as Vector4, ae as UniformsUtils, aq as CoordinationType, aB as WebGLMultipleRenderTargets, aC as RGBAFormat, av as Scene, W as OrthographicCamera, ad as ShaderMaterial, z as Mesh, aD as PlaneGeometry, aE as useEventCallback, ao as jsxRuntimeExports, aF as GLSL3, am as BackSide } from "./index-DKpg3n-y.js";
 import { useRef, useState, useMemo, useEffect, Suspense } from "react";
-import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-BpeUSyh9.js";
+import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-DcLq7d8o.js";
 const LogLevel = {
   INFO: "info",
   WARN: "warn",

package/dist/index.js

@@ -1,4 +1,4 @@
-import { bR, bP, bN, bQ, bO, bM, bS } from "./index-B-aCUFst.js";
+import { bR, bP, bN, bQ, bO, bM, bS } from "./index-DKpg3n-y.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 export {
   bR as PluginAsyncFunction,

package/dist/{jpeg-BZSLq5O3.js → jpeg-DeFocpVz.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-BZk5g5T2.js → lerc-BCstSar4.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aG as getDefaultExportFromCjs, aX as BaseDecoder, aY as LercParameters, aZ as LercAddCompression } from "./index-B-aCUFst.js";
+import { aG as getDefaultExportFromCjs, aX as BaseDecoder, aY as LercParameters, aZ as LercAddCompression } from "./index-DKpg3n-y.js";
 var LercDecode = { exports: {} };
 var hasRequiredLercDecode;
 function requireLercDecode() {

package/dist/{lzw-fa9yKTSy.js → lzw-CMvKxrGF.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-8C0e8lDT.js → packbits-Crf3i8qg.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-fm6sEfJs.js → raw-QxVylWDO.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{troika-three-text.esm-Cf8otk5M.js → troika-three-text.esm-1SLW0Iby.js}

@@ -1,4 +1,4 @@
-import { bH as MeshDistanceMaterial, bI as MeshDepthMaterial, bJ as RGBADepthPacking, ae as UniformsUtils, bK as ShaderChunk, a9 as InstancedBufferGeometry, a8 as Sphere, a7 as Box3, am as BackSide, u as DoubleSide, z as Mesh, a5 as FrontSide, v as MeshBasicMaterial, C as Color, e as Vector3, M as Matrix4, V as Vector2, ap as Matrix3, ag as Vector4, a1 as Texture, l as LinearFilter, aD as PlaneGeometry, x as BufferGeometry, aa as Float32BufferAttribute, bL as InstancedBufferAttribute } from "./index-B-aCUFst.js";
+import { bH as MeshDistanceMaterial, bI as MeshDepthMaterial, bJ as RGBADepthPacking, ae as UniformsUtils, bK as ShaderChunk, a9 as InstancedBufferGeometry, a8 as Sphere, a7 as Box3, am as BackSide, u as DoubleSide, z as Mesh, a5 as FrontSide, v as MeshBasicMaterial, C as Color, e as Vector3, M as Matrix4, V as Vector2, ap as Matrix3, ag as Vector4, a1 as Texture, l as LinearFilter, aD as PlaneGeometry, x as BufferGeometry, aa as Float32BufferAttribute, bL as InstancedBufferAttribute } from "./index-DKpg3n-y.js";
 function workerBootstrap() {
   var modules = /* @__PURE__ */ Object.create(null);
   function registerModule(ref, callback) {

package/dist/{webimage-CyRSWQVR.js → webimage-DJBIWr5d.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-B-aCUFst.js";
+import { aX as BaseDecoder } from "./index-DKpg3n-y.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.9.1",
+  "version": "3.9.2",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,38 +17,38 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/styles": "3.9.1",
-    "@vitessce/abstract": "3.9.1",
-    "@vitessce/constants-internal": "3.9.1",
-    "@vitessce/error": "3.9.1",
-    "@vitessce/description": "3.9.1",
-    "@vitessce/feature-list": "3.9.1",
-    "@vitessce/genomic-profiles": "3.9.1",
-    "@vitessce/csv": "3.9.1",
-    "@vitessce/heatmap": "3.9.1",
-    "@vitessce/json": "3.9.1",
-    "@vitessce/layer-controller": "3.9.1",
-    "@vitessce/link-controller": "3.9.1",
-    "@vitessce/glb": "3.9.1",
-    "@vitessce/obs-sets-manager": "3.9.1",
-    "@vitessce/ome-tiff": "3.9.1",
-    "@vitessce/layer-controller-beta": "3.9.1",
-    "@vitessce/plugins": "3.9.1",
-    "@vitessce/scatterplot-gating": "3.9.1",
-    "@vitessce/scatterplot-embedding": "3.9.1",
-    "@vitessce/schemas": "3.9.1",
-    "@vitessce/statistical-plots": "3.9.1",
-    "@vitessce/spatial": "3.9.1",
-    "@vitessce/spatial-beta": "3.9.1",
-    "@vitessce/vit-s": "3.9.1",
-    "@vitessce/status": "3.9.1",
-    "@vitessce/zarr": "3.9.1",
-    "@vitessce/spatial-zarr": "3.9.1",
-    "@vitessce/globals": "3.9.1",
-    "@vitessce/spatial-three": "3.9.1",
-    "@vitessce/spatial-accelerated": "3.9.1",
-    "@vitessce/biomarker-select": "3.9.1",
-    "@vitessce/neuroglancer": "3.9.1"
+    "@vitessce/constants-internal": "3.9.2",
+    "@vitessce/abstract": "3.9.2",
+    "@vitessce/styles": "3.9.2",
+    "@vitessce/error": "3.9.2",
+    "@vitessce/csv": "3.9.2",
+    "@vitessce/description": "3.9.2",
+    "@vitessce/genomic-profiles": "3.9.2",
+    "@vitessce/feature-list": "3.9.2",
+    "@vitessce/heatmap": "3.9.2",
+    "@vitessce/glb": "3.9.2",
+    "@vitessce/json": "3.9.2",
+    "@vitessce/layer-controller": "3.9.2",
+    "@vitessce/layer-controller-beta": "3.9.2",
+    "@vitessce/plugins": "3.9.2",
+    "@vitessce/obs-sets-manager": "3.9.2",
+    "@vitessce/ome-tiff": "3.9.2",
+    "@vitessce/link-controller": "3.9.2",
+    "@vitessce/scatterplot-gating": "3.9.2",
+    "@vitessce/scatterplot-embedding": "3.9.2",
+    "@vitessce/spatial": "3.9.2",
+    "@vitessce/schemas": "3.9.2",
+    "@vitessce/statistical-plots": "3.9.2",
+    "@vitessce/status": "3.9.2",
+    "@vitessce/vit-s": "3.9.2",
+    "@vitessce/globals": "3.9.2",
+    "@vitessce/spatial-beta": "3.9.2",
+    "@vitessce/spatial-zarr": "3.9.2",
+    "@vitessce/spatial-three": "3.9.2",
+    "@vitessce/zarr": "3.9.2",
+    "@vitessce/spatial-accelerated": "3.9.2",
+    "@vitessce/biomarker-select": "3.9.2",
+    "@vitessce/neuroglancer": "3.9.2"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",