@vitessce/all 3.6.10 → 3.6.12

package/dist/{ReactNeuroglancer-DXQIZ-nA.js → ReactNeuroglancer-ClJTnYLU.js}

@@ -1,4 +1,4 @@
-import { g as getDefaultExportFromCjs, aV as requireAssign, aW as require_export, aX as require_core, aY as require_fails, aZ as require_toObject, a_ as require_objectKeys, a$ as require_cof, b0 as require_wks, b1 as require_iterators, b2 as requireWeb_dom_iterable, b3 as requireEs6_string_iterator, b4 as require_anObject, b5 as require_hide, b6 as require_ctx, b7 as require_toLength, b8 as require_global, b9 as require_objectDp, ba as require_descriptors, bb as require_isObject, bc as require_objectCreate, bd as require_iterDefine, be as require_iterStep, bf as require_meta, bg as require_isArray, bh as require_iobject, bi as require_setToStringTag, bj as require_aFunction, bk as requireIterator, bl as require_propertyDesc, aS as commonjsGlobal, bm as requireEs6_symbol, bn as requireDefineProperty, bo as require_toIobject, bp as require_objectGopd, bq as require_html, br as require_domCreate, bs as require_library, bt as requireSymbol, bu as require_objectPie, bv as require_has, bw as require_redefine, bx as require_objectAssign, by as getAugmentedNamespace, bz as requirePropTypes, aI as jsxRuntimeExports } from "./index-DaWuEqkA.js";
+import { g as getDefaultExportFromCjs, aV as requireAssign, aW as require_export, aX as require_core, aY as require_fails, aZ as require_toObject, a_ as require_objectKeys, a$ as require_cof, b0 as require_wks, b1 as require_iterators, b2 as requireWeb_dom_iterable, b3 as requireEs6_string_iterator, b4 as require_anObject, b5 as require_hide, b6 as require_ctx, b7 as require_toLength, b8 as require_global, b9 as require_objectDp, ba as require_descriptors, bb as require_isObject, bc as require_objectCreate, bd as require_iterDefine, be as require_iterStep, bf as require_meta, bg as require_isArray, bh as require_iobject, bi as require_setToStringTag, bj as require_aFunction, bk as requireIterator, bl as require_propertyDesc, aS as commonjsGlobal, bm as requireEs6_symbol, bn as requireDefineProperty, bo as require_toIobject, bp as require_objectGopd, bq as require_html, br as require_domCreate, bs as require_library, bt as requireSymbol, bu as require_objectPie, bv as require_has, bw as require_redefine, bx as require_objectAssign, by as getAugmentedNamespace, bz as requirePropTypes, aI as jsxRuntimeExports } from "./index-C4jXHZ0b.js";
 import React__default from "react";
 var lib = {};
 var assignExports = requireAssign();

package/dist/{deflate-BvInAYNe.js → deflate-m7-w-RAu.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{higlass-CgAQbB3K.js → higlass-BzR8ZcgQ.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 { aS as commonjsGlobal$1, aT as requireObjectAssign, g as getDefaultExportFromCjs$1, aU as earcut } from "./index-DaWuEqkA.js";
+import { aS as commonjsGlobal$1, aT as requireObjectAssign, g as getDefaultExportFromCjs$1, aU as earcut } from "./index-C4jXHZ0b.js";
 var promise = {};
 var hasRequiredPromise;
 function requirePromise() {

package/dist/{index-DaWuEqkA.js → index-C4jXHZ0b.js}

@@ -207897,7 +207897,8 @@ const PIXELATED_TEXTURE_PARAMETERS = {
 const GLSL_COLORMAPS = [
   "plasma",
   "viridis",
-  "jet"
+  "jet",
+  "greys"
 ];
 const GLSL_COLORMAP_DEFAULT = "plasma";
 const COLORMAP_SHADER_PLACEHOLDER = "COLORMAP_FUNC";
@@ -209668,22 +209669,22 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-fCTZmYt9.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-BMACI29v.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-3qJospDt.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-BwTxxip3.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-ChPg2CE2.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-BvInAYNe.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-IhnVESwp.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-Co9uTOBm.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-m7-w-RAu.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-1Z8M_gwl.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-C2XErs4B.js").then(async (m2) => {
+  () => import("./lerc-CAmIGmmt.js").then(async (m2) => {
     await m2.zstd.init();
     return m2;
   }).then((m2) => m2.default)
 );
-addDecoder(50001, () => import("./webimage-z9CP0_uw.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-BF_dP3bA.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -231817,6 +231818,9 @@ function Legend(props) {
       featureSelectionLabelRawStr = featureSelectionLabelRaw == null ? void 0 : featureSelectionLabelRaw[0];
     } else if (featureAggregationStrategy === "last") {
       featureSelectionLabelRawStr = featureSelectionLabelRaw == null ? void 0 : featureSelectionLabelRaw.at(-1);
+    } else if (typeof featureAggregationStrategy === "number") {
+      const i2 = featureAggregationStrategy;
+      featureSelectionLabelRawStr = featureSelectionLabelRaw == null ? void 0 : featureSelectionLabelRaw[i2];
     } else if (featureAggregationStrategy === "sum") {
       featureSelectionLabelRawStr = "Sum of features";
     } else if (featureAggregationStrategy === "mean") {
@@ -232231,7 +232235,7 @@ function EmbeddingScatterplotSubscriber(props) {
     return [1, 10, 100];
   }, [contourPercentiles, sortedWeights]);
   const circleInfo = useMemo$1(() => {
-    if (!originalViewState || !width2 || !height2) {
+    if (!originalViewState || !width2 || !height2 || !xRange || !yRange) {
       return null;
     }
     const center2 = [
@@ -232242,7 +232246,8 @@ function EmbeddingScatterplotSubscriber(props) {
     if (!(typeof scaleFactor === "number" && typeof center2[0] === "number" && typeof center2[1] === "number") || Number.isNaN(scaleFactor)) {
       return null;
     }
-    const radius2 = Math.min(width2, height2) / 2 / scaleFactor;
+    const size2 = Math.max(xRange, yRange);
+    const radius2 = size2 * Math.sqrt(2) / 2 * 0.8;
     const numPoints = 96;
     const options = { steps: numPoints, units: "degrees" };
     const circlePolygon = circle$5(center2, radius2, options);
@@ -232252,7 +232257,7 @@ function EmbeddingScatterplotSubscriber(props) {
       polygon: circlePolygon,
       steps: numPoints
     };
-  }, [originalViewState, width2, height2]);
+  }, [originalViewState, width2, height2, xRange, yRange]);
   const [alignedEmbeddingIndex, alignedEmbeddingData] = useMemo$1(() => {
     if ((obsEmbedding == null ? void 0 : obsEmbedding.data) && obsEmbeddingIndex && matrixObsIndex) {
       const matrixIndexMap = new Map(matrixObsIndex.map((key2, i2) => [key2, i2]));
@@ -247588,6 +247593,61 @@ function abbreviateNumber(value2) {
     return naive;
   return value2.toExponential(0);
 }
+class DAG {
+  /**
+     * DAG constructor.
+     * @param {{ from: string, to: string, attributes: any}[]} edges
+     */
+  constructor(edges) {
+    this.graph = /* @__PURE__ */ new Map();
+    this.edgeData = new InternMap$1([], JSON.stringify);
+    edges.forEach((edge) => {
+      const { from: from2, to } = edge;
+      if (!this.graph.has(from2)) {
+        this.graph.set(from2, []);
+      }
+      this.graph.get(from2).push(to);
+      this.edgeData.set([from2, to], edge.attributes);
+    });
+  }
+  /**
+   * Find a path from start to end using DFS.
+   * @param {string} start
+   * @param {string} end
+   * @returns {{ from: string, to: string, attributes: any }[] | null} Returns
+   * the path as an array of edges or null if no path exists.
+   */
+  findPath(start2, end2) {
+    const path2 = [];
+    const visited = /* @__PURE__ */ new Set();
+    const dfs = (node2) => {
+      if (node2 === end2) {
+        return true;
+      }
+      visited.add(node2);
+      const neighbors = this.graph.get(node2) || [];
+      for (const neighbor of neighbors) {
+        if (!visited.has(neighbor)) {
+          path2.push([node2, neighbor]);
+          if (dfs(neighbor)) {
+            return true;
+          }
+          path2.pop();
+        }
+      }
+      return false;
+    };
+    const found = dfs(start2);
+    if (found) {
+      return path2.map(([from2, to]) => ({
+        from: from2,
+        to,
+        attributes: this.edgeData.get([from2, to])
+      }));
+    }
+    return null;
+  }
+}
 function getSourceFromLoader(loader2, level) {
   const { data: data2 } = loader2;
   const source2 = Array.isArray(data2) ? data2[data2.length - 1] : data2;
@@ -247899,8 +247959,14 @@ function coordinateTransformationsToMatrix(coordinateTransformations, axes) {
           }
         } else if (spatialOutputAxes.length === 2) {
           const nextMat = new Matrix4$1().fromArray([
-            ...filteredAffine[0],
-            ...filteredAffine[1],
+            filteredAffine[0][0],
+            filteredAffine[0][1],
+            0,
+            filteredAffine[0][2],
+            filteredAffine[1][0],
+            filteredAffine[1][1],
+            0,
+            filteredAffine[1][2],
             0,
             0,
             1,
@@ -247916,6 +247982,7 @@ function coordinateTransformationsToMatrix(coordinateTransformations, axes) {
             const swapMat = new Matrix4$1().fromArray(swapMatNested.flat());
             mat = mat.multiplyLeft(swapMat);
           }
+          mat = mat.transpose();
         } else {
           throw new Error("Affine transformation must have 2 or 3 rows.");
         }
@@ -247942,6 +248009,9 @@ function coordinateTransformationsToMatrix(coordinateTransformations, axes) {
       }
     });
   }
+  if (mat.some((value2) => Number.isNaN(value2))) {
+    throw new Error("Matrix contains NaN values");
+  }
   return mat;
 }
 function hexToRgb(hex2) {
@@ -247960,6 +248030,9 @@ function normalizeAxes(axes) {
     return axisInfo;
   });
 }
+function getIntrinsicCoordinateSystem(normAxes) {
+  return normAxes.map((axis2) => axis2.name).join("");
+}
 function normalizeCoordinateTransformations(coordinateTransformations, datasets) {
   var _a3;
   let result = [];
@@ -247967,35 +248040,13 @@ function normalizeCoordinateTransformations(coordinateTransformations, datasets)
     result = coordinateTransformations.flatMap((transform3) => {
       if (transform3.input && transform3.output) {
         const { type: type2 } = transform3;
-        if (type2 === "translation") {
-          return {
-            type: type2,
-            translation: transform3.translation
-          };
-        }
-        if (type2 === "scale") {
-          return {
-            type: type2,
-            scale: transform3.scale
-          };
-        }
-        if (type2 === "affine") {
-          return {
-            type: type2,
-            affine: transform3.affine,
-            // Affine transformations can potentially swap axes,
-            // so we need to include the input and output axes.
-            input: transform3.input,
-            output: transform3.output
-          };
-        }
-        if (type2 === "identity") {
-          return { type: type2 };
-        }
         if (type2 === "sequence") {
-          return normalizeCoordinateTransformations(transform3.transformations, datasets);
+          return normalizeCoordinateTransformations(transform3.transformations, null);
+        }
+        if (type2 === "affine" || type2 === "translation" || type2 === "scale" || type2 === "identity") {
+          return transform3;
         }
-        log$b.warn(`Coordinate transformation type "${type2}" is not supported.`);
+        log$b.error(`Coordinate transformation type "${type2}" is not supported.`);
       }
       return transform3;
     });
@@ -248008,6 +248059,27 @@ function normalizeCoordinateTransformations(coordinateTransformations, datasets)
   }
   return result;
 }
+function coordinateTransformationsToMatrixForSpatialData(ngffMetadata, targetCoordinateSystem) {
+  const { datasets, coordinateTransformations, axes } = ngffMetadata;
+  const normAxes = normalizeAxes(axes);
+  const intrinsicCoordinateSystem = getIntrinsicCoordinateSystem(normAxes);
+  const edges = coordinateTransformations.map((ct) => ({
+    from: ct.input.name,
+    to: ct.output.name,
+    attributes: ct
+  }));
+  const dag = new DAG(edges);
+  const ctPath = dag.findPath(intrinsicCoordinateSystem, targetCoordinateSystem);
+  if (!ctPath) {
+    if (!coordinateTransformations.find((ct) => ct.output.name === targetCoordinateSystem)) {
+      throw new Error(`No coordinate transformation found with output.name "${targetCoordinateSystem}".`);
+    }
+    throw new Error(`No path found from "${intrinsicCoordinateSystem}" to "${targetCoordinateSystem}".`);
+  }
+  const filteredTransformations = ctPath.map((ctEdge) => ctEdge.attributes);
+  const normalizedTransformations = normalizeCoordinateTransformations(filteredTransformations, datasets);
+  return coordinateTransformationsToMatrix(normalizedTransformations, normAxes);
+}
 class NodeNotFoundError extends Error {
   constructor(context2, options = {}) {
     super(`Node not found: ${context2}`, options);
@@ -253488,7 +253560,7 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-CTf4FMp2.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-D1PvvaWO.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 }) }) }) }));
@@ -265329,7 +265401,7 @@ function HiglassGlobalStyles(props) {
 }
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-CgAQbB3K.js");
+  const { HiGlassComponent } = await import("./higlass-BzR8ZcgQ.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -268273,7 +268345,7 @@ function NeuroglancerGlobalStyles(props) {
   const { classes: classes2 } = props;
   return jsxRuntimeExports.jsxs(jsxRuntimeExports.Fragment, { children: [jsxRuntimeExports.jsx(GlobalStyles$3, { styles: globalNeuroglancerCss }), jsxRuntimeExports.jsx(ScopedGlobalStyles, { styles: globalNeuroglancerStyles, parentClassName: classes2.neuroglancerWrapper })] });
 }
-const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-DXQIZ-nA.js"));
+const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-ClJTnYLU.js"));
 function createWorker() {
   return new WorkerFactory();
 }
@@ -321761,26 +321833,7 @@ function ExpressionHistogramSubscriber(props) {
   return jsxRuntimeExports.jsx(TitleInfo, { title: `Histogram${firstGeneSelected ? ` (${firstGeneSelected})` : ""}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, errors, children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes2.vegaContainer, children: jsxRuntimeExports.jsx(ExpressionHistogram, { geneSelection, obsType, featureType, featureValueType, onSelect, data: data2, theme, width: width2, height: height2 }) }) });
 }
 function DotPlot(props) {
-  const {
-    isStratified,
-    transpose: transpose2,
-    data: rawData,
-    theme,
-    width: width2,
-    height: height2,
-    marginRight,
-    marginBottom,
-    obsType,
-    sampleType,
-    keyLength = 36,
-    featureType,
-    featureValueType,
-    featureValueTransformName,
-    // TODO: re-enable featureValueColormap coordination
-    // featureValueColormap,
-    obsSetSelection,
-    obsSetColor
-  } = props;
+  const { isStratified, transpose: transpose2, data: rawData, theme, width: width2, height: height2, marginRight, marginBottom, obsType, sampleType, keyLength = 36, featureType, featureValueType, featureValueTransformName, featureValueColormap, obsSetSelection, obsSetColor, onDotSelect } = props;
   const vegaContainerRef = useRef();
   const data2 = rawData.map((d) => ({
     ...d,
@@ -321818,6 +321871,26 @@ function DotPlot(props) {
       // Reference: https://vega.github.io/vega-lite/docs/mark.html
       opacity: 1
     },
+    params: [
+      {
+        name: "dot_select",
+        select: {
+          type: "point",
+          on: "click[event.shiftKey === false]",
+          fields: ["feature"],
+          empty: "none"
+        }
+      },
+      {
+        name: "shift_dot_select",
+        select: {
+          type: "point",
+          on: "click[event.shiftKey]",
+          fields: ["feature"],
+          empty: "none"
+        }
+      }
+    ],
     encoding: {
       [transpose2 ? "y" : "x"]: {
         field: "keyFeature",
@@ -321839,8 +321912,7 @@ function DotPlot(props) {
         type: "quantitative",
         title: meanTransform,
         scale: {
-          // scheme: featureValueColormap,
-          scheme: "greys"
+          scheme: featureValueColormap
         },
         legend: {
           direction: "horizontal",
@@ -321882,6 +321954,14 @@ function DotPlot(props) {
       } : {}
     }
   };
+  const handleSignal = (name2, value2) => {
+    if (name2 === "dot_select") {
+      onDotSelect(value2.feature);
+    } else if (name2 === "shift_dot_select") {
+      onDotSelect(value2.feature, true);
+    }
+  };
+  const signalListeners = { dot_select: handleSignal, shift_dot_select: handleSignal };
   const getTooltipText = useCallback((item) => ({
     [`${capitalize$3(featureType)}`]: item.datum.feature,
     [`${capitalize$3(obsType)} Set`]: item.datum.group,
@@ -321906,7 +321986,7 @@ function DotPlot(props) {
   useEffect(() => {
     setVegaRenderIncrement((prev2) => prev2 + 1);
   }, [rawData]);
-  return jsxRuntimeExports.jsx("div", { ref: vegaContainerRef, children: jsxRuntimeExports.jsx(VegaPlot, { data: data2, spec, onNewView, getTooltipText, renderer: "svg" }) });
+  return jsxRuntimeExports.jsx("div", { ref: vegaContainerRef, children: jsxRuntimeExports.jsx(VegaPlot, { data: data2, spec, onNewView, signalListeners, getTooltipText, renderer: "svg" }) });
 }
 function useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, posThreshold, featureLabelsMap) {
   const mergedCellSets = useMemo$1(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
@@ -321962,7 +322042,24 @@ function DotPlotSubscriber(props) {
   const { coordinationScopes, removeGridComponent, theme, title: title2 = "Dot Plot", transpose: transpose2 = true, helpText = ViewHelpMapping.DOT_PLOT } = props;
   const { classes: classes2 } = useStyles$3();
   const loaders = useLoaders();
-  const [{ dataset, obsType, featureType, featureValueType, featureSelection: geneSelection, featureValueTransform, featureValueTransformCoefficient, featureValuePositivityThreshold: posThreshold, featureValueColormap, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, sampleType, sampleSetSelection }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, setFeatureValuePositivityThreshold: setPosThreshold, setFeatureValueColormap }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.DOT_PLOT], coordinationScopes);
+  const [{
+    dataset,
+    obsType,
+    featureType,
+    featureValueType,
+    featureSelection: geneSelection,
+    featureValueTransform,
+    featureValueTransformCoefficient,
+    featureValuePositivityThreshold: posThreshold,
+    featureValueColormap,
+    obsSetSelection: cellSetSelection,
+    obsSetColor: cellSetColor,
+    additionalObsSets: additionalCellSets,
+    sampleType,
+    sampleSetSelection,
+    // eslint-disable-next-line no-unused-vars
+    featureAggregationStrategy
+  }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, setFeatureValuePositivityThreshold: setPosThreshold, setFeatureValueColormap, setFeatureAggregationStrategy }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.DOT_PLOT], coordinationScopes);
   const [width2, height2, containerRef] = useGridItemSize();
   const transformOptions = VALUE_TRANSFORM_OPTIONS;
   const isStratified = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 1;
@@ -322003,7 +322100,13 @@ function DotPlotSubscriber(props) {
   ]);
   const [resultArr, meanExpressionMax] = useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, posThreshold, featureLabelsMap);
   const selectedTransformName = (_a3 = transformOptions.find((o2) => o2.value === featureValueTransform)) == null ? void 0 : _a3.name;
-  return jsxRuntimeExports.jsx(TitleInfo, { title: title2, removeGridComponent, urls: urls2, theme, isReady, helpText, errors, options: jsxRuntimeExports.jsx(CellSetExpressionPlotOptions, { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, featureValuePositivityThreshold: posThreshold, setFeatureValuePositivityThreshold: setPosThreshold, featureValueColormap, setFeatureValueColormap }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes2.vegaContainer, children: resultArr ? jsxRuntimeExports.jsx(DotPlot, { isStratified, transpose: transpose2, domainMax: meanExpressionMax, data: resultArr, theme, width: width2, height: height2, obsType, sampleType, featureType, featureValueType, featureValueTransformName: selectedTransformName, featureValueColormap, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }) : jsxRuntimeExports.jsxs("span", { children: ["Select at least one ", featureType, "."] }) }) });
+  const onDotSelect = useCallback((featureName, isShiftDown = false) => {
+    const featureI = geneSelection.indexOf(featureName == null ? void 0 : featureName[0]);
+    if (featureI >= 0) {
+      setFeatureAggregationStrategy(featureI);
+    }
+  }, [setFeatureAggregationStrategy, geneSelection]);
+  return jsxRuntimeExports.jsx(TitleInfo, { title: title2, removeGridComponent, urls: urls2, theme, isReady, helpText, errors, options: jsxRuntimeExports.jsx(CellSetExpressionPlotOptions, { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, featureValuePositivityThreshold: posThreshold, setFeatureValuePositivityThreshold: setPosThreshold, featureValueColormap, setFeatureValueColormap }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes2.vegaContainer, children: resultArr ? jsxRuntimeExports.jsx(DotPlot, { isStratified, transpose: transpose2, domainMax: meanExpressionMax, data: resultArr, theme, width: width2, height: height2, obsType, sampleType, featureType, featureValueType, featureValueTransformName: selectedTransformName, featureValueColormap, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, onDotSelect }) : jsxRuntimeExports.jsxs("span", { children: ["Select at least one ", featureType, "."] }) }) });
 }
 const scaleBand = scale$6("band");
 const OBS_KEY = "obsId";
@@ -325787,13 +325890,22 @@ class ImageWrapper {
     return this.modelMatrix;
   }
   _getModelMatrix() {
-    const { coordinateTransformations: coordinateTransformationsFromOptions } = this.options;
+    const { coordinateSystem = "global", coordinateTransformations: coordinateTransformationsFromOptions } = this.options;
     if ("multiscales" in this.vivLoader.metadata) {
       const { multiscales: [{ datasets, coordinateTransformations: coordinateTransformationsFromFile, axes }] } = this.vivLoader.metadata;
       const ngffAxes = getNgffAxes(axes);
       const transformMatrixFromOptions = coordinateTransformationsToMatrix(coordinateTransformationsFromOptions, ngffAxes);
-      const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, datasets);
-      const transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, ngffAxes);
+      let transformMatrixFromFile;
+      if ("spatialdata_attrs" in this.vivLoader.metadata) {
+        transformMatrixFromFile = coordinateTransformationsToMatrixForSpatialData(
+          // Pass the first multiscales element.
+          this.vivLoader.metadata.multiscales[0],
+          coordinateSystem
+        );
+      } else {
+        const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, datasets);
+        transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, ngffAxes);
+      }
       const transformMatrix = transformMatrixFromFile.multiplyLeft(transformMatrixFromOptions);
       return transformMatrix;
     }
@@ -326285,16 +326397,7 @@ class SpatialDataLabelsLoader extends SpatialDataImageLoader {
     return result;
   }
 }
-function getCoordsPath(path2) {
-  return `${path2}/coords`;
-}
-function getRadiusPath(path2) {
-  return `${path2}/radius`;
-}
-function getGeometryPath$1(path2) {
-  return `${path2}/geometry`;
-}
-const DEFAULT_AXES$1 = [
+const OLD_SHAPES_DEFAULT_AXES = [
   {
     name: "x",
     type: "space",
@@ -326306,7 +326409,7 @@ const DEFAULT_AXES$1 = [
     unit: "unit"
   }
 ];
-const DEFAULT_COORDINATE_TRANSFORMATIONS$1 = [
+const OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS = [
   {
     input: {
       axes: [
@@ -326341,6 +326444,15 @@ const DEFAULT_COORDINATE_TRANSFORMATIONS$1 = [
     type: "identity"
   }
 ];
+function getCoordsPath(path2) {
+  return `${path2}/coords`;
+}
+function getRadiusPath(path2) {
+  return `${path2}/radius`;
+}
+function getGeometryPath$1(path2) {
+  return `${path2}/geometry`;
+}
 class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
   async loadModelMatrix() {
     const { path: path2, coordinateSystem = "global" } = this.options;
@@ -326348,12 +326460,9 @@ class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
       return this.modelMatrix;
     }
     const zattrs = await this.dataSource.loadSpatialDataElementAttrs(path2);
-    const coordinateTransformationsFromFile = ((zattrs == null ? void 0 : zattrs.coordinateTransformations) || DEFAULT_COORDINATE_TRANSFORMATIONS$1).filter(({ input: { name: inputName }, output: { name: outputName } }) => inputName === "xy" && outputName === coordinateSystem);
-    const axes = (zattrs == null ? void 0 : zattrs.axes) ?? DEFAULT_AXES$1;
-    const normAxes = normalizeAxes(axes);
-    const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, null);
-    const transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, normAxes);
-    this.modelMatrix = transformMatrixFromFile;
+    const coordinateTransformations = (zattrs == null ? void 0 : zattrs.coordinateTransformations) ?? OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS;
+    const axes = (zattrs == null ? void 0 : zattrs.axes) ?? OLD_SHAPES_DEFAULT_AXES;
+    this.modelMatrix = coordinateTransformationsToMatrixForSpatialData({ axes, coordinateTransformations }, coordinateSystem);
     return this.modelMatrix;
   }
   /**
@@ -326452,53 +326561,6 @@ class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
 function getGeometryPath(path2) {
   return `${path2}/geometry`;
 }
-const DEFAULT_AXES = [
-  {
-    name: "x",
-    type: "space",
-    unit: "unit"
-  },
-  {
-    name: "y",
-    type: "space",
-    unit: "unit"
-  }
-];
-const DEFAULT_COORDINATE_TRANSFORMATIONS = [
-  {
-    input: {
-      axes: [
-        {
-          name: "x",
-          type: "space",
-          unit: "unit"
-        },
-        {
-          name: "y",
-          type: "space",
-          unit: "unit"
-        }
-      ],
-      name: "xy"
-    },
-    output: {
-      axes: [
-        {
-          name: "x",
-          type: "space",
-          unit: "unit"
-        },
-        {
-          name: "y",
-          type: "space",
-          unit: "unit"
-        }
-      ],
-      name: "global"
-    },
-    type: "identity"
-  }
-];
 class SpatialDataObsSegmentationsLoader extends AbstractTwoStepLoader {
   async loadModelMatrix() {
     const { path: path2, coordinateSystem = "global" } = this.options;
@@ -326506,12 +326568,9 @@ class SpatialDataObsSegmentationsLoader extends AbstractTwoStepLoader {
       return this.modelMatrix;
     }
     const zattrs = await this.dataSource.loadSpatialDataElementAttrs(path2);
-    const coordinateTransformationsFromFile = ((zattrs == null ? void 0 : zattrs.coordinateTransformations) ?? DEFAULT_COORDINATE_TRANSFORMATIONS).filter(({ input: { name: inputName }, output: { name: outputName } }) => inputName === "xy" && outputName === coordinateSystem);
-    const axes = (zattrs == null ? void 0 : zattrs.axes) ?? DEFAULT_AXES;
-    const normAxes = normalizeAxes(axes);
-    const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, null);
-    const transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, normAxes);
-    this.modelMatrix = transformMatrixFromFile;
+    const coordinateTransformations = (zattrs == null ? void 0 : zattrs.coordinateTransformations) ?? OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS;
+    const axes = (zattrs == null ? void 0 : zattrs.axes) ?? OLD_SHAPES_DEFAULT_AXES;
+    this.modelMatrix = coordinateTransformationsToMatrixForSpatialData({ axes, coordinateTransformations }, coordinateSystem);
     return this.modelMatrix;
   }
   /**
@@ -326588,11 +326647,7 @@ class SpatialDataObsPointsLoader extends AbstractTwoStepLoader {
     if (!coordinateTransformations) {
       throw new Error("The coordinate transformations metadata must be defined for point elements.");
     }
-    const normAxes = normalizeAxes(axes);
-    const coordinateTransformationsFromFile = coordinateTransformations.filter(({ input: { name: inputName }, output: { name: outputName } }) => inputName === "xyz" && outputName === coordinateSystem);
-    const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, null);
-    const transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, normAxes);
-    this.modelMatrix = transformMatrixFromFile;
+    this.modelMatrix = coordinateTransformationsToMatrixForSpatialData({ axes, coordinateTransformations }, coordinateSystem);
     return this.modelMatrix;
   }
   /**
@@ -336224,7 +336279,7 @@ class SpatialDataTableSource extends AnnDataSource {
         const schemaBytes = await this.loadParquetSchemaBytes(parquetPath);
         if (schemaBytes) {
           const wasmSchema = readSchema(schemaBytes);
-          const arrowTableForSchema = tableFromIPC(wasmSchema.intoIPCStream());
+          const arrowTableForSchema = await tableFromIPC(wasmSchema.intoIPCStream());
           indexColumnName = tableToIndexColumnName(arrowTableForSchema);
         }
       } catch (e3) {
@@ -336240,14 +336295,14 @@ class SpatialDataTableSource extends AnnDataSource {
     }
     if (columns2 && !indexColumnName) {
       const wasmSchema = readSchema(parquetBytes);
-      const arrowTableForSchema = tableFromIPC(wasmSchema.intoIPCStream());
+      const arrowTableForSchema = await tableFromIPC(wasmSchema.intoIPCStream());
       indexColumnName = tableToIndexColumnName(arrowTableForSchema);
     }
     if (options.columns && indexColumnName) {
       options.columns = [...options.columns, indexColumnName];
     }
     const wasmTable = readParquet(parquetBytes, options);
-    const arrowTable = tableFromIPC(wasmTable.intoIPCStream());
+    const arrowTable = await tableFromIPC(wasmTable.intoIPCStream());
     return arrowTable;
   }
   // TABLE-SPECIFIC METHODS

package/dist/{index-CTf4FMp2.js → index-D1PvvaWO.js}

@@ -1,4 +1,4 @@
-import { g as getDefaultExportFromCjs, R as Raycaster, O as OrthographicCamera, P as PerspectiveCamera, S as Scene, a as PCFSoftShadowMap, V as VSMShadowMap, b as PCFShadowMap, B as BasicShadowMap, N as NoToneMapping, A as ACESFilmicToneMapping, c as Vector3, d as Vector2, C as Clock, W as WebGLRenderer, e as Camera, f as BufferGeometry, M as Material, L as Layers, T as Texture, h as RGBAFormat, U as UnsignedByteType, i as Color, _ as _extends, j as THREE, G as Group, k as Matrix4, l as TrianglesDrawMode, m as TriangleFanDrawMode, n as TriangleStripDrawMode, o as REVISION, E as EventDispatcher, p as MOUSE, q as TOUCH, r as Spherical, Q as Quaternion, s as Ray$1, t as Plane, u as Loader, v as LoaderUtils, F as FileLoader, w as MeshPhysicalMaterial, x as SpotLight, y as PointLight, D as DirectionalLight, I as InstancedMesh, z as Object3D, H as TextureLoader, J as ImageBitmapLoader, K as BufferAttribute, X as InterleavedBuffer, Y as LinearMipmapLinearFilter, Z as NearestMipmapLinearFilter, $ as LinearMipmapNearestFilter, a0 as NearestMipmapNearestFilter, a1 as LinearFilter, a2 as NearestFilter, a3 as RepeatWrapping, a4 as MirroredRepeatWrapping, a5 as ClampToEdgeWrapping, a6 as PointsMaterial, a7 as LineBasicMaterial, a8 as MeshStandardMaterial, a9 as DoubleSide, aa as MeshBasicMaterial, ab as PropertyBinding, ac as SkinnedMesh, ad as Mesh, ae as LineSegments, af as Line$1, ag as LineLoop, ah as Points, ai as MathUtils, aj as Skeleton, ak as InterpolateDiscrete, al as InterpolateLinear, am as AnimationClip, an as Bone, ao as InterleavedBufferAttribute, ap as VectorKeyframeTrack, aq as QuaternionKeyframeTrack, ar as NumberKeyframeTrack, as as FrontSide, at as Interpolant, au as Box3, av as Sphere, aw as InstancedBufferGeometry, ax as Float32BufferAttribute, ay as InstancedInterleavedBuffer, az as WireframeGeometry, aA as ShaderMaterial, aB as UniformsUtils, aC as UniformsLib, aD as Vector4, aE as Line3, aF as SphereGeometry, aG as Triangle, aH as BackSide, aI as jsxRuntimeExports, aJ as Matrix3, aK as CoordinationType, aL as Data3DTexture, aM as RedFormat, aN as FloatType, aO as getImageSize } from "./index-DaWuEqkA.js";
+import { g as getDefaultExportFromCjs, R as Raycaster, O as OrthographicCamera, P as PerspectiveCamera, S as Scene, a as PCFSoftShadowMap, V as VSMShadowMap, b as PCFShadowMap, B as BasicShadowMap, N as NoToneMapping, A as ACESFilmicToneMapping, c as Vector3, d as Vector2, C as Clock, W as WebGLRenderer, e as Camera, f as BufferGeometry, M as Material, L as Layers, T as Texture, h as RGBAFormat, U as UnsignedByteType, i as Color, _ as _extends, j as THREE, G as Group, k as Matrix4, l as TrianglesDrawMode, m as TriangleFanDrawMode, n as TriangleStripDrawMode, o as REVISION, E as EventDispatcher, p as MOUSE, q as TOUCH, r as Spherical, Q as Quaternion, s as Ray$1, t as Plane, u as Loader, v as LoaderUtils, F as FileLoader, w as MeshPhysicalMaterial, x as SpotLight, y as PointLight, D as DirectionalLight, I as InstancedMesh, z as Object3D, H as TextureLoader, J as ImageBitmapLoader, K as BufferAttribute, X as InterleavedBuffer, Y as LinearMipmapLinearFilter, Z as NearestMipmapLinearFilter, $ as LinearMipmapNearestFilter, a0 as NearestMipmapNearestFilter, a1 as LinearFilter, a2 as NearestFilter, a3 as RepeatWrapping, a4 as MirroredRepeatWrapping, a5 as ClampToEdgeWrapping, a6 as PointsMaterial, a7 as LineBasicMaterial, a8 as MeshStandardMaterial, a9 as DoubleSide, aa as MeshBasicMaterial, ab as PropertyBinding, ac as SkinnedMesh, ad as Mesh, ae as LineSegments, af as Line$1, ag as LineLoop, ah as Points, ai as MathUtils, aj as Skeleton, ak as InterpolateDiscrete, al as InterpolateLinear, am as AnimationClip, an as Bone, ao as InterleavedBufferAttribute, ap as VectorKeyframeTrack, aq as QuaternionKeyframeTrack, ar as NumberKeyframeTrack, as as FrontSide, at as Interpolant, au as Box3, av as Sphere, aw as InstancedBufferGeometry, ax as Float32BufferAttribute, ay as InstancedInterleavedBuffer, az as WireframeGeometry, aA as ShaderMaterial, aB as UniformsUtils, aC as UniformsLib, aD as Vector4, aE as Line3, aF as SphereGeometry, aG as Triangle, aH as BackSide, aI as jsxRuntimeExports, aJ as Matrix3, aK as CoordinationType, aL as Data3DTexture, aM as RedFormat, aN as FloatType, aO as getImageSize } from "./index-C4jXHZ0b.js";
 import * as React from "react";
 import React__default, { useReducer, useRef, useEffect, useLayoutEffect, useDebugValue, useState, useMemo, forwardRef } from "react";
 var constants = { exports: {} };
@@ -23637,7 +23637,7 @@ const Text = /* @__PURE__ */ React.forwardRef(({
   const {
     Text: TextMeshImpl,
     preloadFont
-  } = suspend(async () => import("./troika-three-text.esm-DE8UoVN4.js"), []);
+  } = suspend(async () => import("./troika-three-text.esm-DxxlvoUc.js"), []);
   const invalidate2 = useThree(({
     invalidate: invalidate3
   }) => invalidate3);

package/dist/index.js

@@ -1,4 +1,4 @@
-import { bL, bJ, bH, bK, bI, bG, bM } from "./index-DaWuEqkA.js";
+import { bL, bJ, bH, bK, bI, bG, bM } from "./index-C4jXHZ0b.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 export {
   bL as PluginAsyncFunction,

package/dist/{jpeg-ChPg2CE2.js → jpeg-Co9uTOBm.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-C2XErs4B.js → lerc-CAmIGmmt.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-DaWuEqkA.js";
+import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-C4jXHZ0b.js";
 var LercDecode = { exports: {} };
 var hasRequiredLercDecode;
 function requireLercDecode() {

package/dist/{lzw-BMACI29v.js → lzw-BwTxxip3.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-IhnVESwp.js → packbits-1Z8M_gwl.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-fCTZmYt9.js → raw-3qJospDt.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{troika-three-text.esm-DE8UoVN4.js → troika-three-text.esm-DxxlvoUc.js}

@@ -1,4 +1,4 @@
-import { bA as MeshDistanceMaterial, bB as MeshDepthMaterial, bC as RGBADepthPacking, aB as UniformsUtils, bD as ShaderChunk, aw as InstancedBufferGeometry, av as Sphere, au as Box3, aH as BackSide, a9 as DoubleSide, ad as Mesh, as as FrontSide, aa as MeshBasicMaterial, i as Color, c as Vector3, k as Matrix4, d as Vector2, aJ as Matrix3, aD as Vector4, T as Texture, a1 as LinearFilter, bE as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, bF as InstancedBufferAttribute } from "./index-DaWuEqkA.js";
+import { bA as MeshDistanceMaterial, bB as MeshDepthMaterial, bC as RGBADepthPacking, aB as UniformsUtils, bD as ShaderChunk, aw as InstancedBufferGeometry, av as Sphere, au as Box3, aH as BackSide, a9 as DoubleSide, ad as Mesh, as as FrontSide, aa as MeshBasicMaterial, i as Color, c as Vector3, k as Matrix4, d as Vector2, aJ as Matrix3, aD as Vector4, T as Texture, a1 as LinearFilter, bE as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, bF as InstancedBufferAttribute } from "./index-C4jXHZ0b.js";
 function workerBootstrap() {
   var modules = /* @__PURE__ */ Object.create(null);
   function registerModule(ref, callback) {

package/dist/{webimage-z9CP0_uw.js → webimage-BF_dP3bA.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-DaWuEqkA.js";
+import { aP as BaseDecoder } from "./index-C4jXHZ0b.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.6.10",
+  "version": "3.6.12",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,37 +17,37 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/styles": "3.6.10",
-    "@vitessce/constants-internal": "3.6.10",
-    "@vitessce/abstract": "3.6.10",
-    "@vitessce/error": "3.6.10",
-    "@vitessce/csv": "3.6.10",
-    "@vitessce/description": "3.6.10",
-    "@vitessce/feature-list": "3.6.10",
-    "@vitessce/genomic-profiles": "3.6.10",
-    "@vitessce/heatmap": "3.6.10",
-    "@vitessce/glb": "3.6.10",
-    "@vitessce/json": "3.6.10",
-    "@vitessce/layer-controller": "3.6.10",
-    "@vitessce/layer-controller-beta": "3.6.10",
-    "@vitessce/link-controller": "3.6.10",
-    "@vitessce/obs-sets-manager": "3.6.10",
-    "@vitessce/ome-tiff": "3.6.10",
-    "@vitessce/plugins": "3.6.10",
-    "@vitessce/scatterplot-embedding": "3.6.10",
-    "@vitessce/scatterplot-gating": "3.6.10",
-    "@vitessce/schemas": "3.6.10",
-    "@vitessce/spatial": "3.6.10",
-    "@vitessce/spatial-beta": "3.6.10",
-    "@vitessce/statistical-plots": "3.6.10",
-    "@vitessce/status": "3.6.10",
-    "@vitessce/vit-s": "3.6.10",
-    "@vitessce/zarr": "3.6.10",
-    "@vitessce/globals": "3.6.10",
-    "@vitessce/spatial-zarr": "3.6.10",
-    "@vitessce/spatial-three": "3.6.10",
-    "@vitessce/biomarker-select": "3.6.10",
-    "@vitessce/neuroglancer": "3.6.10"
+    "@vitessce/styles": "3.6.12",
+    "@vitessce/constants-internal": "3.6.12",
+    "@vitessce/abstract": "3.6.12",
+    "@vitessce/error": "3.6.12",
+    "@vitessce/csv": "3.6.12",
+    "@vitessce/description": "3.6.12",
+    "@vitessce/feature-list": "3.6.12",
+    "@vitessce/genomic-profiles": "3.6.12",
+    "@vitessce/heatmap": "3.6.12",
+    "@vitessce/glb": "3.6.12",
+    "@vitessce/json": "3.6.12",
+    "@vitessce/layer-controller": "3.6.12",
+    "@vitessce/layer-controller-beta": "3.6.12",
+    "@vitessce/link-controller": "3.6.12",
+    "@vitessce/obs-sets-manager": "3.6.12",
+    "@vitessce/ome-tiff": "3.6.12",
+    "@vitessce/plugins": "3.6.12",
+    "@vitessce/scatterplot-embedding": "3.6.12",
+    "@vitessce/scatterplot-gating": "3.6.12",
+    "@vitessce/schemas": "3.6.12",
+    "@vitessce/spatial": "3.6.12",
+    "@vitessce/spatial-beta": "3.6.12",
+    "@vitessce/statistical-plots": "3.6.12",
+    "@vitessce/status": "3.6.12",
+    "@vitessce/vit-s": "3.6.12",
+    "@vitessce/zarr": "3.6.12",
+    "@vitessce/globals": "3.6.12",
+    "@vitessce/spatial-zarr": "3.6.12",
+    "@vitessce/spatial-three": "3.6.12",
+    "@vitessce/biomarker-select": "3.6.12",
+    "@vitessce/neuroglancer": "3.6.12"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",