@vitessce/all 3.5.11 → 3.5.12

package/dist/{deflate-916bb37d.js → deflate-327fa967.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{higlass-5022c0ac.js → higlass-a114d38b.js}

@@ -1,6 +1,6 @@
 import React__default, { createElement, isValidElement, PureComponent, Component } from "react";
 import ReactDOM__default, { findDOMNode as findDOMNode$1 } from "react-dom";
-import { aS as commonjsGlobal$1, aT as objectAssign, g as getDefaultExportFromCjs$1, aU as earcut } from "./index-b2384476.js";
+import { aS as commonjsGlobal$1, aT as objectAssign, g as getDefaultExportFromCjs$1, aU as earcut } from "./index-c7da990c.js";
 import "@vitessce/vit-s";
 var promise = {};
 (function(exports2) {

package/dist/{index-9fa0b8f0.js → index-9c4bd1c8.js}

@@ -1,4 +1,4 @@
-import { aV as _export, aW as _coreExports, aX as _fails, aY as _toObject, aZ as _objectKeys, g as getDefaultExportFromCjs, a_ as _wksExports, a$ as _cof, b0 as _iterators, b1 as _anObject, b2 as _hide, b3 as _ctx, b4 as _toLength, b5 as _globalExports, b6 as _objectDp, b7 as _descriptors, b8 as _isObject, b9 as _metaExports, ba as _objectCreate, bb as _iterDefine, bc as _iterStep, bd as _isArray, be as _iobject, bf as _setToStringTag, bg as _aFunction, bh as _propertyDesc, bi as _root, bj as _baseGetTag, bk as isObjectLike_1, bl as isObject_1, bm as _Symbol$iterator, bn as _Object$assign, bo as _objectGopd, bp as _toIobject, bq as _html, br as _domCreate, bs as _library, bt as _Object$defineProperty, bu as _Symbol, bv as _objectPie, bw as _has, bx as _redefine, by as _objectAssign, aS as commonjsGlobal, bz as getAugmentedNamespace, bA as propTypesExports } from "./index-b2384476.js";
+import { aV as _export, aW as _coreExports, aX as _fails, aY as _toObject, aZ as _objectKeys, g as getDefaultExportFromCjs, a_ as _wksExports, a$ as _cof, b0 as _iterators, b1 as _anObject, b2 as _hide, b3 as _ctx, b4 as _toLength, b5 as _globalExports, b6 as _objectDp, b7 as _descriptors, b8 as _isObject, b9 as _metaExports, ba as _objectCreate, bb as _iterDefine, bc as _iterStep, bd as _isArray, be as _iobject, bf as _setToStringTag, bg as _aFunction, bh as _propertyDesc, bi as _root, bj as _baseGetTag, bk as isObjectLike_1, bl as isObject_1, bm as _Symbol$iterator, bn as _Object$assign, bo as _objectGopd, bp as _toIobject, bq as _html, br as _domCreate, bs as _library, bt as _Object$defineProperty, bu as _Symbol, bv as _objectPie, bw as _has, bx as _redefine, by as _objectAssign, aS as commonjsGlobal, bz as getAugmentedNamespace, bA as propTypesExports } from "./index-c7da990c.js";
 import React__default from "react";
 function _mergeNamespaces(n, m) {
   for (var i = 0; i < m.length; i++) {

package/dist/{index-b2384476.js → index-c7da990c.js}

@@ -10820,7 +10820,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.MOLECULE_HIGHLIGHT,
-    CoordinationType$1.TOOLTIPS_VISIBLE
+    CoordinationType$1.TOOLTIPS_VISIBLE,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.SPATIAL_BETA]: [
     CoordinationType$1.META_COORDINATION_SCOPES,
@@ -10893,7 +10894,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.LEGEND_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_ORIENTATION,
-    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE
+    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.HEATMAP]: [
     CoordinationType$1.DATASET,
@@ -11008,7 +11010,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_ROTATION_Y,
     CoordinationType$1.SPATIAL_ROTATION_Z,
     CoordinationType$1.SPATIAL_ROTATION_ORBIT,
-    CoordinationType$1.SPATIAL_ORBIT_AXIS
+    CoordinationType$1.SPATIAL_ORBIT_AXIS,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.LAYER_CONTROLLER_BETA]: [
     CoordinationType$1.META_COORDINATION_SCOPES,
@@ -177346,16 +177349,16 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-7ad8e084.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-ffd426d3.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-1af0a143.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-615797a2.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-8687eb38.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-916bb37d.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-3388263e.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-42867a4a.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-60247a11.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-32441425.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-327fa967.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-b9451794.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-84a2944c.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-40ad658c.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -213005,9 +213008,6 @@ function physicalSizeToMatrix(xSize, ySize, zSize, xUnit, yUnit, zUnit) {
     sizes.push(unit$1(`${zSize} ${zUnit}`.replace("µ", "u")));
   }
   const scale2 = sizes.map((i2) => divide(i2, unit$1("1 um")));
-  if (!sizes[0].equals(sizes[1])) {
-    scale2[1] = divide(sizes[1], sizes[0]);
-  }
   if (!scale2[2]) {
     scale2[2] = 1;
   }
@@ -216511,6 +216511,7 @@ let Spatial$1 = class Spatial extends AbstractSpatialOrScatterplot {
     return null;
   }
   createRasterLayer(rawLayerDef, loader2, i2) {
+    const { photometricInterpretation } = this.props;
     const layerDef = {
       ...rawLayerDef,
       channels: rawLayerDef.channels.filter((channel) => channel.selection && channel.color && channel.slider)
@@ -216589,6 +216590,23 @@ let Spatial$1 = class Spatial extends AbstractSpatialOrScatterplot {
     if (isInterleaved$1((Array.isArray(data2) ? data2[0] : data2).shape)) {
       rgbInterleavedProps.visible = layerDef.visible;
     }
+    const rgbProps = photometricInterpretation === "RGB" ? {
+      colors: [
+        [255, 0, 0],
+        [0, 255, 0],
+        [0, 0, 255]
+      ],
+      contrastLimits: [
+        [0, 255],
+        [0, 255],
+        [0, 255]
+      ],
+      channelsVisible: [
+        true,
+        true,
+        true
+      ]
+    } : {};
     return new Layer2({
       loader: layerLoader,
       id: `${layerDef.use3d ? "volume" : "image"}-layer-${layerDef.index}-${i2}`,
@@ -216610,7 +216628,8 @@ let Spatial$1 = class Spatial extends AbstractSpatialOrScatterplot {
       onViewportLoad: layerProps.callback,
       excludeBackground: layerProps.excludeBackground,
       extensions,
-      ...rgbInterleavedProps
+      ...rgbInterleavedProps,
+      ...rgbProps
     });
   }
   use3d() {
@@ -216829,7 +216848,8 @@ let Spatial$1 = class Spatial extends AbstractSpatialOrScatterplot {
       "geneExpressionColormapRange",
       "expressionData",
       "imageLayerCallbacks",
-      "geneExpressionColormap"
+      "geneExpressionColormap",
+      "photometricInterpretation"
     ].some(shallowDiff)) {
       this.onUpdateImages();
       forceUpdate = true;
@@ -216928,7 +216948,7 @@ function SpatialSubscriber$1(props) {
   const loaders = useLoaders();
   const setComponentHover = useSetComponentHover();
   const setComponentViewInfo = useSetComponentViewInfo(uuid);
-  const [{ dataset, obsType, featureType, featureValueType, spatialZoom: zoom2, spatialTargetX: targetX2, spatialTargetY: targetY2, spatialTargetZ: targetZ, spatialRotationX: rotationX, spatialRotationY: rotationY, spatialRotationZ: rotationZ, spatialRotationOrbit: rotationOrbit, spatialOrbitAxis: orbitAxis, spatialImageLayer: imageLayers, spatialSegmentationLayer: cellsLayer, spatialPointLayer: moleculesLayer, spatialNeighborhoodLayer: neighborhoodsLayer, obsFilter: cellFilter, obsHighlight: cellHighlight, moleculeHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, spatialAxisFixed, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible }, { setSpatialZoom: setZoom, setSpatialTargetX: setTargetX, setSpatialTargetY: setTargetY, setSpatialTargetZ: setTargetZ, setSpatialRotationX: setRotationX, setSpatialRotationOrbit: setRotationOrbit, setSpatialOrbitAxis: setOrbitAxis, setSpatialImageLayer: setRasterLayers, setSpatialSegmentationLayer: setCellsLayer, setSpatialPointLayer: setMoleculesLayer, setSpatialNeighborhoodLayer: setNeighborhoodsLayer, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setMoleculeHighlight, setSpatialAxisFixed, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SPATIAL], coordinationScopes);
+  const [{ dataset, obsType, featureType, featureValueType, spatialZoom: zoom2, spatialTargetX: targetX2, spatialTargetY: targetY2, spatialTargetZ: targetZ, spatialRotationX: rotationX, spatialRotationY: rotationY, spatialRotationZ: rotationZ, spatialRotationOrbit: rotationOrbit, spatialOrbitAxis: orbitAxis, spatialImageLayer: imageLayers, spatialSegmentationLayer: cellsLayer, spatialPointLayer: moleculesLayer, spatialNeighborhoodLayer: neighborhoodsLayer, obsFilter: cellFilter, obsHighlight: cellHighlight, moleculeHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, spatialAxisFixed, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, photometricInterpretation: photometricInterpretationFromCoordination }, { setSpatialZoom: setZoom, setSpatialTargetX: setTargetX, setSpatialTargetY: setTargetY, setSpatialTargetZ: setTargetZ, setSpatialRotationX: setRotationX, setSpatialRotationOrbit: setRotationOrbit, setSpatialOrbitAxis: setOrbitAxis, setSpatialImageLayer: setRasterLayers, setSpatialSegmentationLayer: setCellsLayer, setSpatialPointLayer: setMoleculesLayer, setSpatialNeighborhoodLayer: setNeighborhoodsLayer, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setMoleculeHighlight, setSpatialAxisFixed, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SPATIAL], coordinationScopes);
   const { spatialZoom: initialZoom, spatialTargetX: initialTargetX, spatialTargetY: initialTargetY, spatialTargetZ: initialTargetZ } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SPATIAL], coordinationScopes);
   const observationsLabel = observationsLabelOverride || obsType;
   const [{ imageLayerCallbacks, segmentationLayerCallbacks }] = useAuxiliaryCoordination(COMPONENT_COORDINATION_TYPES.layerController, coordinationScopes);
@@ -216948,10 +216968,11 @@ function SpatialSubscriber$1(props) {
   const [expressionData, loadedFeatureSelection, featureSelectionStatus] = useFeatureSelection(loaders, dataset, false, geneSelection, { obsType, featureType, featureValueType });
   const [{ obsIndex: matrixObsIndex }, matrixIndicesStatus, matrixIndicesUrls] = useObsFeatureMatrixIndices(loaders, dataset, false, { obsType, featureType, featureValueType });
   const [{ image: image2 }, imageStatus, imageUrls] = useImageData(loaders, dataset, false, { setSpatialImageLayer: setRasterLayers }, { spatialImageLayer: imageLayers }, {});
-  const { loaders: imageLayerLoaders = [], meta: meta2 = [] } = image2 || {};
+  const { loaders: imageLayerLoaders = [], meta: meta2 = [], instance: instance2 } = image2 || {};
   const [neighborhoods, neighborhoodsStatus, neighborhoodsUrls] = useNeighborhoodsData(loaders, dataset, false, { setSpatialNeighborhoodLayer: setNeighborhoodsLayer }, { spatialNeighborhoodLayer: neighborhoodsLayer });
   const [{ featureLabelsMap: featureLabelsMapOrig }, featureLabelsStatus, featureLabelsUrls] = useFeatureLabelsData(loaders, dataset, false, {}, {}, { featureType });
   const [featureLabelsMap, expandedFeatureLabelsStatus] = useExpandedFeatureLabelsMap(featureType, featureLabelsMapOrig, { stripCuriePrefixes: true });
+  const photometricInterpretation = photometricInterpretationFromCoordination ?? (instance2 == null ? void 0 : instance2.getPhotometricInterpretation());
   const isReady = useReady([
     obsLocationsStatus,
     obsLabelsStatus,
@@ -217204,7 +217225,7 @@ function SpatialSubscriber$1(props) {
     orbitAxis
   }, setViewState, originalViewState, imageLayerDefs: imageLayers, obsSegmentationsLayerDefs: cellsLayer, obsLocationsLayerDefs: moleculesLayer, neighborhoodLayerDefs: neighborhoodsLayer, obsLocationsIndex, obsSegmentationsIndex, obsLocations, obsLocationsLabels, obsLocationsFeatureIndex, hasSegmentations: hasSegmentationsData, obsSegmentations, obsSegmentationsType, obsCentroids, obsCentroidsIndex, cellFilter, cellSelection, cellHighlight, cellColors, neighborhoods, imageLayerLoaders: resolutionFilteredImageLayerLoaders, setCellFilter, setCellSelection: setCellSelectionProp, setCellHighlight, setHoverInfo, setMoleculeHighlight, setComponentHover: () => {
     setComponentHover(uuid);
-  }, updateViewInfo: setComponentViewInfo, imageLayerCallbacks, segmentationLayerCallbacks, spatialAxisFixed, geneExpressionColormap, geneExpressionColormapRange, expressionData: shiftedExpressionDataForBitmask, cellColorEncoding, getExpressionValue, theme, useFullResolutionImage }), tooltipsVisible && jsxRuntimeExports.jsx(SpatialTooltipSubscriber$1, { parentUuid: uuid, obsHighlight: cellHighlight || moleculeHighlight, width: width2, height: height2, getObsInfo: getTooltipObsInfo, useHoverInfoForTooltip, hoverData, hoverCoord, hoverMode, getObsIdFromHoverData, featureType, featureLabelsMap }), jsxRuntimeExports.jsx(Legend, {
+  }, updateViewInfo: setComponentViewInfo, imageLayerCallbacks, segmentationLayerCallbacks, spatialAxisFixed, geneExpressionColormap, geneExpressionColormapRange, expressionData: shiftedExpressionDataForBitmask, cellColorEncoding, getExpressionValue, theme, useFullResolutionImage, photometricInterpretation }), tooltipsVisible && jsxRuntimeExports.jsx(SpatialTooltipSubscriber$1, { parentUuid: uuid, obsHighlight: cellHighlight || moleculeHighlight, width: width2, height: height2, getObsInfo: getTooltipObsInfo, useHoverInfoForTooltip, hoverData, hoverCoord, hoverMode, getObsIdFromHoverData, featureType, featureLabelsMap }), jsxRuntimeExports.jsx(Legend, {
     visible: true,
     // Fix to dark theme due to black background of spatial plot.
     theme: "dark",
@@ -218637,7 +218658,7 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-1de95a31.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-fd7c132d.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 }) }) }) }));
@@ -225150,7 +225171,7 @@ const buttonStyles = {
 };
 function LayerController$1(props) {
   var _a3;
-  const { layer, name: name2, loader: loader2, theme, handleLayerRemove, handleLayerChange, shouldShowTransparentColor, shouldShowDomain, shouldShowColormap, ChannelController, setViewState, disable3d, setImageLayerCallback, setAreLayerChannelsLoading, areLayerChannelsLoading, disabled, spatialHeight, spatialWidth, disableChannelsIfRgbDetected, shouldShowRemoveLayerButton } = props;
+  const { layer, name: name2, loader: loader2, theme, handleLayerRemove, handleLayerChange, shouldShowTransparentColor, shouldShowDomain, shouldShowColormap, ChannelController, setViewState, disable3d, setImageLayerCallback, setAreLayerChannelsLoading, areLayerChannelsLoading, disabled, spatialHeight, spatialWidth, photometricInterpretation, shouldShowRemoveLayerButton } = props;
   const { colormap, opacity: opacity2, channels: channels2, transparentColor, renderingMode, xSlice, ySlice, zSlice, resolution, use3d, modelMatrix: modelMatrix2 } = layer;
   const channelRef = useRef(channels2);
   useEffect(() => {
@@ -225365,7 +225386,7 @@ function LayerController$1(props) {
     handleColormapChange: setColormap,
     handleGlobalChannelsSelectionChange,
     handleTransparentColorChange: setTransparentColor,
-    disableChannelsIfRgbDetected: isRgb(loader2, channels2) && disableChannelsIfRgbDetected,
+    disableChannelsIfRgbDetected: photometricInterpretation === "RGB",
     handleDomainChange,
     shouldShowTransparentColor,
     shouldShowDomain,
@@ -225381,7 +225402,7 @@ function LayerController$1(props) {
     spatialHeight,
     spatialWidth,
     modelMatrix: modelMatrix2
-  }), isRgb(loader2, channels2) && disableChannelsIfRgbDetected ? null : channelControllers, isRgb(loader2, channels2) && disableChannelsIfRgbDetected ? null : jsxRuntimeExports.jsx(Button$1, { disabled: channels2.length === MAX_CHANNELS$1, onClick: handleChannelAdd, fullWidth: true, variant: "outlined", style: buttonStyles, startIcon: jsxRuntimeExports.jsx(AddIcon, {}), size: "small", children: "Add Channel" })] });
+  }), photometricInterpretation === "RGB" ? null : channelControllers, photometricInterpretation === "RGB" ? null : jsxRuntimeExports.jsx(Button$1, { disabled: channels2.length === MAX_CHANNELS$1, onClick: handleChannelAdd, fullWidth: true, variant: "outlined", style: buttonStyles, startIcon: jsxRuntimeExports.jsx(AddIcon, {}), size: "small", children: "Add Channel" })] });
   return jsxRuntimeExports.jsxs(Accordion$1, { className: controllerSectionClasses.layerControllerRoot, onChange: (e3, expanded) => {
     var _a4, _b3, _c3;
     return !disabled && setIsExpanded(expanded && ((_c3 = (_b3 = (_a4 = e3 == null ? void 0 : e3.target) == null ? void 0 : _a4.attributes) == null ? void 0 : _b3.role) == null ? void 0 : _c3.value) === "presentation");
@@ -225458,6 +225479,7 @@ const LayerControllerMemoized = React__default.memo(forwardRef((props, ref2) =>
     setAreLoadingImageChannels,
     handleRasterLayerChange,
     handleRasterLayerRemove,
+    photometricInterpretation,
     obsSegmentationsType,
     segmentationLayerLoaders,
     segmentationLayerMeta,
@@ -225579,6 +225601,7 @@ const LayerControllerMemoized = React__default.memo(forwardRef((props, ref2) =>
         disable3d: globalDisable3d || (disable3d || []).indexOf(layerMeta.name) >= 0 || typeof layerIs3DIndex === "number" && layerIs3DIndex !== -1 && layerIs3DIndex !== i2,
         disabled: typeof layerIs3DIndex === "number" && layerIs3DIndex !== -1 && layerIs3DIndex !== i2,
         disableChannelsIfRgbDetected,
+        photometricInterpretation,
         imageLayerCallbacks,
         setImageLayerCallback,
         setViewState: ({ zoom: newZoom, target: target2, rotationX: newRotationX, rotationOrbit: newRotationOrbit }) => {
@@ -225602,7 +225625,7 @@ const LayerControllerMemoized = React__default.memo(forwardRef((props, ref2) =>
 function LayerControllerSubscriber$1(props) {
   const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: title2 = "Spatial Layers", disable3d, globalDisable3d, disableChannelsIfRgbDetected, enableLayerButtonsWithOneLayer, helpText = ViewHelpMapping.LAYER_CONTROLLER } = props;
   const loaders = useLoaders();
-  const [{ dataset, obsType, spatialImageLayer: rasterLayers, spatialSegmentationLayer: cellsLayer, spatialPointLayer: moleculesLayer }, { setSpatialImageLayer: setRasterLayers, setSpatialSegmentationLayer: setCellsLayer, setSpatialPointLayer: setMoleculesLayer, setSpatialTargetX: setTargetX, setSpatialTargetY: setTargetY, setSpatialTargetZ: setTargetZ, setSpatialRotationX: setRotationX, setSpatialRotationOrbit: setRotationOrbit, setSpatialZoom: setZoom }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.LAYER_CONTROLLER], coordinationScopes);
+  const [{ dataset, obsType, spatialImageLayer: rasterLayers, spatialSegmentationLayer: cellsLayer, spatialPointLayer: moleculesLayer, photometricInterpretation: photometricInterpretationFromCoordination }, { setSpatialImageLayer: setRasterLayers, setSpatialSegmentationLayer: setCellsLayer, setSpatialPointLayer: setMoleculesLayer, setSpatialTargetX: setTargetX, setSpatialTargetY: setTargetY, setSpatialTargetZ: setTargetZ, setSpatialRotationX: setRotationX, setSpatialRotationOrbit: setRotationOrbit, setSpatialZoom: setZoom }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.LAYER_CONTROLLER], coordinationScopes);
   const [{ imageLayerCallbacks, areLoadingImageChannels, segmentationLayerCallbacks, areLoadingSegmentationChannels }, { setImageLayerCallbacks, setAreLoadingImageChannels, setSegmentationLayerCallbacks, setAreLoadingSegmentationChannels }] = useAuxiliaryCoordination(COMPONENT_COORDINATION_TYPES.layerController, coordinationScopes);
   const [spatialLayout] = useComponentLayout("spatial", ["spatialImageLayer"], coordinationScopes);
   const layerControllerRef = useRef();
@@ -225611,12 +225634,13 @@ function LayerControllerSubscriber$1(props) {
   const [obsLocationsData, obsLocationsStatus] = useObsLocationsData(loaders, dataset, false, { setSpatialPointLayer: setMoleculesLayer }, { spatialPointLayer: moleculesLayer }, {});
   const [{ obsSegmentations, obsSegmentationsType }, obsSegmentationsStatus] = useObsSegmentationsData(loaders, dataset, false, { setSpatialSegmentationLayer: setCellsLayer }, { spatialSegmentationLayer: cellsLayer }, {});
   const [{ image: image2 }, imageStatus] = useImageData(loaders, dataset, false, { setSpatialImageLayer: setRasterLayers }, { spatialImageLayer: rasterLayers }, {});
-  const { loaders: imageLayerLoaders, meta: imageLayerMeta } = image2 || {};
+  const { loaders: imageLayerLoaders, meta: imageLayerMeta, instance: instance2 } = image2 || {};
   const isReady = useReady([
     obsLocationsStatus,
     obsSegmentationsStatus,
     imageStatus
   ]);
+  const photometricInterpretation = photometricInterpretationFromCoordination ?? (instance2 == null ? void 0 : instance2.getPhotometricInterpretation());
   const segmentationLayerLoaders = obsSegmentations && obsSegmentationsType === "bitmask" ? obsSegmentations.loaders : null;
   const segmentationLayerMeta = obsSegmentations && obsSegmentationsType === "bitmask" ? obsSegmentations.meta : null;
   const handleImageAdd = useCallback(async (index2) => {
@@ -225678,6 +225702,7 @@ function LayerControllerSubscriber$1(props) {
     setAreLoadingImageChannels,
     handleRasterLayerChange,
     handleRasterLayerRemove,
+    photometricInterpretation,
     obsSegmentationsType,
     segmentationLayerLoaders,
     segmentationLayerMeta,
@@ -229496,7 +229521,7 @@ const useStyles$6 = makeStyles((theme) => ({
 }));
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-5022c0ac.js");
+  const { HiGlassComponent } = await import("./higlass-a114d38b.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -232444,7 +232469,7 @@ const useStyles$5 = makeStyles(() => ({
   }
 }));
 const LazyReactNeuroglancer = React__default.lazy(async () => {
-  const ReactNeuroglancer = await import("./index-9fa0b8f0.js").then((n3) => n3.i);
+  const ReactNeuroglancer = await import("./index-9c4bd1c8.js").then((n3) => n3.i);
   return ReactNeuroglancer;
 });
 function createWorker() {

package/dist/{index-1de95a31.js → index-fd7c132d.js}

@@ -1,4 +1,4 @@
-import { g as getDefaultExportFromCjs, R as Raycaster, O as OrthographicCamera, P as PerspectiveCamera, S as Scene, a as PCFSoftShadowMap, N as NoToneMapping, A as ACESFilmicToneMapping, V as Vector2, b as Vector3, L as Layers, T as Texture, c as RGBAFormat, U as UnsignedByteType, W as WebGLRenderer, C as Camera, B as BasicShadowMap, d as PCFShadowMap, e as VSMShadowMap, f as BufferGeometry, M as Material, h as Color, i as Clock, _ as _extends, j as THREE, G as Group, k as Matrix4, l as TrianglesDrawMode, m as TriangleFanDrawMode, n as TriangleStripDrawMode, o as REVISION, p as Ray$1, q as Plane, E as EventDispatcher, r as MOUSE, s as TOUCH, Q as Quaternion, t as Spherical, u as Loader, v as LoaderUtils, F as FileLoader, w as SpotLight, x as PointLight, D as DirectionalLight, y as MeshBasicMaterial, z as MeshPhysicalMaterial, I as InstancedMesh, H as Object3D, J as TextureLoader, K as ImageBitmapLoader, X as BufferAttribute, Y as InterleavedBuffer, Z as LinearFilter, $ as LinearMipmapLinearFilter, a0 as RepeatWrapping, a1 as PointsMaterial, a2 as LineBasicMaterial, a3 as MeshStandardMaterial, a4 as DoubleSide, a5 as PropertyBinding, a6 as SkinnedMesh, a7 as Mesh, a8 as LineSegments, a9 as Line$1, aa as LineLoop, ab as Points, ac as MathUtils, ad as Skeleton, ae as InterpolateLinear, af as AnimationClip, ag as Bone, ah as NearestFilter, ai as NearestMipmapNearestFilter, aj as LinearMipmapNearestFilter, ak as NearestMipmapLinearFilter, al as ClampToEdgeWrapping, am as MirroredRepeatWrapping, an as InterpolateDiscrete, ao as FrontSide, ap as InterleavedBufferAttribute, aq as VectorKeyframeTrack, ar as QuaternionKeyframeTrack, as as NumberKeyframeTrack, at as Box3, au as Sphere, av as Interpolant, 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-b2384476.js";
+import { g as getDefaultExportFromCjs, R as Raycaster, O as OrthographicCamera, P as PerspectiveCamera, S as Scene, a as PCFSoftShadowMap, N as NoToneMapping, A as ACESFilmicToneMapping, V as Vector2, b as Vector3, L as Layers, T as Texture, c as RGBAFormat, U as UnsignedByteType, W as WebGLRenderer, C as Camera, B as BasicShadowMap, d as PCFShadowMap, e as VSMShadowMap, f as BufferGeometry, M as Material, h as Color, i as Clock, _ as _extends, j as THREE, G as Group, k as Matrix4, l as TrianglesDrawMode, m as TriangleFanDrawMode, n as TriangleStripDrawMode, o as REVISION, p as Ray$1, q as Plane, E as EventDispatcher, r as MOUSE, s as TOUCH, Q as Quaternion, t as Spherical, u as Loader, v as LoaderUtils, F as FileLoader, w as SpotLight, x as PointLight, D as DirectionalLight, y as MeshBasicMaterial, z as MeshPhysicalMaterial, I as InstancedMesh, H as Object3D, J as TextureLoader, K as ImageBitmapLoader, X as BufferAttribute, Y as InterleavedBuffer, Z as LinearFilter, $ as LinearMipmapLinearFilter, a0 as RepeatWrapping, a1 as PointsMaterial, a2 as LineBasicMaterial, a3 as MeshStandardMaterial, a4 as DoubleSide, a5 as PropertyBinding, a6 as SkinnedMesh, a7 as Mesh, a8 as LineSegments, a9 as Line$1, aa as LineLoop, ab as Points, ac as MathUtils, ad as Skeleton, ae as InterpolateLinear, af as AnimationClip, ag as Bone, ah as NearestFilter, ai as NearestMipmapNearestFilter, aj as LinearMipmapNearestFilter, ak as NearestMipmapLinearFilter, al as ClampToEdgeWrapping, am as MirroredRepeatWrapping, an as InterpolateDiscrete, ao as FrontSide, ap as InterleavedBufferAttribute, aq as VectorKeyframeTrack, ar as QuaternionKeyframeTrack, as as NumberKeyframeTrack, at as Box3, au as Sphere, av as Interpolant, 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-c7da990c.js";
 import * as React from "react";
 import React__default, { useReducer, useRef, useDebugValue, useEffect, useLayoutEffect, useState, useMemo, forwardRef } from "react";
 import "@vitessce/vit-s";
@@ -23800,7 +23800,7 @@ const Text = /* @__PURE__ */ React.forwardRef(({
   const {
     Text: TextMeshImpl,
     preloadFont
-  } = suspend(async () => import("./troika-three-text.esm-1b1516c6.js"), []);
+  } = suspend(async () => import("./troika-three-text.esm-c7a0339e.js"), []);
   const invalidate2 = useThree(({
     invalidate: invalidate3
   }) => invalidate3);

package/dist/index.js

@@ -1,4 +1,4 @@
-import { bM, bK, bI, bL, bJ, bH, bN } from "./index-b2384476.js";
+import { bM, bK, bI, bL, bJ, bH, bN } from "./index-c7da990c.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 import "react";
 import "react-dom";

package/dist/{jpeg-8687eb38.js → jpeg-32441425.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-42867a4a.js → lerc-84a2944c.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-b2384476.js";
+import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-ffd426d3.js → lzw-615797a2.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-3388263e.js → packbits-b9451794.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-7ad8e084.js → raw-1af0a143.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{troika-three-text.esm-1b1516c6.js → troika-three-text.esm-c7a0339e.js}

@@ -1,4 +1,4 @@
-import { aB as UniformsUtils, bB as MeshDepthMaterial, bC as RGBADepthPacking, bD as MeshDistanceMaterial, bE as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, bF as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, bG as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-b2384476.js";
+import { aB as UniformsUtils, bB as MeshDepthMaterial, bC as RGBADepthPacking, bD as MeshDistanceMaterial, bE as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, bF as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, bG as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-60247a11.js → webimage-40ad658c.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-b2384476.js";
+import { aP as BaseDecoder } from "./index-c7da990c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.5.11",
+  "version": "3.5.12",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,35 +18,35 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.5.11",
-    "@vitessce/abstract": "3.5.11",
-    "@vitessce/csv": "3.5.11",
-    "@vitessce/description": "3.5.11",
-    "@vitessce/feature-list": "3.5.11",
-    "@vitessce/genomic-profiles": "3.5.11",
-    "@vitessce/heatmap": "3.5.11",
-    "@vitessce/glb": "3.5.11",
-    "@vitessce/json": "3.5.11",
-    "@vitessce/layer-controller": "3.5.11",
-    "@vitessce/layer-controller-beta": "3.5.11",
-    "@vitessce/link-controller": "3.5.11",
-    "@vitessce/obs-sets-manager": "3.5.11",
-    "@vitessce/ome-tiff": "3.5.11",
-    "@vitessce/plugins": "3.5.11",
-    "@vitessce/scatterplot-embedding": "3.5.11",
-    "@vitessce/scatterplot-gating": "3.5.11",
-    "@vitessce/schemas": "3.5.11",
-    "@vitessce/spatial": "3.5.11",
-    "@vitessce/spatial-beta": "3.5.11",
-    "@vitessce/statistical-plots": "3.5.11",
-    "@vitessce/status": "3.5.11",
-    "@vitessce/vit-s": "3.5.11",
-    "@vitessce/zarr": "3.5.11",
-    "@vitessce/globals": "3.5.11",
-    "@vitessce/spatial-zarr": "3.5.11",
-    "@vitessce/spatial-three": "3.5.11",
-    "@vitessce/biomarker-select": "3.5.11",
-    "@vitessce/neuroglancer": "3.5.11"
+    "@vitessce/constants-internal": "3.5.12",
+    "@vitessce/abstract": "3.5.12",
+    "@vitessce/csv": "3.5.12",
+    "@vitessce/description": "3.5.12",
+    "@vitessce/feature-list": "3.5.12",
+    "@vitessce/genomic-profiles": "3.5.12",
+    "@vitessce/heatmap": "3.5.12",
+    "@vitessce/glb": "3.5.12",
+    "@vitessce/json": "3.5.12",
+    "@vitessce/layer-controller": "3.5.12",
+    "@vitessce/layer-controller-beta": "3.5.12",
+    "@vitessce/link-controller": "3.5.12",
+    "@vitessce/obs-sets-manager": "3.5.12",
+    "@vitessce/ome-tiff": "3.5.12",
+    "@vitessce/plugins": "3.5.12",
+    "@vitessce/scatterplot-embedding": "3.5.12",
+    "@vitessce/scatterplot-gating": "3.5.12",
+    "@vitessce/schemas": "3.5.12",
+    "@vitessce/spatial": "3.5.12",
+    "@vitessce/spatial-beta": "3.5.12",
+    "@vitessce/statistical-plots": "3.5.12",
+    "@vitessce/status": "3.5.12",
+    "@vitessce/vit-s": "3.5.12",
+    "@vitessce/zarr": "3.5.12",
+    "@vitessce/globals": "3.5.12",
+    "@vitessce/spatial-zarr": "3.5.12",
+    "@vitessce/spatial-three": "3.5.12",
+    "@vitessce/biomarker-select": "3.5.12",
+    "@vitessce/neuroglancer": "3.5.12"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",