@vitessce/all 3.8.4 → 3.8.6

package/dist/{OrbitControls-CYynRaKW.js → OrbitControls-blC-_luf.js}

@@ -1,4 +1,4 @@
-import { aF as getDefaultExportFromCjs, aG as Raycaster, W as OrthographicCamera, K as PerspectiveCamera, av as Scene, aH as PCFSoftShadowMap, aI as VSMShadowMap, aJ as PCFShadowMap, aK as BasicShadowMap, aL as NoToneMapping, aM as ACESFilmicToneMapping, e as Vector3, V as Vector2, aN as Clock, aO as WebGLRenderer, aP as Camera, x as BufferGeometry, r as Material, aQ as Layers, a1 as Texture, aC as RGBAFormat, ay as UnsignedByteType, C as Color, aj as _extends, aR as THREE, aS as EventDispatcher, aT as MOUSE, aU as TOUCH, aV as Spherical, Q as Quaternion, an as Ray, ak as Plane } from "./index-se6p8sp4.js";
+import { aF as getDefaultExportFromCjs, aG as Raycaster, W as OrthographicCamera, K as PerspectiveCamera, av as Scene, aH as PCFSoftShadowMap, aI as VSMShadowMap, aJ as PCFShadowMap, aK as BasicShadowMap, aL as NoToneMapping, aM as ACESFilmicToneMapping, e as Vector3, V as Vector2, aN as Clock, aO as WebGLRenderer, aP as Camera, x as BufferGeometry, r as Material, aQ as Layers, a1 as Texture, aC as RGBAFormat, ay as UnsignedByteType, C as Color, aj as _extends, aR as THREE, aS as EventDispatcher, aT as MOUSE, aU as TOUCH, aV as Spherical, Q as Quaternion, an as Ray, ak as Plane } from "./index-Z-pD1WnL.js";
 import * as React from "react";
 import React__default, { useReducer, useRef, useEffect, useLayoutEffect, useDebugValue, useState, useMemo } from "react";
 var constants = { exports: {} };

package/dist/{ReactNeuroglancer-B784BBrr.js → ReactNeuroglancer-BV_821il.js}

@@ -1,4 +1,4 @@
-import { aF as getDefaultExportFromCjs, b0 as requireAssign, b1 as require_export, b2 as require_core, b3 as require_fails, b4 as require_toObject, b5 as require_objectKeys, b6 as require_cof, b7 as require_wks, b8 as require_iterators, b9 as requireWeb_dom_iterable, ba as requireEs6_string_iterator, bb as require_anObject, bc as require_hide, bd as require_ctx, be as require_toLength, bf as require_global, bg as require_objectDp, bh as require_descriptors, bi as require_isObject, bj as require_objectCreate, bk as require_iterDefine, bl as require_iterStep, bm as require_meta, bn as require_isArray, bo as require_iobject, bp as require_setToStringTag, bq as require_aFunction, br as requireIterator, bs as require_propertyDesc, aZ as commonjsGlobal, bt as requireEs6_symbol, bu as requireDefineProperty, bv as require_toIobject, bw as require_objectGopd, bx as require_html, by as require_domCreate, bz as require_library, bA as requireSymbol, bB as require_objectPie, bC as require_has, bD as require_redefine, bE as require_objectAssign, bF as diffCameraState, ao as jsxRuntimeExports } from "./index-se6p8sp4.js";
+import { aF as getDefaultExportFromCjs, b0 as requireAssign, b1 as require_export, b2 as require_core, b3 as require_fails, b4 as require_toObject, b5 as require_objectKeys, b6 as require_cof, b7 as require_wks, b8 as require_iterators, b9 as requireWeb_dom_iterable, ba as requireEs6_string_iterator, bb as require_anObject, bc as require_hide, bd as require_ctx, be as require_toLength, bf as require_global, bg as require_objectDp, bh as require_descriptors, bi as require_isObject, bj as require_objectCreate, bk as require_iterDefine, bl as require_iterStep, bm as require_meta, bn as require_isArray, bo as require_iobject, bp as require_setToStringTag, bq as require_aFunction, br as requireIterator, bs as require_propertyDesc, aZ as commonjsGlobal, bt as requireEs6_symbol, bu as requireDefineProperty, bv as require_toIobject, bw as require_objectGopd, bx as require_html, by as require_domCreate, bz as require_library, bA as requireSymbol, bB as require_objectPie, bC as require_has, bD as require_redefine, bE as require_objectAssign, bF as diffCameraState, ao as jsxRuntimeExports } from "./index-Z-pD1WnL.js";
 import React__default from "react";
 var assignExports = requireAssign();
 const _Object$assign = /* @__PURE__ */ getDefaultExportFromCjs(assignExports);

package/dist/{deflate-Bi9jTZa_.js → deflate-CsetZFHb.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{higlass-DlJQBL8o.js → higlass-BYlgWL_Y.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 { aZ as commonjsGlobal$1, a_ as requireObjectAssign, aF as getDefaultExportFromCjs$1, a$ as earcut } from "./index-se6p8sp4.js";
+import { aZ as commonjsGlobal$1, a_ as requireObjectAssign, aF as getDefaultExportFromCjs$1, a$ as earcut } from "./index-Z-pD1WnL.js";
 var promise = {};
 var hasRequiredPromise;
 function requirePromise() {

package/dist/{index-BiA0XI99.js → index-CHxaVZhJ.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, ao as jsxRuntimeExports, aE as GLSL3, am as BackSide } from "./index-se6p8sp4.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, ao as jsxRuntimeExports, aE as GLSL3, am as BackSide } from "./index-Z-pD1WnL.js";
 import { useRef, useState, useMemo, useEffect, useCallback } from "react";
-import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-CYynRaKW.js";
+import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-blC-_luf.js";
 const LogLevel = {
   INFO: "info",
   WARN: "warn",
@@ -220,6 +220,7 @@ function _requestBufferToRequestObjects(buffer, k) {
 class VolumeDataManager {
   constructor(glParam) {
     logWithColor$2("CLASS INITIALIZING");
+    log.debug("VolumeDataManager constructor", { glParam, glParamContext: glParam.getContext?.() });
     const gl = glParam.getContext?.() || glParam;
     const renderer = glParam;
     if (gl.domElement && gl.getContext) {
@@ -242,12 +243,20 @@ class VolumeDataManager {
           };
           return defaults[param] || 0;
         },
+        isContextLost: () => false,
         MAX_TEXTURE_SIZE: "MAX_TEXTURE_SIZE",
         MAX_3D_TEXTURE_SIZE: "MAX_3D_TEXTURE_SIZE",
         MAX_RENDERBUFFER_SIZE: "MAX_RENDERBUFFER_SIZE",
         MAX_UNIFORM_BUFFER_BINDINGS: "MAX_UNIFORM_BUFFER_BINDINGS"
       };
     }
+    this._originalGlParam = glParam;
+    this._isContextLost = false;
+    this._contextRestoredCallbacks = [];
+    if (this.gl && this.gl.canvas) {
+      this.gl.canvas.addEventListener("webglcontextlost", this._handleContextLost.bind(this));
+      this.gl.canvas.addEventListener("webglcontextrestored", this._handleContextRestored.bind(this));
+    }
     log.debug("GL CONSTANTS");
     log.debug(this.gl);
     log.debug(this.gl.TEXTURE0);
@@ -339,8 +348,78 @@ class VolumeDataManager {
     this.needsBailout = false;
     this.initStatus = INIT_STATUS.NOT_STARTED;
     this.initError = null;
+    this._lastChannelConfig = null;
     logWithColor$2("VolumeDataManager constructor complete");
   }
+  /**
+   * Handle WebGL context loss
+   */
+  _handleContextLost(event) {
+    logWithColor$2("CONTEXT LOST");
+    log.warn("WebGL context lost, preventing default and setting flag");
+    event.preventDefault();
+    this._isContextLost = true;
+    if (this.channels && this.channels.zarrMappings) {
+      this._lastChannelConfig = {
+        zarrMappings: [...this.channels.zarrMappings],
+        colorMappings: [...this.channels.colorMappings],
+        downsampleMin: [...this.channels.downsampleMin],
+        downsampleMax: [...this.channels.downsampleMax]
+      };
+    }
+  }
+  /**
+   * Handle WebGL context restoration
+   */
+  _handleContextRestored(event) {
+    logWithColor$2("CONTEXT RESTORED");
+    log.warn("WebGL context restored, reinitializing textures");
+    this._isContextLost = false;
+    if (this._originalGlParam && this._originalGlParam.getContext) {
+      this.gl = this._originalGlParam.getContext();
+    }
+    if (this._lastChannelConfig) {
+      this.channels.zarrMappings = [...this._lastChannelConfig.zarrMappings];
+      this.channels.colorMappings = [...this._lastChannelConfig.colorMappings];
+      this.channels.downsampleMin = [...this._lastChannelConfig.downsampleMin];
+      this.channels.downsampleMax = [...this._lastChannelConfig.downsampleMax];
+      log.debug("Restored channel configuration after context loss");
+    }
+    if (this.PT && this.zarrStore && this.zarrStore.brickLayout) {
+      try {
+        this.initMRMCPT();
+        log.debug("Successfully reinitialized MRMCPT after context restoration");
+      } catch (error) {
+        log.error("Failed to reinitialize MRMCPT after context restoration:", error);
+      }
+    }
+    this._contextRestoredCallbacks.forEach((callback) => {
+      try {
+        callback();
+      } catch (error) {
+        log.error("Error in context restored callback:", error);
+      }
+    });
+  }
+  /**
+   * Check if WebGL context is lost
+   */
+  isContextLost() {
+    if (this._isContextLost)
+      return true;
+    if (this.gl && typeof this.gl.isContextLost === "function") {
+      return this.gl.isContextLost();
+    }
+    return false;
+  }
+  /**
+   * Register a callback to be called when context is restored
+   */
+  onContextRestored(callback) {
+    if (typeof callback === "function") {
+      this._contextRestoredCallbacks.push(callback);
+    }
+  }
   initImages(images, imageLayerScopes) {
     logWithColor$2("INIT IMAGES");
     this.images = images;
@@ -629,6 +708,12 @@ class VolumeDataManager {
     log.debug("newColorMappings", newColorMappings);
     this.channels.colorMappings = newColorMappings;
     log.debug("updatedChannels", this.channels);
+    this._lastChannelConfig = {
+      zarrMappings: [...this.channels.zarrMappings],
+      colorMappings: [...this.channels.colorMappings],
+      downsampleMin: [...this.channels.downsampleMin],
+      downsampleMax: [...this.channels.downsampleMax]
+    };
   }
   /**
    * Try to load a resolution level
@@ -746,6 +831,10 @@ class VolumeDataManager {
       log.debug("processRequestData: already busy, skipping");
       return;
     }
+    if (this.isContextLost()) {
+      log.debug("processRequestData: WebGL context is lost, skipping");
+      return;
+    }
     this.isBusy = true;
     this.triggerRequest = false;
     const { requests, origRequestCount } = _requestBufferToRequestObjects(buffer, this.k);
@@ -763,6 +852,10 @@ class VolumeDataManager {
       this.needsBailout = true;
       return;
     }
+    if (this.isContextLost()) {
+      log.debug("processUsageData: WebGL context is lost, skipping");
+      return;
+    }
     this.isBusy = true;
     this.triggerUsage = false;
     const now = ++this.timeStamp;
@@ -804,6 +897,10 @@ class VolumeDataManager {
       log.error("pagetable texture not initialized");
       return;
     }
+    if (this.isContextLost()) {
+      log.warn("WebGL context is lost, skipping channel purge");
+      return;
+    }
     this.channels.downsampleMin[ptChannelIndex] = void 0;
     this.channels.downsampleMax[ptChannelIndex] = void 0;
     this.channels.zarrMappings[ptChannelIndex] = void 0;
@@ -833,6 +930,10 @@ class VolumeDataManager {
   _updatePTEntry(ptX, ptY, ptZ, ptVal) {
     if (!this.ptTHREE)
       return;
+    if (this.isContextLost()) {
+      log.warn("WebGL context is lost, skipping PT entry update");
+      return;
+    }
     const { gl } = this;
     const texPT = this.renderer.properties.get(this.ptTHREE).__webglTexture;
     gl.activeTexture(gl.TEXTURE0);
@@ -883,16 +984,51 @@ class VolumeDataManager {
   * 4. Upload one brick + PT entry                                *
   * ------------------------------------------------------------- */
   async _uploadBrick(ptCoord, bcSlot) {
+    log.debug("uploading brick", ptCoord, bcSlot);
+    if (this.isContextLost()) {
+      log.warn("WebGL context is lost, skipping brick upload");
+      return;
+    }
     if (ptCoord.x >= this.PT.xExtent || ptCoord.y >= this.PT.yExtent || ptCoord.z >= this.PT.zTotal || ptCoord.x < 0 || ptCoord.y < 0 || ptCoord.z < 0) {
       log.error("this.PT", this.PT);
       log.error("ptCoord out of bounds", ptCoord);
       return;
     }
     const { channel, resolution, x, y, z } = _ptToZarr(ptCoord.x, ptCoord.y, ptCoord.z, { PT_zExtent: this.PT.zExtent, PT_z0Extent: this.PT.z0Extent, PT_anchors: this.PT.anchors });
+    if (!this.channels || !this.channels.zarrMappings || this.channels.zarrMappings.length === 0) {
+      log.error("Channel mappings not initialized, skipping brick upload");
+      return;
+    }
+    if (channel < 0 || channel >= this.channels.zarrMappings.length) {
+      log.error("Channel index out of bounds", { channel, mappingsLength: this.channels.zarrMappings.length });
+      return;
+    }
     const zarrChannel = this.channels.zarrMappings[channel];
     if (zarrChannel === void 0 || zarrChannel === -1) {
-      log.error("zarrChannel is undefined or -1", zarrChannel);
-      return;
+      log.warn("zarrChannel is undefined or -1", {
+        zarrChannel,
+        channel,
+        ptCoord,
+        channelMappings: this.channels.zarrMappings,
+        contextLost: this.isContextLost()
+      });
+      if (this._lastChannelConfig && this._lastChannelConfig.zarrMappings[channel] !== void 0) {
+        log.warn("Attempting to use last known channel config");
+        this.channels.zarrMappings = [...this._lastChannelConfig.zarrMappings];
+        this.channels.colorMappings = [...this._lastChannelConfig.colorMappings];
+        this.channels.downsampleMin = [...this._lastChannelConfig.downsampleMin];
+        this.channels.downsampleMax = [...this._lastChannelConfig.downsampleMax];
+        const restoredZarrChannel = this.channels.zarrMappings[channel];
+        if (restoredZarrChannel !== void 0 && restoredZarrChannel !== -1) {
+          log.debug("Successfully restored channel mapping, continuing with upload");
+        } else {
+          log.error("Could not restore valid channel mapping, aborting brick upload");
+          return;
+        }
+      } else {
+        log.error("No fallback channel config available, aborting brick upload");
+        return;
+      }
     }
     log.debug("starting to load zarr chunk", { resolution, z, y, x, zarrChannel });
     let chunk = await this.loadZarrChunk(0, zarrChannel, z, y, x, resolution);
@@ -962,6 +1098,7 @@ class VolumeDataManager {
     if (ptRequests.length === 0)
       return;
     const slots = this._allocateBCSlots(ptRequests.length);
+    log.debug("Handling brick requests:", { requestCount: ptRequests.length, slotCount: slots.length });
     log.debug("handleBrickRequests: starting for loop");
     for (let i = 0; i < ptRequests.length; ++i) {
       log.debug("uploading brick", ptRequests[i], slots[i]);
@@ -3464,6 +3601,8 @@ function VolumeView(props) {
   useFrame((state, delta, xrFrame) => {
     if (!mrtRef.current || !dataManager || !renderManager)
       return;
+    if (!renderState.shader)
+      return;
     const { gl: frameGl, camera: frameCamera, scene: frameScene, clock } = state;
     if (!stillRef.current) {
       performGeometryPass(frameGl, frameCamera, frameScene, { mrtRef });

package/dist/{index-SV2fA7OO.js → index-VG1RjUEu.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-se6p8sp4.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-Z-pD1WnL.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-CYynRaKW.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-blC-_luf.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-BtJXS2ob.js"), []);
+  } = suspend(async () => import("./troika-three-text.esm-BsP89YlX.js"), []);
   const invalidate = useThree(({
     invalidate: invalidate2
   }) => invalidate2);

package/dist/{index-se6p8sp4.js → index-Z-pD1WnL.js}

@@ -10157,6 +10157,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     // TODO: CoordinationType.FEATURE_COLOR_ENCODING,
     // TODO: CoordinationType.ADDITIONAL_FEATURE_SETS,
     CoordinationType$1.TOOLTIPS_VISIBLE,
@@ -209322,22 +209323,22 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-CGkykmix.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-KgXyy-19.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-CRt4_45v.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-CE0HuE9L.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-BUtzsoPi.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-Bi9jTZa_.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-Bmv1iZNF.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-DdeYvQ7M.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-CsetZFHb.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-z6O-xEjB.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-B9pxOoW2.js").then(async (m2) => {
+  () => import("./lerc-D1O_lzXu.js").then(async (m2) => {
     await m2.zstd.init();
     return m2;
   }).then((m2) => m2.default)
 );
-addDecoder(50001, () => import("./webimage-C9QSeLIa.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-CLacHpNV.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -231711,7 +231712,9 @@ function EmbeddingScatterplotSubscriber(props) {
     // Average fill density for dynamic opacity calculation.
     averageFillDensity,
     // For the dual scatterplot:
-    sampleSetSelection: sampleSetSelectionFromProps
+    sampleSetSelection: sampleSetSelectionFromProps,
+    // Circle scale factor:
+    circleScaleFactor = 0.8
   } = props;
   const loaders = useLoaders();
   const coordinationScopes = useCoordinationScopes(coordinationScopesRaw);
@@ -231916,7 +231919,7 @@ function EmbeddingScatterplotSubscriber(props) {
       return null;
     }
     const size2 = Math.max(xRange, yRange);
-    const radius2 = size2 * Math.sqrt(2) / 2 * 0.8;
+    const radius2 = size2 * Math.sqrt(2) / 2 * circleScaleFactor;
     const numPoints = 96;
     const options = { steps: numPoints, units: "degrees" };
     const circlePolygon = circle$5(center2, radius2, options);
@@ -231926,7 +231929,7 @@ function EmbeddingScatterplotSubscriber(props) {
       polygon: circlePolygon,
       steps: numPoints
     };
-  }, [originalViewState, width2, height2, xRange, yRange]);
+  }, [originalViewState, width2, height2, xRange, yRange, circleScaleFactor]);
   const [alignedEmbeddingIndex, alignedEmbeddingData] = useMemo$1(() => {
     if (obsEmbedding?.data && obsEmbeddingIndex && matrixObsIndex) {
       const matrixIndexMap = new Map(matrixObsIndex.map((key2, i2) => [key2, i2]));
@@ -247754,7 +247757,7 @@ function uri2href(url) {
   }
   throw Error(`Protocol not supported, got: ${JSON.stringify(protocol)}`);
 }
-function fetch_range$1(url, offset2, length2, opts2 = {}) {
+function fetch_range(url, offset2, length2, opts2 = {}) {
   if (offset2 !== void 0 && length2 !== void 0) {
     opts2 = {
       ...opts2,
@@ -247766,7 +247769,7 @@ function fetch_range$1(url, offset2, length2, opts2 = {}) {
   }
   return fetch(url, opts2);
 }
-function merge_init$1(storeOverrides, requestOverrides) {
+function merge_init(storeOverrides, requestOverrides) {
   return {
     ...storeOverrides,
     ...requestOverrides,
@@ -247780,7 +247783,7 @@ function assert$5(expression2, msg = "") {
   if (!expression2)
     throw new Error(msg);
 }
-function resolve$2(root2, path2) {
+function resolve$1(root2, path2) {
   const base2 = typeof root2 === "string" ? new URL(root2) : root2;
   if (!base2.pathname.endsWith("/")) {
     base2.pathname += "/";
@@ -247789,7 +247792,7 @@ function resolve$2(root2, path2) {
   resolved.search = base2.search;
   return resolved;
 }
-async function handle_response$1(response) {
+async function handle_response(response) {
   if (response.status === 404) {
     return void 0;
   }
@@ -247798,7 +247801,7 @@ async function handle_response$1(response) {
   }
   throw new Error(`Unexpected response status ${response.status} ${response.statusText}`);
 }
-async function fetch_suffix$1(url, suffix_length, init2, use_suffix_request) {
+async function fetch_suffix(url, suffix_length, init2, use_suffix_request) {
   if (use_suffix_request) {
     return fetch(url, {
       ...init2,
@@ -247811,9 +247814,9 @@ async function fetch_suffix$1(url, suffix_length, init2, use_suffix_request) {
   }
   let content_length = response.headers.get("Content-Length");
   let length2 = Number(content_length);
-  return fetch_range$1(url, length2 - suffix_length, length2, init2);
+  return fetch_range(url, length2 - suffix_length, length2, init2);
 }
-let FetchStore$1 = class FetchStore {
+class FetchStore {
   #overrides;
   #use_suffix_request;
   constructor(url, options = {}) {
@@ -247822,25 +247825,25 @@ let FetchStore$1 = class FetchStore {
     this.#use_suffix_request = options.useSuffixRequest ?? false;
   }
   #merge_init(overrides) {
-    return merge_init$1(this.#overrides, overrides);
+    return merge_init(this.#overrides, overrides);
   }
   async get(key2, options = {}) {
-    let href2 = resolve$2(this.url, key2).href;
+    let href2 = resolve$1(this.url, key2).href;
     let response = await fetch(href2, this.#merge_init(options));
-    return handle_response$1(response);
+    return handle_response(response);
   }
   async getRange(key2, range2, options = {}) {
-    let url = resolve$2(this.url, key2);
+    let url = resolve$1(this.url, key2);
     let init2 = this.#merge_init(options);
     let response;
     if ("suffixLength" in range2) {
-      response = await fetch_suffix$1(url, range2.suffixLength, init2, this.#use_suffix_request);
+      response = await fetch_suffix(url, range2.suffixLength, init2, this.#use_suffix_request);
     } else {
-      response = await fetch_range$1(url, range2.offset, range2.length, init2);
+      response = await fetch_range(url, range2.offset, range2.length, init2);
     }
-    return handle_response$1(response);
+    return handle_response(response);
   }
-};
+}
 let BoolArray$1 = class BoolArray {
   #bytes;
   constructor(x2, byteOffset, length2) {
@@ -250132,7 +250135,7 @@ class HTTPRangeReader {
     if (size2 === 0) {
       return new Uint8Array(0);
     }
-    const req = await fetch_range$1(this.url, offset2, size2, this.#overrides);
+    const req = await fetch_range(this.url, offset2, size2, this.#overrides);
     assert$5(req.ok, `failed http request ${this.url}, status: ${req.status} offset: ${offset2} size: ${size2}: ${req.statusText}`);
     return new Uint8Array(await req.arrayBuffer());
   }
@@ -250400,7 +250403,7 @@ class ReferenceStore {
     if (!url) {
       throw Error(`No url for key ${key2}, and no target url provided.`);
     }
-    let res = await fetch_range$1(uri2href(url), offset2, size2, merge_init$1(this.#overrides, opts2));
+    let res = await fetch_range(uri2href(url), offset2, size2, merge_init(this.#overrides, opts2));
     if (res.status === 200 || res.status === 206) {
       return new Uint8Array(await res.arrayBuffer());
     }
@@ -250415,7 +250418,7 @@ class ReferenceStore {
     return ReferenceStore.fromSpec(spec, opts2);
   }
 }
-class RelaxedFetchStore extends FetchStore$1 {
+class RelaxedFetchStore extends FetchStore {
   // This allows returning `undefined` for 403 responses,
   // as opposed to completely erroring.
   // Needed due to https://github.com/manzt/zarrita.js/pull/212
@@ -253033,12 +253036,12 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-SV2fA7OO.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-VG1RjUEu.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-BiA0XI99.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-CHxaVZhJ.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 }) }) }) }));
@@ -265935,89 +265938,6 @@ function set_from_chunk_binary(dest, src, bytes_per_element2, projections2) {
     }, bytes_per_element2, projs);
   }
 }
-function fetch_range(url, offset2, length2, opts2 = {}) {
-  if (offset2 !== void 0 && length2 !== void 0) {
-    opts2 = {
-      ...opts2,
-      headers: {
-        ...opts2.headers,
-        Range: `bytes=${offset2}-${offset2 + length2 - 1}`
-      }
-    };
-  }
-  return fetch(url, opts2);
-}
-function merge_init(storeOverrides, requestOverrides) {
-  return {
-    ...storeOverrides,
-    ...requestOverrides,
-    headers: {
-      ...storeOverrides.headers,
-      ...requestOverrides.headers
-    }
-  };
-}
-function resolve$1(root2, path2) {
-  const base2 = typeof root2 === "string" ? new URL(root2) : root2;
-  if (!base2.pathname.endsWith("/")) {
-    base2.pathname += "/";
-  }
-  const resolved = new URL(path2.slice(1), base2);
-  resolved.search = base2.search;
-  return resolved;
-}
-async function handle_response(response) {
-  if (response.status === 404) {
-    return void 0;
-  }
-  if (response.status === 200 || response.status === 206) {
-    return new Uint8Array(await response.arrayBuffer());
-  }
-  throw new Error(`Unexpected response status ${response.status} ${response.statusText}`);
-}
-async function fetch_suffix(url, suffix_length, init2, use_suffix_request) {
-  if (use_suffix_request) {
-    return fetch(url, {
-      ...init2,
-      headers: { ...init2.headers, Range: `bytes=-${suffix_length}` }
-    });
-  }
-  let response = await fetch(url, { ...init2, method: "HEAD" });
-  if (!response.ok) {
-    return response;
-  }
-  let content_length = response.headers.get("Content-Length");
-  let length2 = Number(content_length);
-  return fetch_range(url, length2 - suffix_length, length2, init2);
-}
-class FetchStore2 {
-  #overrides;
-  #use_suffix_request;
-  constructor(url, options = {}) {
-    this.url = url;
-    this.#overrides = options.overrides ?? {};
-    this.#use_suffix_request = options.useSuffixRequest ?? false;
-  }
-  #merge_init(overrides) {
-    return merge_init(this.#overrides, overrides);
-  }
-  async get(key2, options = {}) {
-    let href2 = resolve$1(this.url, key2).href;
-    let response = await fetch(href2, this.#merge_init(options));
-    return handle_response(response);
-  }
-  async getRange(key2, range2, options = {}) {
-    let url = resolve$1(this.url, key2);
-    let init2 = this.#merge_init(options);
-    let response;
-    if ("suffixLength" in range2) {
-      response = await fetch_suffix(url, range2.suffixLength, init2, this.#use_suffix_request);
-    } else {
-      response = await fetch_range(url, range2.offset, range2.length, init2);
-    }
-    return handle_response(response);
-  }
-}
 function multivecChunksToTileDenseArray(chunks, tileShape, isRow) {
   const fullTileLength = isRow ? tileShape[1] : tileShape[0] * tileShape[1];
   const fullTileArray = new Float32Array(fullTileLength);
@@ -266063,7 +265983,7 @@ var ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher2(HGC, ...args) {
         this.storeRoot = Promise.resolve(ZarrMultivecDataFetcher2.urlToStoreRoot[dataConfig.url]);
       } else if (dataConfig.url) {
         const { url, options = {} } = dataConfig;
-        this.store = new FetchStore2(url, options);
+        this.store = new FetchStore(url, options);
         this.storeRoot = Promise.resolve(root(this.store));
       }
       if (dataConfig.row !== void 0) {
@@ -266239,7 +266159,7 @@ function HiglassGlobalStyles(props) {
 }
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-DlJQBL8o.js");
+  const { HiGlassComponent } = await import("./higlass-BYlgWL_Y.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -269186,7 +269106,7 @@ 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-B784BBrr.js"));
+const LazyReactNeuroglancer = React__default.lazy(() => import("./ReactNeuroglancer-BV_821il.js"));
 function createWorker() {
   return new WorkerFactory();
 }
@@ -299439,6 +299359,7 @@ accessor$1(() => 0, [], "zero");
 accessor$1(() => 1, [], "one");
 accessor$1(() => true, [], "true");
 accessor$1(() => false, [], "false");
+/* @__PURE__ */ new Set([...Object.getOwnPropertyNames(Object.prototype).filter((name2) => typeof Object.prototype[name2] === "function"), "__proto__"]);
 var isArray$2 = Array.isArray;
 function peek$2(array2) {
   return array2[array2.length - 1];
@@ -301721,8 +301642,7 @@ function splitAccessPath(p) {
   for (i2 = j = 0; j < n3; ++j) {
     c2 = p[j];
     if (c2 === "\\") {
-      s2 += p.substring(i2, j);
-      s2 += p.substring(++j, ++j);
+      s2 += p.substring(i2, j++);
       i2 = j;
     } else if (c2 === q) {
       push2();
@@ -301780,7 +301700,8 @@ const Error$1 = 1;
 const Warn = 2;
 const Info2 = 3;
 const Debug = 4;
-function logger(_, method2, handler = log$1$1) {
+function logger(_, method2) {
+  let handler = arguments.length > 2 && arguments[2] !== void 0 ? arguments[2] : log$1$1;
   let level = _ || None$2;
   return {
     level(_2) {
@@ -301814,7 +301735,10 @@ function isObject$2(_) {
   return _ === Object(_);
 }
 const isLegalKey = (key2) => key2 !== "__proto__";
-function mergeConfig(...configs) {
+function mergeConfig() {
+  for (var _len = arguments.length, configs = new Array(_len), _key = 0; _key < _len; _key++) {
+    configs[_key] = arguments[_key];
+  }
   return configs.reduce((out, source2) => {
     for (const key2 in source2) {
       if (key2 === "signals") {
@@ -302052,9 +301976,8 @@ function extentIndex(array2, f2) {
   }
   return [u2, v];
 }
-const hop = Object.prototype.hasOwnProperty;
 function has$1(object2, property2) {
-  return hop.call(object2, property2);
+  return Object.hasOwn(object2, property2);
 }
 const NULL = {};
 function fastmap(input) {
@@ -353838,7 +353761,7 @@ const initialState$1 = {
 };
 const pageSizeOptions$1 = [10];
 function FeatureStatsTable(props) {
-  const { obsType, featureType, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, data: data2, setFeatureSelection, featurePointSignificanceThreshold, featurePointFoldChangeThreshold } = props;
+  const { obsType, featureType, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, data: data2, setFeatureSelection, setFeatureAggregationStrategy, featurePointSignificanceThreshold, featurePointFoldChangeThreshold } = props;
   const [
     // eslint-disable-next-line no-unused-vars
     computedData,
@@ -353898,6 +353821,7 @@ function FeatureStatsTable(props) {
   }, [filteredData, obsSetsColumnNameMappingReversed]);
   const onSelectionModelChange = useCallback((rowIds) => {
     const featureIds = Array.from(rowIds.ids).map((rowId) => rowId.split(ROW_ID_DELIMITER)[0]);
+    setFeatureAggregationStrategy(null);
     setFeatureSelection(featureIds);
   }, []);
   const rowSelectionModel = useMemo$1(() => ({ ids: /* @__PURE__ */ new Set([]), type: "include" }), []);
@@ -353921,7 +353845,7 @@ function FeatureStatsTableSubscriber(props) {
   const { title: title2 = "Differential Expression Results", coordinationScopes: coordinationScopesRaw, removeGridComponent, theme, helpText = ViewHelpMapping.FEATURE_STATS_TABLE } = props;
   const loaders = useLoaders();
   const coordinationScopes = useCoordinationScopes(coordinationScopesRaw);
-  const [{ dataset, obsType, sampleType, featureType, featureValueType, obsFilter: cellFilter, obsHighlight: cellHighlight, obsSetSelection, obsSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureValueTransform, featureValueTransformCoefficient, gatingFeatureSelectionX, gatingFeatureSelectionY, featureSelection, sampleSetSelection, sampleSetColor }, { setObsFilter: setCellFilter, setObsSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setFeaturePointSignificanceThreshold, setFeaturePointFoldChangeThreshold, setFeatureValueTransform, setFeatureValueTransformCoefficient, setGatingFeatureSelectionX, setGatingFeatureSelectionY, setFeatureSelection, setSampleSetSelection, setSampleSetColor }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.FEATURE_STATS_TABLE], coordinationScopes);
+  const [{ dataset, obsType, sampleType, featureType, featureValueType, obsFilter: cellFilter, obsHighlight: cellHighlight, obsSetSelection, obsSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureValueTransform, featureValueTransformCoefficient, featureAggregationStrategy, gatingFeatureSelectionX, gatingFeatureSelectionY, featureSelection, sampleSetSelection, sampleSetColor }, { setObsFilter: setCellFilter, setObsSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setFeaturePointSignificanceThreshold, setFeaturePointFoldChangeThreshold, setFeatureValueTransform, setFeatureValueTransformCoefficient, setFeatureAggregationStrategy, setGatingFeatureSelectionX, setGatingFeatureSelectionY, setFeatureSelection, setSampleSetSelection, setSampleSetColor }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.FEATURE_STATS_TABLE], coordinationScopes);
   const obsSetsLoader = useMatchingLoader(loaders, dataset, DataType$3.OBS_SETS, { obsType });
   const sampleSetsLoader = useMatchingLoader(loaders, dataset, DataType$3.SAMPLE_SETS, { sampleType });
   const obsSetsColumnNameMapping = useColumnNameMapping(obsSetsLoader);
@@ -353944,7 +353868,7 @@ function FeatureStatsTableSubscriber(props) {
   const isReady = useReady([
     featureStatsStatus
   ]);
-  return jsxRuntimeExports.jsx(TitleInfo, { title: title2, removeGridComponent, theme, isReady, helpText, errors, withPadding: false, children: featureStats ? jsxRuntimeExports.jsx(FeatureStatsTable, { theme, obsType, featureType, obsSetsColumnNameMapping, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMapping, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: featureStats, featureSelection, setFeatureSelection, featurePointSignificanceThreshold, featurePointFoldChangeThreshold }) : jsxRuntimeExports.jsxs("p", { style: { padding: "12px" }, children: ["Select at least one ", obsType, " set."] }) });
+  return jsxRuntimeExports.jsx(TitleInfo, { title: title2, removeGridComponent, theme, isReady, helpText, errors, withPadding: false, children: featureStats ? jsxRuntimeExports.jsx(FeatureStatsTable, { theme, obsType, featureType, obsSetsColumnNameMapping, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMapping, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: featureStats, featureSelection, setFeatureSelection, setFeatureAggregationStrategy, featurePointSignificanceThreshold, featurePointFoldChangeThreshold }) : jsxRuntimeExports.jsxs("p", { style: { padding: "12px" }, children: ["Select at least one ", obsType, " set."] }) });
 }
 class CsvSource {
   constructor({ url, requestInit: requestInit2 }) {
@@ -354080,6 +354004,24 @@ class ObsLabelsCsvLoader extends CsvLoader {
     return this.cachedResult;
   }
 }
+class VitessceConfigViewHConcat {
+  constructor(views) {
+    this.views = views;
+  }
+}
+class VitessceConfigViewVConcat {
+  constructor(views) {
+    this.views = views;
+  }
+}
+function hconcat(...views) {
+  const vcvhc = new VitessceConfigViewHConcat(views);
+  return vcvhc;
+}
+function vconcat(...views) {
+  const vcvvc = new VitessceConfigViewVConcat(views);
+  return vcvvc;
+}
 class CoordinationLevel {
   constructor(value2) {
     this.value = value2;
@@ -354098,6 +354040,233 @@ class CoordinationLevel {
 function CL(value2) {
   return new CoordinationLevel(value2);
 }
+class AbstractAutoConfig {
+  constructor(parsedStore) {
+    const { url, fileType, zmetadata } = parsedStore;
+    this.url = url;
+    this.fileType = fileType;
+    this.zmetadata = zmetadata;
+  }
+  // eslint-disable-next-line class-methods-use-this
+  addFiles(vc, dataset) {
+    throw new Error("The addFiles() method has not been implemented.");
+  }
+  // eslint-disable-next-line class-methods-use-this
+  addViews(vc, dataset, layoutOption) {
+    throw new Error("The addViews() method has not been implemented.");
+  }
+}
+class AnnDataAutoConfig extends AbstractAutoConfig {
+  getOptions() {
+    const { zmetadata } = this;
+    const options = {
+      obsEmbedding: [],
+      obsSets: []
+    };
+    zmetadata.forEach(({ path: path2, attrs }) => {
+      const lowerPath = path2.toLowerCase();
+      const relPath = path2.substring(1);
+      if (["/x"].includes(lowerPath)) {
+        options.obsFeatureMatrix = {
+          path: relPath
+          // TODO: Also check the shape of X.
+          // If X is very large, try to initialize initial-filtering properties
+          // (will require that /var contains a boolean column however.)
+        };
+      }
+      if (["/obsm/x_spatial", "/obsm/spatial"].includes(lowerPath)) {
+        options.obsLocations = {
+          path: relPath
+        };
+      }
+      if (["/obsm/x_umap", "/obsm/umap"].includes(lowerPath)) {
+        options.obsEmbedding.push({ path: relPath, embeddingType: "UMAP" });
+      }
+      if (["/obsm/x_tsne", "/obsm/tsne"].includes(lowerPath)) {
+        options.obsEmbedding.push({ path: relPath, embeddingType: "t-SNE" });
+      }
+      if (["/obsm/x_pca", "/obsm/pca"].includes(lowerPath)) {
+        options.obsEmbedding.push({ path: relPath, embeddingType: "PCA" });
+      }
+      const supportedObsSetsPaths = [
+        "cluster",
+        "clusters",
+        "subcluster",
+        "cell_type",
+        "celltype",
+        "leiden",
+        "louvain",
+        "disease",
+        "organism",
+        "self_reported_ethnicity",
+        "tissue",
+        "sex"
+      ].map((colname) => `/obs/${colname}`);
+      if (supportedObsSetsPaths.includes(lowerPath)) {
+        const name2 = relPath.split("/").at(-1);
+        options.obsSets.push({ path: relPath, name: name2 });
+      }
+    });
+    return options;
+  }
+  addFiles(vc, dataset) {
+    const { url, fileType } = this;
+    dataset.addFile({
+      url,
+      fileType,
+      options: this.getOptions()
+      // TODO: coordination values?
+    });
+  }
+  // eslint-disable-next-line class-methods-use-this
+  addViews(vc, dataset, layoutOption) {
+  }
+}
+class SpatialDataAutoConfig extends AbstractAutoConfig {
+  getOptions() {
+    const { zmetadata } = this;
+    const options = {};
+    const availableElements = zmetadata.filter(({ path: path2 }) => {
+      const relPath = path2.substring(1);
+      return relPath.match(/^(tables|table|images|labels|shapes|points)\/([^/]*)$/);
+    });
+    availableElements.forEach(({ path: path2, attrs }) => {
+      const relPath = path2.substring(1);
+      const firstCoordinateSystem = attrs?.multiscales?.[0]?.coordinateTransformations?.[0]?.output?.name;
+      if (relPath.match(/^(images)\/([^/]*)$/)) {
+        options.image = {
+          path: relPath,
+          coordinateSystem: firstCoordinateSystem
+          // TODO: support a fileUid property in the schema?
+        };
+      }
+      if (relPath.match(/^(labels)\/([^/]*)$/)) {
+        options.obsSegmentations = {
+          path: relPath,
+          coordinateSystem: firstCoordinateSystem
+          // TODO: support a fileUid property in the schema?
+        };
+      }
+      if (relPath.match(/^(shapes)\/([^/]*)$/)) {
+        options.obsSpots = {
+          path: relPath,
+          coordinateSystem: firstCoordinateSystem
+        };
+      }
+      if (relPath.match(/^(points)\/([^/]*)$/)) {
+        options.obsPoints = {
+          path: relPath,
+          coordinateSystem: firstCoordinateSystem
+        };
+      }
+      if (relPath.match(/^(tables|table)\/([^/]*)$/)) {
+        const tableEls = zmetadata.filter(({ path: subpath }) => subpath.startsWith(path2));
+        const hasX = tableEls.find((el) => el.path === `${path2}/X`);
+        if (hasX) {
+          options.obsFeatureMatrix = {
+            path: hasX.path.substring(1)
+            // region: null,
+          };
+        }
+        const hasObs = tableEls.find((el) => el.path === `${path2}/obs`);
+        if (hasObs) {
+          const columnOrder = hasObs.attrs?.["column-order"];
+          options.obsSets = {
+            // region: null,
+            tablePath: relPath,
+            obsSets: columnOrder.map((c2) => ({
+              // TODO: determine whether this column is string/categorical.
+              // TODO: determine whether this column contains too many
+              // categories to make sense to consider a cell set.
+              path: `${hasObs.path.substring(1)}/${c2}`,
+              name: c2
+            }))
+          };
+        }
+      }
+    });
+    return options;
+  }
+  addFiles(vc, dataset) {
+    const { url, fileType } = this;
+    dataset.addFile({
+      url,
+      fileType,
+      options: this.getOptions()
+      // TODO: coordination values?
+    });
+  }
+  // eslint-disable-next-line class-methods-use-this
+  addViews(vc, dataset, layoutOption) {
+    const options = this.getOptions();
+    const spatialView = vc.addView(dataset, "spatialBeta");
+    const lcView = vc.addView(dataset, "layerControllerBeta");
+    const controlViews = [lcView];
+    if (options.obsSets) {
+      const obsSets = vc.addView(dataset, "obsSets");
+      controlViews.push(obsSets);
+    }
+    if (options.obsFeatureMatrix) {
+      const featureList = vc.addView(dataset, "featureList");
+      controlViews.push(featureList);
+    }
+    vc.layout(hconcat(spatialView, vconcat(...controlViews)));
+  }
+}
+class OmeAutoConfig extends AbstractAutoConfig {
+  addFiles(vc, dataset) {
+    const { url, fileType } = this;
+    dataset.addFile({
+      url,
+      fileType
+      // TODO: options?
+      // TODO: coordination values?
+    });
+  }
+  // eslint-disable-next-line class-methods-use-this
+  addViews(vc, dataset, layoutOption) {
+    const spatialView = vc.addView(dataset, "spatialBeta");
+    const lcView = vc.addView(dataset, "layerControllerBeta");
+    vc.layout(hconcat(spatialView, lcView));
+  }
+}
+({
+  [FileType$1.IMAGE_OME_TIFF]: [".ome.tif", ".ome.tiff", ".ome.tf2", ".ome.tf8"],
+  [FileType$1.IMAGE_OME_ZARR]: [".ome.zarr"],
+  [FileType$1.IMAGE_OME_ZARR_ZIP]: [".ome.zarr.zip"],
+  [FileType$1.ANNDATA_ZARR]: [".ad.zarr", ".h5ad.zarr", ".adata.zarr", ".anndata.zarr"],
+  [FileType$1.ANNDATA_ZARR_ZIP]: [".ad.zarr.zip", ".h5ad.zarr.zip", ".adata.zarr.zip", ".anndata.zarr.zip"],
+  // TODO: how to handle h5ad-based AnnData (since needs reference JSON file).
+  // Perhaps just assume one H5AD+one JSON (or .ref.json) file correspond to each other?
+  [FileType$1.SPATIALDATA_ZARR]: [".sd.zarr", ".sdata.zarr", ".spatialdata.zarr"],
+  [FileType$1.SPATIALDATA_ZARR_ZIP]: [".sd.zarr.zip", ".sdata.zarr.zip", ".spatialdata.zarr.zip"]
+});
+({
+  // OME-TIFF
+  [FileType$1.IMAGE_OME_TIFF]: OmeAutoConfig,
+  [FileType$1.OBS_SEGMENTATIONS_OME_TIFF]: OmeAutoConfig,
+  // OME-Zarr
+  [FileType$1.IMAGE_OME_ZARR]: OmeAutoConfig,
+  [FileType$1.IMAGE_OME_ZARR_ZIP]: OmeAutoConfig,
+  [FileType$1.OBS_SEGMENTATIONS_OME_ZARR]: OmeAutoConfig,
+  [FileType$1.OBS_SEGMENTATIONS_OME_ZARR_ZIP]: OmeAutoConfig,
+  // AnnData
+  [FileType$1.ANNDATA_ZARR]: AnnDataAutoConfig,
+  [FileType$1.ANNDATA_ZARR_ZIP]: AnnDataAutoConfig,
+  // SpatialData
+  [FileType$1.SPATIALDATA_ZARR]: SpatialDataAutoConfig,
+  [FileType$1.SPATIALDATA_ZARR_ZIP]: SpatialDataAutoConfig
+});
+[
+  FileType$1.ANNDATA_ZARR,
+  FileType$1.ANNDATA_ZARR_ZIP,
+  FileType$1.SPATIALDATA_ZARR,
+  FileType$1.SPATIALDATA_ZARR_ZIP,
+  FileType$1.IMAGE_OME_ZARR,
+  FileType$1.IMAGE_OME_ZARR_ZIP,
+  FileType$1.OBS_SEGMENTATIONS_OME_ZARR,
+  FileType$1.OBS_SEGMENTATIONS_OME_ZARR_ZIP
+];
 class ObsSpotsCsvLoader extends CsvLoader {
   loadFromCache(data2) {
     if (this.cachedResult) {

package/dist/index.js

@@ -1,4 +1,4 @@
-import { bQ, bO, bM, bP, bN, bL, bR } from "./index-se6p8sp4.js";
+import { bQ, bO, bM, bP, bN, bL, bR } from "./index-Z-pD1WnL.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 export {
   bQ as PluginAsyncFunction,

package/dist/{jpeg-BUtzsoPi.js → jpeg-DdeYvQ7M.js}

@@ -1,4 +1,4 @@
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-B9pxOoW2.js → lerc-D1O_lzXu.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aF as getDefaultExportFromCjs, aW as BaseDecoder, aX as LercParameters, aY as LercAddCompression } from "./index-se6p8sp4.js";
+import { aF as getDefaultExportFromCjs, aW as BaseDecoder, aX as LercParameters, aY as LercAddCompression } from "./index-Z-pD1WnL.js";
 var LercDecode = { exports: {} };
 var hasRequiredLercDecode;
 function requireLercDecode() {

package/dist/{lzw-KgXyy-19.js → lzw-CE0HuE9L.js}

@@ -1,4 +1,4 @@
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-Bmv1iZNF.js → packbits-z6O-xEjB.js}

@@ -1,4 +1,4 @@
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-CGkykmix.js → raw-CRt4_45v.js}

@@ -1,4 +1,4 @@
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{troika-three-text.esm-BtJXS2ob.js → troika-three-text.esm-BsP89YlX.js}

@@ -1,4 +1,4 @@
-import { bG as MeshDistanceMaterial, bH as MeshDepthMaterial, bI as RGBADepthPacking, ae as UniformsUtils, bJ 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, bK as InstancedBufferAttribute } from "./index-se6p8sp4.js";
+import { bG as MeshDistanceMaterial, bH as MeshDepthMaterial, bI as RGBADepthPacking, ae as UniformsUtils, bJ 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, bK as InstancedBufferAttribute } from "./index-Z-pD1WnL.js";
 function workerBootstrap() {
   var modules = /* @__PURE__ */ Object.create(null);
   function registerModule(ref, callback) {

package/dist/{webimage-C9QSeLIa.js → webimage-CLacHpNV.js}

@@ -1,4 +1,4 @@
-import { aW as BaseDecoder } from "./index-se6p8sp4.js";
+import { aW as BaseDecoder } from "./index-Z-pD1WnL.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.8.4",
+  "version": "3.8.6",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,38 +17,38 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/styles": "3.8.4",
-    "@vitessce/constants-internal": "3.8.4",
-    "@vitessce/abstract": "3.8.4",
-    "@vitessce/error": "3.8.4",
-    "@vitessce/csv": "3.8.4",
-    "@vitessce/description": "3.8.4",
-    "@vitessce/feature-list": "3.8.4",
-    "@vitessce/genomic-profiles": "3.8.4",
-    "@vitessce/heatmap": "3.8.4",
-    "@vitessce/glb": "3.8.4",
-    "@vitessce/json": "3.8.4",
-    "@vitessce/layer-controller": "3.8.4",
-    "@vitessce/layer-controller-beta": "3.8.4",
-    "@vitessce/link-controller": "3.8.4",
-    "@vitessce/obs-sets-manager": "3.8.4",
-    "@vitessce/ome-tiff": "3.8.4",
-    "@vitessce/plugins": "3.8.4",
-    "@vitessce/scatterplot-embedding": "3.8.4",
-    "@vitessce/scatterplot-gating": "3.8.4",
-    "@vitessce/schemas": "3.8.4",
-    "@vitessce/spatial": "3.8.4",
-    "@vitessce/spatial-beta": "3.8.4",
-    "@vitessce/statistical-plots": "3.8.4",
-    "@vitessce/status": "3.8.4",
-    "@vitessce/vit-s": "3.8.4",
-    "@vitessce/zarr": "3.8.4",
-    "@vitessce/globals": "3.8.4",
-    "@vitessce/spatial-zarr": "3.8.4",
-    "@vitessce/spatial-three": "3.8.4",
-    "@vitessce/spatial-accelerated": "3.8.4",
-    "@vitessce/biomarker-select": "3.8.4",
-    "@vitessce/neuroglancer": "3.8.4"
+    "@vitessce/styles": "3.8.6",
+    "@vitessce/constants-internal": "3.8.6",
+    "@vitessce/abstract": "3.8.6",
+    "@vitessce/error": "3.8.6",
+    "@vitessce/csv": "3.8.6",
+    "@vitessce/description": "3.8.6",
+    "@vitessce/feature-list": "3.8.6",
+    "@vitessce/genomic-profiles": "3.8.6",
+    "@vitessce/heatmap": "3.8.6",
+    "@vitessce/glb": "3.8.6",
+    "@vitessce/json": "3.8.6",
+    "@vitessce/layer-controller": "3.8.6",
+    "@vitessce/layer-controller-beta": "3.8.6",
+    "@vitessce/link-controller": "3.8.6",
+    "@vitessce/obs-sets-manager": "3.8.6",
+    "@vitessce/ome-tiff": "3.8.6",
+    "@vitessce/plugins": "3.8.6",
+    "@vitessce/scatterplot-embedding": "3.8.6",
+    "@vitessce/scatterplot-gating": "3.8.6",
+    "@vitessce/schemas": "3.8.6",
+    "@vitessce/spatial": "3.8.6",
+    "@vitessce/spatial-beta": "3.8.6",
+    "@vitessce/statistical-plots": "3.8.6",
+    "@vitessce/status": "3.8.6",
+    "@vitessce/vit-s": "3.8.6",
+    "@vitessce/zarr": "3.8.6",
+    "@vitessce/globals": "3.8.6",
+    "@vitessce/spatial-zarr": "3.8.6",
+    "@vitessce/spatial-three": "3.8.6",
+    "@vitessce/spatial-accelerated": "3.8.6",
+    "@vitessce/biomarker-select": "3.8.6",
+    "@vitessce/neuroglancer": "3.8.6"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",