@vitessce/all 3.4.12 → 3.5.0

package/dist/index.js

@@ -1,4 +1,4 @@
-import { b4, b2, b0, b3, b1, a$, b5 } from "./index-8ed3997f.js";
+import { b4, b2, b0, b3, b1, a$, b5 } from "./index-509a394d.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull } from "@vitessce/vit-s";
 import "react";
 import "react-dom";

package/dist/{jpeg-e383d75a.js → jpeg-924502fe.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-8ed3997f.js";
+import { aP as BaseDecoder } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-e0ea6e91.js → lerc-1339f69d.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-8ed3997f.js";
+import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-9502d20a.js → lzw-098e43e6.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-8ed3997f.js";
+import { aP as BaseDecoder } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-b61051af.js → packbits-eecc1015.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-8ed3997f.js";
+import { aP as BaseDecoder } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-54997420.js → raw-9c07a573.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-8ed3997f.js";
+import { aP as BaseDecoder } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{troika-three-text.esm-315428f3.js → troika-three-text.esm-aadb7de3.js}

@@ -1,4 +1,4 @@
-import { aB as UniformsUtils, aV as MeshDepthMaterial, aW as RGBADepthPacking, aX as MeshDistanceMaterial, aY as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, aZ as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, a_ as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-8ed3997f.js";
+import { aB as UniformsUtils, aV as MeshDepthMaterial, aW as RGBADepthPacking, aX as MeshDistanceMaterial, aY as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, aZ as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, a_ as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-e4eb8c23.js → webimage-ebd59020.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-8ed3997f.js";
+import { aP as BaseDecoder } from "./index-509a394d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

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

@@ -1 +1 @@
-{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAgBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,2CAiElC"}
+{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAiBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,2CAmElC"}

package/dist-tsc/Vitessce.js

@@ -3,9 +3,9 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { useMemo } from 'react';
 import { VitS, logConfig, } from '@vitessce/vit-s';
 import { upgradeAndParse, } from '@vitessce/schemas';
-import { baseViewTypes, baseFileTypes, baseJointFileTypes, baseCoordinationTypes, } from './base-plugins.js';
+import { baseViewTypes, baseFileTypes, baseJointFileTypes, baseCoordinationTypes, baseAsyncFunctions, } from './base-plugins.js';
 export function Vitessce(props) {
-    const { config, onConfigUpgrade, pluginViewTypes: pluginViewTypesProp, pluginFileTypes: pluginFileTypesProp, pluginCoordinationTypes: pluginCoordinationTypesProp, pluginJointFileTypes: pluginJointFileTypesProp, pluginAsyncFunctions, } = props;
+    const { config, onConfigUpgrade, pluginViewTypes: pluginViewTypesProp, pluginFileTypes: pluginFileTypesProp, pluginCoordinationTypes: pluginCoordinationTypesProp, pluginJointFileTypes: pluginJointFileTypesProp, pluginAsyncFunctions: pluginAsyncFunctionsProp, } = props;
     // If config.uid exists, then use it for hook dependencies to detect changes
     // (controlled component case). If not, then use the config object itself
     // and assume the un-controlled component case.
@@ -41,6 +41,8 @@ export function Vitessce(props) {
     const mergedPluginCoordinationTypes = useMemo(() => ([
         ...baseCoordinationTypes, ...(pluginCoordinationTypesProp || []),
     ]), [pluginCoordinationTypesProp]);
-    // TODO: merge with a set of "base" async functions
-    return (_jsx(VitS, { ...props, config: configOrWarning, viewTypes: mergedPluginViewTypes, fileTypes: mergedPluginFileTypes, jointFileTypes: mergedPluginJointFileTypes, coordinationTypes: mergedPluginCoordinationTypes, asyncFunctions: pluginAsyncFunctions, warning: (success ? null : configOrWarning) }));
+    const mergedPluginAsyncFunctions = useMemo(() => ([
+        ...baseAsyncFunctions, ...(pluginAsyncFunctionsProp || []),
+    ]), [pluginAsyncFunctionsProp]);
+    return (_jsx(VitS, { ...props, config: configOrWarning, viewTypes: mergedPluginViewTypes, fileTypes: mergedPluginFileTypes, jointFileTypes: mergedPluginJointFileTypes, coordinationTypes: mergedPluginCoordinationTypes, asyncFunctions: mergedPluginAsyncFunctions, warning: (success ? null : configOrWarning) }));
 }

package/dist-tsc/base-plugins.d.ts

@@ -1,4 +1,4 @@
-import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType } from '@vitessce/plugins';
+import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, PluginAsyncFunction } from '@vitessce/plugins';
 import type { DataLoader, DataSource } from '@vitessce/plugins';
 import { z } from '@vitessce/schemas';
 export declare const baseViewTypes: PluginViewType[];
@@ -228,87 +228,59 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
     } | undefined;
 }>> | PluginJointFileType<z.ZodObject<{
     image: z.ZodOptional<z.ZodObject<{
-        coordinateTransformations: z.ZodOptional<z.ZodArray<z.ZodUnion<[z.ZodObject<{
-            type: z.ZodLiteral<"identity">;
-        }, "strip", z.ZodTypeAny, {
-            type: "identity";
-        }, {
-            type: "identity";
-        }>, z.ZodObject<{
-            type: z.ZodLiteral<"translation">;
-            translation: z.ZodArray<z.ZodNumber, "many">;
-        }, "strip", z.ZodTypeAny, {
-            type: "translation";
-            translation: number[];
-        }, {
-            type: "translation";
-            translation: number[];
-        }>, z.ZodObject<{
-            type: z.ZodLiteral<"scale">;
-            scale: z.ZodArray<z.ZodNumber, "many">;
-        }, "strip", z.ZodTypeAny, {
-            type: "scale";
-            scale: number[];
-        }, {
-            type: "scale";
-            scale: number[];
-        }>]>, "many">>;
         path: z.ZodString;
+        coordinateSystem: z.ZodOptional<z.ZodString>;
     }, "strip", z.ZodTypeAny, {
         path: string;
-        coordinateTransformations?: ({
-            type: "identity";
-        } | {
-            type: "translation";
-            translation: number[];
-        } | {
-            type: "scale";
-            scale: number[];
-        })[] | undefined;
+        coordinateSystem?: string | undefined;
     }, {
         path: string;
-        coordinateTransformations?: ({
-            type: "identity";
-        } | {
-            type: "translation";
-            translation: number[];
-        } | {
-            type: "scale";
-            scale: number[];
-        })[] | undefined;
+        coordinateSystem?: string | undefined;
     }>>;
     labels: z.ZodOptional<z.ZodObject<{
         path: z.ZodString;
+        tablePath: z.ZodOptional<z.ZodString>;
+        coordinateSystem: z.ZodOptional<z.ZodString>;
     }, "strip", z.ZodTypeAny, {
         path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     }, {
         path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     }>>;
     obsFeatureMatrix: z.ZodOptional<z.ZodObject<{
         path: z.ZodString;
         featureFilterPath: z.ZodOptional<z.ZodString>;
         initialFeatureFilterPath: z.ZodOptional<z.ZodString>;
         region: z.ZodOptional<z.ZodString>;
+        coordinateSystem: z.ZodOptional<z.ZodString>;
     }, "strip", z.ZodTypeAny, {
         path: string;
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
         region?: string | undefined;
+        coordinateSystem?: string | undefined;
     }, {
         path: string;
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
         region?: string | undefined;
+        coordinateSystem?: string | undefined;
     }>>;
     obsSpots: z.ZodOptional<z.ZodObject<{
         path: z.ZodString;
         tablePath: z.ZodOptional<z.ZodString>;
+        coordinateSystem: z.ZodOptional<z.ZodString>;
     }, "strip", z.ZodTypeAny, {
         path: string;
         tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     }, {
         path: string;
         tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     }>>;
     obsSets: z.ZodOptional<z.ZodObject<{
         region: z.ZodOptional<z.ZodString>;
@@ -343,31 +315,28 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         region?: string | undefined;
         tablePath?: string | undefined;
     }>>;
+    coordinateSystem: z.ZodOptional<z.ZodOptional<z.ZodString>>;
 }, "strip", z.ZodTypeAny, {
     image?: {
         path: string;
-        coordinateTransformations?: ({
-            type: "identity";
-        } | {
-            type: "translation";
-            translation: number[];
-        } | {
-            type: "scale";
-            scale: number[];
-        })[] | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     labels?: {
         path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsFeatureMatrix?: {
         path: string;
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
         region?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsSpots?: {
         path: string;
         tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsSets?: {
         obsSets: {
@@ -378,31 +347,28 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         region?: string | undefined;
         tablePath?: string | undefined;
     } | undefined;
+    coordinateSystem?: string | undefined;
 }, {
     image?: {
         path: string;
-        coordinateTransformations?: ({
-            type: "identity";
-        } | {
-            type: "translation";
-            translation: number[];
-        } | {
-            type: "scale";
-            scale: number[];
-        })[] | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     labels?: {
         path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsFeatureMatrix?: {
         path: string;
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
         region?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsSpots?: {
         path: string;
         tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
     } | undefined;
     obsSets?: {
         obsSets: {
@@ -413,6 +379,7 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         region?: string | undefined;
         tablePath?: string | undefined;
     } | undefined;
+    coordinateSystem?: string | undefined;
 }>> | PluginJointFileType<z.ZodObject<{
     xy: z.ZodOptional<z.ZodString>;
     poly: z.ZodOptional<z.ZodString>;
@@ -1087,4 +1054,5 @@ export declare const baseCoordinationTypes: (PluginCoordinationType<z.ZodNullabl
         }>;
     })[];
 }>>> | PluginCoordinationType<z.ZodNullable<z.ZodUnion<[z.ZodNumber, z.ZodString]>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodNumber, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["BlackIsZero", "RGB"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["2D", "3D"]>>> | PluginCoordinationType<z.ZodEnum<["maximumIntensityProjection", "additive"]>> | PluginCoordinationType<z.ZodEnum<["vertical", "horizontal"]>> | PluginCoordinationType<z.ZodEnum<["cellSetSelection", "sampleSetSelection", "contourColor"]>>)[];
+export declare const baseAsyncFunctions: PluginAsyncFunction[];
 //# sourceMappingURL=base-plugins.d.ts.map

package/dist-tsc/base-plugins.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AAWA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACtB,mBAAmB,EACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EA6CF,MAAM,mBAAmB,CAAC;AAgJ3B,eAAO,MAAM,aAAa,kBAoBzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDAqEzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;yBAoD+B,CAAC;gCAC/B,CAAC;;;yBAC/B,CAAA;gCAAsD,CAAC;;;;;;;;;iBAIf,CAAC;;;;iBAC6C,CAAC;;;;;;;YAG3C,CAAC;;;YAC1B,CAAC;;;;;;;YAEuC,CAAC;;;YAC/B,CAAC;;;;;;;YAQ7B,CAAC;;;YACqC,CAAC;;;;;;;;;;;;;;YAYxC,CAAD;;;YAAmE,CAAC;;;;;;;;YAMjE,CAAH;;;;YAG2B,CAAC;;;;;;;;;;;;;;;;;;;;;;;;yBAkBC,CAAC;gCAAsD,CAAC;;;;;iBAG7D,CAAC;;;;YAKtB,CAAJ;;;;YAEuC,CAAC;;;;YAIpC,CAAH;;;;;;;YAQqB,CAAC;;;;YAKF,CAAC;;;;;;;;;;;;;;;;;;;;yBAiBlB,CAAA;gCAGY,CAAC;;;;;iBAES,CAAC;;;;YACG,CAAC;;;;YACI,CAAC;;;;YACF,CAAC;;;;;;;YAElB,CAAC;;;;YACU,CAAC;;;;;;;;;;;wBA4DglD,CAAC;;;wBAA6E,CAAC;;;;;;;;iBAA8Q,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;yBAAkZ,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;yBAA8E,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;;;;;iBAAgR,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;;;qBAAygB,CAAC;;;;qBAA2J,CAAC;;;;;;qBAAsN,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;qBAA0K,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;wBAAwL,CAAC;;;;iBAA+F,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;wBAAqJ,CAAC;;;;iBAA+F,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAtcr7M,CAAC;;;;;qBAEmE,CAAC;qBAExD,CAAC;;;;;;;;;qBAYtB,CAAC;6BAEM,CAAC;;sBAGV,CAAD;;;;;qBAWC,CADC;qBAEK,CAAC;;;;;;;;;qBAOH,CAAC;6BACe,CAAC;;;;;;;;;;;;;kBAyBC,CAAC;mBAEf,CAAC;gBAGP,CAAC;gBACA,CAAC;uBACgB,CAAC;iBAEK,CAAC;oBAG3B,CAAC;oBAEI,CAAC;qBAKR,CADC;;kBAEwB,CAAC;mBAEX,CAAC;gBAGd,CAAA;gBACiB,CAAC;uBAGlB,CAAF;iBACU,CAAC;oBACgB,CAAC;oBAEjB,CAAC;qBAEE,CAAC;;;;;;gBAOP,CAAC;sBAA0B,CAAC;;;;;qBAIsC,CAAC;qBAG1D,CAAC;;;;;;;;;qBACsE,CAAC;6BAEvD,CAAA;;mBACpB,CAAC;kBAAuB,CAAA;mBAAyC,CAAC;gBAAmD,CAAC;gBAAsC,CAAC;uBAC3I,CAAC;iBAEvB,CAAC;oBAA0C,CAAC;oBAA0C,CAAC;qBAC1D,CAAC;;;;;;gBAGlC,CAAD;sBACC,CAAA;;;;;qBAMgC,CAAC;qBACjB,CAAC;;;;;;;;;qBAIU,CAAC;6BACV,CAAC;;mBACW,CAAC;kBAAsB,CAAC;mBACrB,CAAC;gBACnB,CAAC;gBAAsC,CAAC;uBAClC,CAAC;iBACZ,CAAC;oBAA2C,CAAA;oBACpD,CAAC;qBAA2C,CAAC;;;;;;;;;gBAInD,CAAC;sBAA0B,CAAC;;;;;qBAO5B,CADC;qBACoB,CAAC;;;;;;;;;qBAEe,CAAC;6BAAoD,CAAC;;mBAC7C,CAAC;kBAAsB,CAAC;mBACtE,CAAD;gBAAmD,CAAC;gBAAsC,CAAC;uBAChF,CAAC;iBAAuC,CAAC;oBAA0C,CAAC;oBACvE,CAAC;qBAA2C,CAAC;;;;;;;;;;;gBAEkB,CAAC;sBAA0B,CAAC;;;;;qBAGpE,CAAC;qBAA4C,CAAC;;;;;;;;;qBAGjB,CAAC;6BAAoD,CAAC;;mBAC1F,CAAC;kBAAsB,CAAC;mBAAyC,CAAC;gBACvF,CAAC;gBAAsC,CAAC;uBAA6C,CAAC;iBACvG,CAAC;oBAA0C,CAAC;oBAA0C,CAAC;qBAA2C,CAAC;;;;;;;;;;;;;;OAqErI,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;aAlTtB,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAmCd,CAAC;cACqB,CAAC;eAGnB,CAAA;;;;;;;;;;;;;;;;;;;aASgC,CAAC;cAAsC,CAAC;eAC1C,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;aA7D1B,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAmCd,CAAC;cACqB,CAAC;eAGnB,CAAA;;;;;;;;;;;;;;;;;;;aASgC,CAAC;cAAsC,CAAC;eAC1C,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;4hBA+brC,CAAC;AAEF,eAAO,MAAM,kBAAkB,uBAG9B,CAAC"}

package/dist-tsc/base-plugins.js

@@ -1,5 +1,5 @@
-import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, ALT_ZARR_STORE_TYPES, } from '@vitessce/constants-internal';
-import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
+import { FileType, DataType, ViewType, CoordinationType, AsyncFunctionType, COMPONENT_COORDINATION_TYPES, ALT_ZARR_STORE_TYPES, } from '@vitessce/constants-internal';
+import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, PluginAsyncFunction, } from '@vitessce/plugins';
 import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, sampleSetsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsFeatureColumnsAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, sampleEdgesAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataH5adSchema, spatialdataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsOmeTiffSchema, obsSegmentationsOmeZarrSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, meshGlbSchema, } from '@vitessce/schemas';
 // Register view type plugins
 import { DescriptionSubscriber } from '@vitessce/description';
@@ -38,8 +38,10 @@ ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, }
 import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
 import { GlbSource, GlbLoader, } from '@vitessce/glb';
 // Joint file types
+import { BiomarkerSelectSubscriber, autocompleteFeature, transformFeature, } from '@vitessce/biomarker-select';
 import { expandAnndataZarr, expandSpatialdataZarr, } from './joint-file-types.js';
 import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
+// Biomarker select UI and default async functions.
 // Helper function to use COMPONENT_COORDINATION_TYPES.
 function makeViewType(name, component) {
     return new PluginViewType(name, component, COMPONENT_COORDINATION_TYPES[name]);
@@ -79,6 +81,7 @@ export const baseViewTypes = [
     makeViewType('higlass', HiGlassSubscriber),
     makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
     makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
+    makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
 ];
 export const baseFileTypes = [
     // All CSV file types
@@ -117,9 +120,9 @@ export const baseFileTypes = [
     makeFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource, obsSegmentationsAnndataSchema),
     makeFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource, featureLabelsAnndataSchema),
     // All OME file types
-    makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
+    ...makeZarrFileTypes(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
     makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
-    makeFileType(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
+    ...makeZarrFileTypes(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
     makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, obsSegmentationsOmeTiffSchema),
     // SpatialData file types
     makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
@@ -292,3 +295,7 @@ export const baseCoordinationTypes = [
     new PluginCoordinationType(CoordinationType.CONTOUR_COLOR_ENCODING, 'cellSetSelection', z.enum(['cellSetSelection', 'sampleSetSelection', 'contourColor'])),
     new PluginCoordinationType(CoordinationType.CONTOUR_COLOR, null, rgbArray.nullable()),
 ];
+export const baseAsyncFunctions = [
+    new PluginAsyncFunction(AsyncFunctionType.AUTOCOMPLETE_FEATURE, autocompleteFeature),
+    new PluginAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE, transformFeature),
+];

package/dist-tsc/joint-file-types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AA6B7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAqN7E;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC;;;;;;;;UAhP1E,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;KA2TlB"}
+{"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AA6B7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAqN7E;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC;;;;;;;;UAhP1E,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;KA6UlB"}

package/dist-tsc/joint-file-types.js

@@ -242,8 +242,10 @@ export function expandSpatialdataZarr(fileDef) {
         }
     });
     const { options = {} } = fileDef;
+    const defaultCoordinateSystem = options.coordinateSystem;
     return [
         // obsFeatureMatrix
+        // TODO: handle multiple obsFeatureMatrix?
         ...(options.obsFeatureMatrix ? [{
                 ...baseFileDef,
                 fileType: FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR,
@@ -256,6 +258,7 @@ export function expandSpatialdataZarr(fileDef) {
                 },
             }] : []),
         // obsSets
+        // TODO: handle multiple obsSets?
         ...(options.obsSets ? [{
                 ...baseFileDef,
                 fileType: FileType.OBS_SETS_SPATIALDATA_ZARR,
@@ -266,10 +269,14 @@ export function expandSpatialdataZarr(fileDef) {
                 },
             }] : []),
         // obsSpots
+        // TODO: handle multiple obsSpots?
         ...(options.obsSpots ? [{
                 ...baseFileDef,
                 fileType: FileType.OBS_SPOTS_SPATIALDATA_ZARR,
-                options: options.obsSpots,
+                options: {
+                    coordinateSystem: defaultCoordinateSystem,
+                    ...options.obsSpots,
+                },
                 coordinationValues: {
                     ...extraCoordinationValues,
                     obsType: baseFileDef.coordinationValues.obsType,
@@ -277,11 +284,18 @@ export function expandSpatialdataZarr(fileDef) {
             }] : []),
         // TODO: obsPoints?
         // TODO: obsLocations?
+        // TODO: obsLabels
+        // TODO: featureLabels
+        // TODO: obsEmbedding
         // image
+        // TODO: handle multiple images
         ...(options.image ? [{
                 ...baseFileDef,
                 fileType: FileType.IMAGE_SPATIALDATA_ZARR,
-                options: options.image,
+                options: {
+                    coordinateSystem: defaultCoordinateSystem,
+                    ...options.image,
+                },
                 coordinationValues: {
                     ...extraCoordinationValues,
                     featureType: baseFileDef.coordinationValues.featureType,
@@ -289,10 +303,14 @@ export function expandSpatialdataZarr(fileDef) {
                 },
             }] : []),
         // labels
+        // TODO: handle multiple labels?
         ...(options.labels ? [{
                 ...baseFileDef,
                 fileType: FileType.LABELS_SPATIALDATA_ZARR,
-                options: options.labels,
+                options: {
+                    coordinateSystem: defaultCoordinateSystem,
+                    ...options.labels,
+                },
                 coordinationValues: {
                     ...extraCoordinationValues,
                     obsType: baseFileDef.coordinationValues.obsType,

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@vitessce/all",
-  "version": "3.4.12",
-  "author": "Gehlenborg Lab",
+  "version": "3.5.0",
+  "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
     "type": "git",
@@ -18,29 +18,30 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.4.12",
-    "@vitessce/csv": "3.4.12",
-    "@vitessce/description": "3.4.12",
-    "@vitessce/feature-list": "3.4.12",
-    "@vitessce/genomic-profiles": "3.4.12",
-    "@vitessce/heatmap": "3.4.12",
-    "@vitessce/glb": "3.4.12",
-    "@vitessce/json": "3.4.12",
-    "@vitessce/layer-controller": "3.4.12",
-    "@vitessce/layer-controller-beta": "3.4.12",
-    "@vitessce/obs-sets-manager": "3.4.12",
-    "@vitessce/ome-tiff": "3.4.12",
-    "@vitessce/plugins": "3.4.12",
-    "@vitessce/scatterplot-embedding": "3.4.12",
-    "@vitessce/scatterplot-gating": "3.4.12",
-    "@vitessce/schemas": "3.4.12",
-    "@vitessce/spatial": "3.4.12",
-    "@vitessce/spatial-beta": "3.4.12",
-    "@vitessce/statistical-plots": "3.4.12",
-    "@vitessce/status": "3.4.12",
-    "@vitessce/vit-s": "3.4.12",
-    "@vitessce/zarr": "3.4.12",
-    "@vitessce/spatial-three": "3.4.12"
+    "@vitessce/constants-internal": "3.5.0",
+    "@vitessce/csv": "3.5.0",
+    "@vitessce/description": "3.5.0",
+    "@vitessce/feature-list": "3.5.0",
+    "@vitessce/genomic-profiles": "3.5.0",
+    "@vitessce/heatmap": "3.5.0",
+    "@vitessce/glb": "3.5.0",
+    "@vitessce/json": "3.5.0",
+    "@vitessce/layer-controller": "3.5.0",
+    "@vitessce/layer-controller-beta": "3.5.0",
+    "@vitessce/obs-sets-manager": "3.5.0",
+    "@vitessce/ome-tiff": "3.5.0",
+    "@vitessce/plugins": "3.5.0",
+    "@vitessce/scatterplot-embedding": "3.5.0",
+    "@vitessce/scatterplot-gating": "3.5.0",
+    "@vitessce/schemas": "3.5.0",
+    "@vitessce/spatial": "3.5.0",
+    "@vitessce/spatial-beta": "3.5.0",
+    "@vitessce/statistical-plots": "3.5.0",
+    "@vitessce/status": "3.5.0",
+    "@vitessce/vit-s": "3.5.0",
+    "@vitessce/zarr": "3.5.0",
+    "@vitessce/spatial-three": "3.5.0",
+    "@vitessce/biomarker-select": "3.5.0"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",

package/src/Vitessce.tsx

@@ -12,6 +12,7 @@ import {
   baseFileTypes,
   baseJointFileTypes,
   baseCoordinationTypes,
+  baseAsyncFunctions,
 } from './base-plugins.js';
 
 export function Vitessce(props: any) {
@@ -22,7 +23,7 @@ export function Vitessce(props: any) {
     pluginFileTypes: pluginFileTypesProp,
     pluginCoordinationTypes: pluginCoordinationTypesProp,
     pluginJointFileTypes: pluginJointFileTypesProp,
-    pluginAsyncFunctions,
+    pluginAsyncFunctions: pluginAsyncFunctionsProp,
   } = props;
 
   // If config.uid exists, then use it for hook dependencies to detect changes
@@ -65,7 +66,9 @@ export function Vitessce(props: any) {
     ...baseCoordinationTypes, ...(pluginCoordinationTypesProp || []),
   ]), [pluginCoordinationTypesProp]);
 
-  // TODO: merge with a set of "base" async functions
+  const mergedPluginAsyncFunctions = useMemo(() => ([
+    ...baseAsyncFunctions, ...(pluginAsyncFunctionsProp || []),
+  ]), [pluginAsyncFunctionsProp]);
 
   return (
     <VitS
@@ -75,7 +78,7 @@ export function Vitessce(props: any) {
       fileTypes={mergedPluginFileTypes}
       jointFileTypes={mergedPluginJointFileTypes}
       coordinationTypes={mergedPluginCoordinationTypes}
-      asyncFunctions={pluginAsyncFunctions}
+      asyncFunctions={mergedPluginAsyncFunctions}
       warning={(success ? null : configOrWarning)}
     />
   );

package/src/base-plugins.ts

@@ -5,6 +5,7 @@ import {
   DataType,
   ViewType,
   CoordinationType,
+  AsyncFunctionType,
   COMPONENT_COORDINATION_TYPES,
   ALT_ZARR_STORE_TYPES,
 } from '@vitessce/constants-internal';
@@ -13,6 +14,7 @@ import {
   PluginJointFileType,
   PluginViewType,
   PluginCoordinationType,
+  PluginAsyncFunction,
 } from '@vitessce/plugins';
 import type {
   DataLoader,
@@ -161,6 +163,11 @@ import {
 } from '@vitessce/glb';
 
 // Joint file types
+import {
+  BiomarkerSelectSubscriber,
+  autocompleteFeature,
+  transformFeature,
+} from '@vitessce/biomarker-select';
 import {
   expandAnndataZarr,
   expandSpatialdataZarr,
@@ -179,6 +186,8 @@ import {
   expandRasterOmeZarr,
 } from './joint-file-types-legacy.js';
 
+// Biomarker select UI and default async functions.
+
 // Helper function to use COMPONENT_COORDINATION_TYPES.
 function makeViewType(name: string, component: any) {
   return new PluginViewType(name, component as ComponentType, COMPONENT_COORDINATION_TYPES[name]);
@@ -220,6 +229,7 @@ export const baseViewTypes = [
   makeViewType('higlass', HiGlassSubscriber),
   makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
   makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
+  makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
 ];
 
 export const baseFileTypes = [
@@ -259,9 +269,9 @@ export const baseFileTypes = [
   makeFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource, obsSegmentationsAnndataSchema),
   makeFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource, featureLabelsAnndataSchema),
   // All OME file types
-  makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
+  ...makeZarrFileTypes(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
   makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
-  makeFileType(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
+  ...makeZarrFileTypes(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
   makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, obsSegmentationsOmeTiffSchema),
   // SpatialData file types
   makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
@@ -517,3 +527,8 @@ export const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType.CONTOUR_COLOR_ENCODING, 'cellSetSelection', z.enum(['cellSetSelection', 'sampleSetSelection', 'contourColor'])),
   new PluginCoordinationType(CoordinationType.CONTOUR_COLOR, null, rgbArray.nullable()),
 ];
+
+export const baseAsyncFunctions = [
+  new PluginAsyncFunction(AsyncFunctionType.AUTOCOMPLETE_FEATURE, autocompleteFeature),
+  new PluginAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE, transformFeature),
+];