@vitessce/all 3.6.3 → 3.6.5

package/dist/index.js

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

package/dist/{jpeg-DJyIIvO7.js → jpeg-Cme28dbT.js}

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

package/dist/{lerc-B0cTVDdb.js → lerc-h4DF1MKc.js}

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

package/dist/{lzw-BWwSMLET.js → lzw-h5wVE82e.js}

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

package/dist/{packbits-CpM-jL5s.js → packbits-PnonD8Iv.js}

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

package/dist/{raw-BnKrggy7.js → raw-D2g6FVg4.js}

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

package/dist/{troika-three-text.esm-C71wQV-C.js → troika-three-text.esm-C3yFpL6B.js}

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

package/dist/{webimage-DkWfOrrK.js → webimage-D3CXqES4.js}

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

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

@@ -49,6 +49,13 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
     }>>;
+    obsFeatureColumns: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        path: z.ZodString;
+    }, "strip", z.ZodTypeAny, {
+        path: string;
+    }, {
+        path: string;
+    }>, "many">>;
     obsSets: z.ZodOptional<z.ZodArray<z.ZodObject<{
         name: z.ZodString;
         path: z.ZodUnion<[z.ZodString, z.ZodArray<z.ZodString, "many">]>;
@@ -146,6 +153,9 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
     } | undefined;
+    obsFeatureColumns?: {
+        path: string;
+    }[] | undefined;
     obsSets?: {
         path: (string | string[]) & (string | string[] | undefined);
         name: string;
@@ -195,6 +205,9 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         featureFilterPath?: string | undefined;
         initialFeatureFilterPath?: string | undefined;
     } | undefined;
+    obsFeatureColumns?: {
+        path: string;
+    }[] | undefined;
     obsSets?: {
         path: (string | string[]) & (string | string[] | undefined);
         name: string;
@@ -250,6 +263,19 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         tablePath?: string | undefined;
         coordinateSystem?: string | undefined;
     }>>;
+    shapes: 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>;
@@ -326,6 +352,11 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         tablePath?: string | undefined;
         coordinateSystem?: string | undefined;
     } | undefined;
+    shapes?: {
+        path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
+    } | undefined;
     obsFeatureMatrix?: {
         path: string;
         featureFilterPath?: string | undefined;
@@ -358,6 +389,11 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
         tablePath?: string | undefined;
         coordinateSystem?: string | undefined;
     } | undefined;
+    shapes?: {
+        path: string;
+        tablePath?: string | undefined;
+        coordinateSystem?: string | undefined;
+    } | undefined;
     obsFeatureMatrix?: {
         path: string;
         featureFilterPath?: string | undefined;

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,EAkDF,MAAM,mBAAmB,CAAC;AAwK3B,eAAO,MAAM,aAAa,kBA8BzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDAwEzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;yBAqFnB,CAAC;gCAAsD,CAAC;;;yBACA,CAAC;gCACxB,CAAC;;;;;;;;;;;;;;;;iBAUN,CAAC;;;;iBAEpB,CAAC;;;;;;;YAMD,CAAC;;;YAGnB,CAAC;;;;;;;YAOS,CAAA;;;YAIT,CAAD;;;;;;;YAIwD,CAAC;;;YAClC,CAAC;;;;;;;;;;;;;;YAWjB,CAAC;;;YAGG,CAAC;;;;;;;;YAMa,CAAC;;;;YAIM,CAAC;;;;;;;;;;;;;;;;;;;;;;;;yBAqBlC,CAAC;gCACwB,CAAC;;;;;;;;iBAUxB,CAAC;;;;YAIG,CAAC;;;;YAGM,CAAC;;;;YAGZ,CAAC;;;;;;;YAEH,CAAD;;;;YACQ,CAAC;;;;;;;;;;;;;;;;;;;;yBAIoE,CAAC;gCACrC,CAAC;;;;;;;;iBAEwC,CAAC;;;;YACd,CAAA;;;;YACC,CAAC;;;;YACI,CAAC;;;;;;;YAEZ,CAAC;;;;YACjC,CAAC;;;;;;;;;;;wBAiEg3C,CAAC;;;wBAA6E,CAAC;;;;;;;;iBAA8Q,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,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;;;;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;;;;iBAA+F,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBArhB76N,CAAC;;;;;qBAGU,CAAC;qBAA4C,CAAC;;;;;;;;;qBAIlD,CAAC;6BACZ,CAAA;;sBAEa,CAAC;;;;;qBAOY,CAAC;qBACK,CAAC;;;;;;;;;qBAa/B,CAAC;6BAEH,CAAC;;;;;;;;;;;;;kBAwBC,CAAC;mBACO,CAAC;gBAEH,CAAC;gBAEd,CAAF;uBACY,CAAC;iBAEX,CAAC;oBACY,CAAC;oBAEb,CAAC;qBACQ,CAAC;;kBAER,CAAC;mBAEC,CAAC;gBAGK,CAAC;gBACA,CAAC;uBAGV,CAAC;iBAGI,CAAC;oBAET,CAAA;oBACgB,CAAC;qBAEV,CAAC;;;;;;gBAMP,CAAC;sBACiB,CAAC;;;;;qBAYf,CAAC;qBACY,CAAC;;;;;;;;;qBAWN,CAAC;6BAEH,CAAC;;mBAGZ,CAAD;kBACC,CAAA;mBACW,CAAC;gBAGX,CAAC;gBACe,CAAC;uBAEK,CAAC;iBAEd,CAAC;oBACb,CAAA;oBAA0C,CAAC;qBACX,CAAC;;;;;;gBAGiC,CAAC;sBAA0B,CAAC;;;;;qBAGlF,CAAC;qBAA4C,CAAC;;;;;;;;;qBAEvB,CAAC;6BAEV,CAAC;;mBAAgE,CAAC;kBAC/E,CAAC;mBAAyC,CAAC;gBACZ,CAAC;gBACrC,CAAA;uBACa,CAAC;iBACa,CAAC;oBAA0C,CAAC;oBAC3E,CAAJ;qBAI2B,CAAC;;;;;;;;;gBAIV,CAAC;sBAA0B,CAAC;;;;;qBAI5C,CAAC;qBAA4C,CAAC;;;;;;;;;qBAInB,CAAC;6BACC,CAAC;;mBAC9B,CAAC;kBAAsB,CAAC;mBACxB,CAAF;gBAAmD,CAAC;gBAC3C,CAAC;uBAA6C,CAAC;iBAC9B,CAAC;oBACJ,CAAC;oBAA0C,CAAC;qBAC3B,CAAC;;;;;;;;;;;gBAIY,CAAC;sBAC1C,CAAC;;;;;qBAGS,CAAC;qBAA4C,CAAC;;;;;;;;;qBAM7D,CAAC;6BAC4B,CAAC;;mBAAgE,CAAC;kBACnF,CAAC;mBAAyC,CAAC;gBAAmD,CAAC;gBACvF,CAAC;uBAA6C,CAAC;iBACtE,CAAC;oBAA0C,CAAC;oBAA0C,CAAC;qBACtE,CAAC;;;;;;;;;;;;;;OAsFrB,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;aA7VtB,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cAEF,CAAD;eAEU,CAAC;;;;;;;;;;;;;;;;;;;aAiB0B,CAAC;cACjB,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;aAlEnD,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cAEF,CAAD;eAEU,CAAC;;;;;;;;;;;;;;;;;;;aAiB0B,CAAC;cACjB,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kzBA4gB9D,CAAC;AAEF,eAAO,MAAM,kBAAkB,uBAK9B,CAAC"}

package/dist-tsc/base-plugins.js

@@ -37,7 +37,7 @@ import {
 // OME
 OmeZarrLoader, OmeZarrAsObsSegmentationsLoader, 
 // SpatialData
-SpatialDataTableSource, SpatialDataShapesSource, SpatialDataImageLoader, SpatialDataLabelsLoader, SpatialDataObsSpotsLoader, SpatialDataObsSetsLoader, } from '@vitessce/spatial-zarr';
+SpatialDataTableSource, SpatialDataShapesSource, SpatialDataImageLoader, SpatialDataLabelsLoader, SpatialDataObsSpotsLoader, SpatialDataObsSegmentationsLoader, SpatialDataObsSetsLoader, } from '@vitessce/spatial-zarr';
 import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
 import { GlbSource, GlbLoader, } from '@vitessce/glb';
 // Joint file types
@@ -144,11 +144,8 @@ export const baseFileTypes = [
     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),
-    // TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
     makeFileType(FileType.LABELS_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataLabelsLoader, ZarrDataSource, obsSegmentationsSpatialdataSchema),
-    // TODO: create a new loader for shapes that returns obsSegmentations with obsSegmentationsType: 'polygon' (or switch this to 'shape' everywhere?)
-    // TODO: create a new source for GeoPandas tables?
-    makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
+    makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataObsSegmentationsLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
     makeFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR, DataType.OBS_SPOTS, SpatialDataObsSpotsLoader, SpatialDataShapesSource, obsSpotsSpatialdataSchema),
     makeFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, SpatialDataTableSource, obsFeatureMatrixSpatialdataSchema),
     makeFileType(FileType.OBS_SETS_SPATIALDATA_ZARR, DataType.OBS_SETS, SpatialDataObsSetsLoader, SpatialDataTableSource, obsSetsSpatialdataSchema),
@@ -175,6 +172,7 @@ export const baseJointFileTypes = [
     new PluginJointFileType(FileType.ANNDATA_ZARR_ZIP, expandAnndataZarr, anndataZarrSchema),
     new PluginJointFileType(FileType.ANNDATA_H5AD, expandAnndataZarr, anndataH5adSchema),
     new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
+    new PluginJointFileType(FileType.SPATIALDATA_ZARR_ZIP, expandSpatialdataZarr, spatialdataZarrSchema),
     // For legacy file types:
     new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
     new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),

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;KA6UlB"}
+{"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,SAsO7E;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC;;;;;;;;UAjQ1E,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;;;;;;;UADX,MAAM;kBACE,GAAG;KA8WlB"}

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

@@ -55,6 +55,23 @@ export function expandAnndataZarr(fileDef) {
                     featureValueType: baseFileDef.coordinationValues.featureValueType,
                 },
             }] : []),
+        // obsFeatureColumns
+        ...(options.obsFeatureColumns ? [{
+                ...baseFileDef,
+                fileType: getFileType(FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR),
+                options: {
+                    ...sharedOptions,
+                    obsFeatureColumns: options.obsFeatureColumns,
+                },
+                coordinationValues: {
+                    ...extraCoordinationValues,
+                    obsType: baseFileDef.coordinationValues.obsType,
+                    // TODO: allow providing a featureType that is scoped to each `obsFeatureColumns` item
+                    // (rather than always using the featureType from the file definition).
+                    featureType: baseFileDef.coordinationValues.featureType,
+                    featureValueType: baseFileDef.coordinationValues.featureValueType,
+                },
+            }] : []),
         // obsSets
         ...(options.obsSets ? [{
                 ...baseFileDef,
@@ -225,6 +242,7 @@ export function expandAnndataZarr(fileDef) {
     ];
 }
 export function expandSpatialdataZarr(fileDef) {
+    const getFileType = createGetFileType(fileDef.fileType);
     const baseFileDef = {
         url: fileDef.url,
         requestInit: fileDef.requestInit,
@@ -248,7 +266,7 @@ export function expandSpatialdataZarr(fileDef) {
         // TODO: handle multiple obsFeatureMatrix?
         ...(options.obsFeatureMatrix ? [{
                 ...baseFileDef,
-                fileType: FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR,
+                fileType: getFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR),
                 options: options.obsFeatureMatrix,
                 coordinationValues: {
                     ...extraCoordinationValues,
@@ -261,7 +279,7 @@ export function expandSpatialdataZarr(fileDef) {
         // TODO: handle multiple obsSets?
         ...(options.obsSets ? [{
                 ...baseFileDef,
-                fileType: FileType.OBS_SETS_SPATIALDATA_ZARR,
+                fileType: getFileType(FileType.OBS_SETS_SPATIALDATA_ZARR),
                 options: options.obsSets,
                 coordinationValues: {
                     ...extraCoordinationValues,
@@ -272,7 +290,7 @@ export function expandSpatialdataZarr(fileDef) {
         // TODO: handle multiple obsSpots?
         ...(options.obsSpots ? [{
                 ...baseFileDef,
-                fileType: FileType.OBS_SPOTS_SPATIALDATA_ZARR,
+                fileType: getFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR),
                 options: {
                     coordinateSystem: defaultCoordinateSystem,
                     ...options.obsSpots,
@@ -288,10 +306,10 @@ export function expandSpatialdataZarr(fileDef) {
         // TODO: featureLabels
         // TODO: obsEmbedding
         // image
-        // TODO: handle multiple images
+        // TODO: handle multiple image elements?
         ...(options.image ? [{
                 ...baseFileDef,
-                fileType: FileType.IMAGE_SPATIALDATA_ZARR,
+                fileType: getFileType(FileType.IMAGE_SPATIALDATA_ZARR),
                 options: {
                     coordinateSystem: defaultCoordinateSystem,
                     ...options.image,
@@ -306,7 +324,7 @@ export function expandSpatialdataZarr(fileDef) {
         // TODO: handle multiple labels?
         ...(options.labels ? [{
                 ...baseFileDef,
-                fileType: FileType.LABELS_SPATIALDATA_ZARR,
+                fileType: getFileType(FileType.LABELS_SPATIALDATA_ZARR),
                 options: {
                     coordinateSystem: defaultCoordinateSystem,
                     ...options.labels,
@@ -317,5 +335,20 @@ export function expandSpatialdataZarr(fileDef) {
                     // TODO: fileUid?
                 },
             }] : []),
+        // shapes
+        // TODO: handle multiple shape elements?
+        ...(options.shapes ? [{
+                ...baseFileDef,
+                fileType: getFileType(FileType.SHAPES_SPATIALDATA_ZARR),
+                options: {
+                    coordinateSystem: defaultCoordinateSystem,
+                    ...options.shapes,
+                },
+                coordinationValues: {
+                    ...extraCoordinationValues,
+                    obsType: baseFileDef.coordinationValues.obsType,
+                    // TODO: fileUid?
+                },
+            }] : []),
     ];
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.6.3",
+  "version": "3.6.5",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,36 +17,36 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/styles": "3.6.3",
-    "@vitessce/constants-internal": "3.6.3",
-    "@vitessce/abstract": "3.6.3",
-    "@vitessce/csv": "3.6.3",
-    "@vitessce/description": "3.6.3",
-    "@vitessce/feature-list": "3.6.3",
-    "@vitessce/genomic-profiles": "3.6.3",
-    "@vitessce/heatmap": "3.6.3",
-    "@vitessce/glb": "3.6.3",
-    "@vitessce/json": "3.6.3",
-    "@vitessce/layer-controller": "3.6.3",
-    "@vitessce/layer-controller-beta": "3.6.3",
-    "@vitessce/link-controller": "3.6.3",
-    "@vitessce/obs-sets-manager": "3.6.3",
-    "@vitessce/ome-tiff": "3.6.3",
-    "@vitessce/plugins": "3.6.3",
-    "@vitessce/scatterplot-embedding": "3.6.3",
-    "@vitessce/scatterplot-gating": "3.6.3",
-    "@vitessce/schemas": "3.6.3",
-    "@vitessce/spatial": "3.6.3",
-    "@vitessce/spatial-beta": "3.6.3",
-    "@vitessce/statistical-plots": "3.6.3",
-    "@vitessce/status": "3.6.3",
-    "@vitessce/vit-s": "3.6.3",
-    "@vitessce/zarr": "3.6.3",
-    "@vitessce/globals": "3.6.3",
-    "@vitessce/spatial-zarr": "3.6.3",
-    "@vitessce/spatial-three": "3.6.3",
-    "@vitessce/biomarker-select": "3.6.3",
-    "@vitessce/neuroglancer": "3.6.3"
+    "@vitessce/styles": "3.6.5",
+    "@vitessce/constants-internal": "3.6.5",
+    "@vitessce/abstract": "3.6.5",
+    "@vitessce/csv": "3.6.5",
+    "@vitessce/description": "3.6.5",
+    "@vitessce/feature-list": "3.6.5",
+    "@vitessce/genomic-profiles": "3.6.5",
+    "@vitessce/heatmap": "3.6.5",
+    "@vitessce/glb": "3.6.5",
+    "@vitessce/json": "3.6.5",
+    "@vitessce/layer-controller": "3.6.5",
+    "@vitessce/layer-controller-beta": "3.6.5",
+    "@vitessce/link-controller": "3.6.5",
+    "@vitessce/obs-sets-manager": "3.6.5",
+    "@vitessce/ome-tiff": "3.6.5",
+    "@vitessce/plugins": "3.6.5",
+    "@vitessce/scatterplot-embedding": "3.6.5",
+    "@vitessce/scatterplot-gating": "3.6.5",
+    "@vitessce/schemas": "3.6.5",
+    "@vitessce/spatial": "3.6.5",
+    "@vitessce/spatial-beta": "3.6.5",
+    "@vitessce/statistical-plots": "3.6.5",
+    "@vitessce/status": "3.6.5",
+    "@vitessce/vit-s": "3.6.5",
+    "@vitessce/zarr": "3.6.5",
+    "@vitessce/globals": "3.6.5",
+    "@vitessce/spatial-zarr": "3.6.5",
+    "@vitessce/spatial-three": "3.6.5",
+    "@vitessce/biomarker-select": "3.6.5",
+    "@vitessce/neuroglancer": "3.6.5"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",

package/src/base-plugins.ts

@@ -173,6 +173,7 @@ import {
   SpatialDataImageLoader,
   SpatialDataLabelsLoader,
   SpatialDataObsSpotsLoader,
+  SpatialDataObsSegmentationsLoader,
   SpatialDataObsSetsLoader,
 } from '@vitessce/spatial-zarr';
 
@@ -319,11 +320,8 @@ export const baseFileTypes = [
   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),
-  // TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
   makeFileType(FileType.LABELS_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataLabelsLoader, ZarrDataSource, obsSegmentationsSpatialdataSchema),
-  // TODO: create a new loader for shapes that returns obsSegmentations with obsSegmentationsType: 'polygon' (or switch this to 'shape' everywhere?)
-  // TODO: create a new source for GeoPandas tables?
-  makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
+  makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataObsSegmentationsLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
   makeFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR, DataType.OBS_SPOTS, SpatialDataObsSpotsLoader, SpatialDataShapesSource, obsSpotsSpatialdataSchema),
   makeFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, SpatialDataTableSource, obsFeatureMatrixSpatialdataSchema),
   makeFileType(FileType.OBS_SETS_SPATIALDATA_ZARR, DataType.OBS_SETS, SpatialDataObsSetsLoader, SpatialDataTableSource, obsSetsSpatialdataSchema),
@@ -352,6 +350,7 @@ export const baseJointFileTypes = [
   new PluginJointFileType(FileType.ANNDATA_ZARR_ZIP, expandAnndataZarr, anndataZarrSchema),
   new PluginJointFileType(FileType.ANNDATA_H5AD, expandAnndataZarr, anndataH5adSchema),
   new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
+  new PluginJointFileType(FileType.SPATIALDATA_ZARR_ZIP, expandSpatialdataZarr, spatialdataZarrSchema),
   // For legacy file types:
   new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
   new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),

package/src/joint-file-types.ts

@@ -67,6 +67,23 @@ export function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>)
         featureValueType: baseFileDef.coordinationValues.featureValueType,
       },
     }] : []),
+    // obsFeatureColumns
+    ...(options.obsFeatureColumns ? [{
+      ...baseFileDef,
+      fileType: getFileType(FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR),
+      options: {
+        ...sharedOptions,
+        obsFeatureColumns: options.obsFeatureColumns,
+      },
+      coordinationValues: {
+        ...extraCoordinationValues,
+        obsType: baseFileDef.coordinationValues.obsType,
+        // TODO: allow providing a featureType that is scoped to each `obsFeatureColumns` item
+        // (rather than always using the featureType from the file definition).
+        featureType: baseFileDef.coordinationValues.featureType,
+        featureValueType: baseFileDef.coordinationValues.featureValueType,
+      },
+    }] : []),
     // obsSets
     ...(options.obsSets ? [{
       ...baseFileDef,
@@ -244,6 +261,7 @@ export function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>)
 }
 
 export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchema>) {
+  const getFileType = createGetFileType(fileDef.fileType);
   const baseFileDef: BaseFileDef = {
     url: fileDef.url,
     requestInit: fileDef.requestInit,
@@ -267,7 +285,7 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
     // TODO: handle multiple obsFeatureMatrix?
     ...(options.obsFeatureMatrix ? [{
       ...baseFileDef,
-      fileType: FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR,
+      fileType: getFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR),
       options: options.obsFeatureMatrix,
       coordinationValues: {
         ...extraCoordinationValues,
@@ -280,7 +298,7 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
     // TODO: handle multiple obsSets?
     ...(options.obsSets ? [{
       ...baseFileDef,
-      fileType: FileType.OBS_SETS_SPATIALDATA_ZARR,
+      fileType: getFileType(FileType.OBS_SETS_SPATIALDATA_ZARR),
       options: options.obsSets,
       coordinationValues: {
         ...extraCoordinationValues,
@@ -291,7 +309,7 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
     // TODO: handle multiple obsSpots?
     ...(options.obsSpots ? [{
       ...baseFileDef,
-      fileType: FileType.OBS_SPOTS_SPATIALDATA_ZARR,
+      fileType: getFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR),
       options: {
         coordinateSystem: defaultCoordinateSystem,
         ...options.obsSpots,
@@ -307,10 +325,10 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
     // TODO: featureLabels
     // TODO: obsEmbedding
     // image
-    // TODO: handle multiple images
+    // TODO: handle multiple image elements?
     ...(options.image ? [{
       ...baseFileDef,
-      fileType: FileType.IMAGE_SPATIALDATA_ZARR,
+      fileType: getFileType(FileType.IMAGE_SPATIALDATA_ZARR),
       options: {
         coordinateSystem: defaultCoordinateSystem,
         ...options.image,
@@ -325,7 +343,7 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
     // TODO: handle multiple labels?
     ...(options.labels ? [{
       ...baseFileDef,
-      fileType: FileType.LABELS_SPATIALDATA_ZARR,
+      fileType: getFileType(FileType.LABELS_SPATIALDATA_ZARR),
       options: {
         coordinateSystem: defaultCoordinateSystem,
         ...options.labels,
@@ -336,5 +354,20 @@ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchem
         // TODO: fileUid?
       },
     }] : []),
+    // shapes
+    // TODO: handle multiple shape elements?
+    ...(options.shapes ? [{
+      ...baseFileDef,
+      fileType: getFileType(FileType.SHAPES_SPATIALDATA_ZARR),
+      options: {
+        coordinateSystem: defaultCoordinateSystem,
+        ...options.shapes,
+      },
+      coordinationValues: {
+        ...extraCoordinationValues,
+        obsType: baseFileDef.coordinationValues.obsType,
+        // TODO: fileUid?
+      },
+    }] : []),
   ];
 }