@vitessce/all 3.2.2 → 3.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/blosc-0acfcf7e.js +975 -0
- package/dist/{deflate-432aacfa.js → deflate-2f8bc9ba.js} +1 -1
- package/dist/gzip-dd5ab7c8.js +28 -0
- package/dist/{hglib-1bae5754.js → hglib-c31dff2a.js} +1 -1
- package/dist/{index-f665a5d4.js → index-bef59a57.js} +4678 -5566
- package/dist/index.js +1 -1
- package/dist/{jpeg-b55e77c5.js → jpeg-92e88990.js} +1 -1
- package/dist/{lerc-2523b21e.js → lerc-7d9f0083.js} +1 -1
- package/dist/lz4-abb4416a.js +919 -0
- package/dist/{lzw-b35f334d.js → lzw-fddb0b81.js} +1 -1
- package/dist/{packbits-6e275aa4.js → packbits-f19f0a34.js} +1 -1
- package/dist/pako.esm-856454b6-c5c8cd15.js +4066 -0
- package/dist/{raw-8dc223b5.js → raw-e3409593.js} +1 -1
- package/dist/{webimage-917679ff.js → webimage-e1f702e2.js} +1 -1
- package/dist/zlib-cd823c38.js +28 -0
- package/dist/zstd-4072ca78.js +919 -0
- package/dist-tsc/Vitessce.d.ts.map +1 -1
- package/dist-tsc/Vitessce.js +1 -1
- package/dist-tsc/base-plugins.d.ts.map +1 -1
- package/dist-tsc/base-plugins.js +14 -1
- package/package.json +22 -22
- package/src/Vitessce.tsx +1 -0
- package/src/base-plugins.ts +23 -0
@@ -1 +1 @@
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-
{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAgBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,
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+
{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAgBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,8CA+DlC"}
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package/dist-tsc/Vitessce.js
CHANGED
@@ -5,7 +5,7 @@ import { VitS, logConfig, } from '@vitessce/vit-s';
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import { upgradeAndParse, } from '@vitessce/schemas';
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import { baseViewTypes, baseFileTypes, baseJointFileTypes, baseCoordinationTypes, } from './base-plugins.js';
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export function Vitessce(props) {
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const { config, onConfigUpgrade, pluginViewTypes: pluginViewTypesProp, pluginFileTypes: pluginFileTypesProp, pluginCoordinationTypes: pluginCoordinationTypesProp, pluginJointFileTypes: pluginJointFileTypesProp, } = props;
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const { config, onConfigUpgrade, pluginViewTypes: pluginViewTypesProp, pluginFileTypes: pluginFileTypesProp, pluginCoordinationTypes: pluginCoordinationTypesProp, pluginJointFileTypes: pluginJointFileTypesProp, stores, } = props;
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// If config.uid exists, then use it for hook dependencies to detect changes
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// (controlled component case). If not, then use the config object itself
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// and assume the un-controlled component case.
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@@ -1 +1 @@
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-
{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,
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+
{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EAqCF,MAAM,mBAAmB,CAAC;AAiH3B,eAAO,MAAM,aAAa,kBAiBzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA8DzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAe9B,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;4WAmLjC,CAAC"}
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package/dist-tsc/base-plugins.js
CHANGED
@@ -1,6 +1,6 @@
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import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, } from '@vitessce/constants-internal';
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import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
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-
import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
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import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
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// Register view type plugins
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import { DescriptionSubscriber } from '@vitessce/description';
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import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
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@@ -31,6 +31,8 @@ AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsSpot
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MuDataSource,
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// OME
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OmeZarrLoader,
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// SpatialData
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SpatialDataTableSource, SpatialDataShapesSource, SpatialDataImageLoader, SpatialDataLabelsLoader, SpatialDataObsSpotsLoader, SpatialDataObsSetsLoader,
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// Legacy
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ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
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import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
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@@ -99,6 +101,16 @@ export const baseFileTypes = [
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makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
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makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
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// SpatialData file types
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makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
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// TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
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makeFileType(FileType.LABELS_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataLabelsLoader, ZarrDataSource, obsSegmentationsSpatialdataSchema),
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// TODO: create a new loader for shapes that returns obsSegmentations with obsSegmentationsType: 'polygon' (or switch this to 'shape' everywhere?)
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// TODO: create a new source for GeoPandas tables?
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makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
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makeFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR, DataType.OBS_SPOTS, SpatialDataObsSpotsLoader, SpatialDataShapesSource, obsSpotsSpatialdataSchema),
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makeFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, SpatialDataTableSource, obsFeatureMatrixSpatialdataSchema),
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makeFileType(FileType.OBS_SETS_SPATIALDATA_ZARR, DataType.OBS_SETS, SpatialDataObsSetsLoader, SpatialDataTableSource, obsSetsSpatialdataSchema),
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// All legacy file types
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makeFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource, z.null()),
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makeFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource, rasterJsonSchema),
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@@ -117,6 +129,7 @@ export const baseFileTypes = [
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];
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export const baseJointFileTypes = [
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new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
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// new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
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// For legacy file types:
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new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
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new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
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package/package.json
CHANGED
@@ -1,6 +1,6 @@
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{
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"name": "@vitessce/all",
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"version": "3.
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"version": "3.3.0",
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"author": "Gehlenborg Lab",
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"homepage": "http://vitessce.io",
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"repository": {
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@@ -18,27 +18,27 @@
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"dependencies": {
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"@material-ui/core": "~4.12.3",
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"zod": "^3.21.4",
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"@vitessce/constants-internal": "3.
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"@vitessce/description": "3.
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"@vitessce/csv": "3.
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/layer-controller": "3.
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"@vitessce/layer-controller-beta": "3.
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"@vitessce/
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"@vitessce/
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"@vitessce/plugins": "3.
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"@vitessce/scatterplot-embedding": "3.
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"@vitessce/scatterplot-gating": "3.
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"@vitessce/schemas": "3.
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"@vitessce/spatial": "3.
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"@vitessce/
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"@vitessce/
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"@vitessce/vit-s": "3.
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"@vitessce/status": "3.
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"@vitessce/zarr": "3.
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"@vitessce/constants-internal": "3.3.0",
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"@vitessce/description": "3.3.0",
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"@vitessce/csv": "3.3.0",
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"@vitessce/feature-list": "3.3.0",
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"@vitessce/heatmap": "3.3.0",
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"@vitessce/genomic-profiles": "3.3.0",
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"@vitessce/json": "3.3.0",
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"@vitessce/layer-controller": "3.3.0",
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"@vitessce/layer-controller-beta": "3.3.0",
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"@vitessce/ome-tiff": "3.3.0",
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"@vitessce/obs-sets-manager": "3.3.0",
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"@vitessce/plugins": "3.3.0",
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"@vitessce/scatterplot-embedding": "3.3.0",
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"@vitessce/scatterplot-gating": "3.3.0",
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"@vitessce/schemas": "3.3.0",
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"@vitessce/spatial": "3.3.0",
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"@vitessce/spatial-beta": "3.3.0",
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"@vitessce/statistical-plots": "3.3.0",
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"@vitessce/vit-s": "3.3.0",
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"@vitessce/status": "3.3.0",
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"@vitessce/zarr": "3.3.0"
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},
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"devDependencies": {
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"@types/react": "^18.0.28",
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package/src/Vitessce.tsx
CHANGED
@@ -22,6 +22,7 @@ export function Vitessce(props: any) {
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pluginFileTypes: pluginFileTypesProp,
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pluginCoordinationTypes: pluginCoordinationTypesProp,
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pluginJointFileTypes: pluginJointFileTypesProp,
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stores,
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} = props;
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// If config.uid exists, then use it for hook dependencies to detect changes
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package/src/base-plugins.ts
CHANGED
@@ -43,6 +43,11 @@ import {
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cellsJsonSchema,
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imageOmeZarrSchema,
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imageOmeTiffSchema,
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imageSpatialdataSchema,
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obsSegmentationsSpatialdataSchema,
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obsFeatureMatrixSpatialdataSchema,
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obsSpotsSpatialdataSchema,
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obsSetsSpatialdataSchema,
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obsSetPath,
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rgbArray,
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obsSetsSchema,
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@@ -118,6 +123,13 @@ import {
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MuDataSource,
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// OME
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OmeZarrLoader,
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// SpatialData
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SpatialDataTableSource,
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SpatialDataShapesSource,
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SpatialDataImageLoader,
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SpatialDataLabelsLoader,
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SpatialDataObsSpotsLoader,
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SpatialDataObsSetsLoader,
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// Legacy
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ZarrDataSource,
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MatrixZarrAsObsFeatureMatrixLoader,
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@@ -212,6 +224,16 @@ export const baseFileTypes = [
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makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
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makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
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// SpatialData file types
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makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
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// TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
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makeFileType(FileType.LABELS_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, SpatialDataLabelsLoader, ZarrDataSource, obsSegmentationsSpatialdataSchema),
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// TODO: create a new loader for shapes that returns obsSegmentations with obsSegmentationsType: 'polygon' (or switch this to 'shape' everywhere?)
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// TODO: create a new source for GeoPandas tables?
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makeFileType(FileType.SHAPES_SPATIALDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, SpatialDataShapesSource, obsSegmentationsSpatialdataSchema),
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makeFileType(FileType.OBS_SPOTS_SPATIALDATA_ZARR, DataType.OBS_SPOTS, SpatialDataObsSpotsLoader, SpatialDataShapesSource, obsSpotsSpatialdataSchema),
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makeFileType(FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, SpatialDataTableSource, obsFeatureMatrixSpatialdataSchema),
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makeFileType(FileType.OBS_SETS_SPATIALDATA_ZARR, DataType.OBS_SETS, SpatialDataObsSetsLoader, SpatialDataTableSource, obsSetsSpatialdataSchema),
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// All legacy file types
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makeFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource, z.null()),
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makeFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource, rasterJsonSchema),
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@@ -231,6 +253,7 @@ export const baseFileTypes = [
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export const baseJointFileTypes = [
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new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
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// new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
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// For legacy file types:
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new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
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new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
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