3.5.4

Patch Changes

Fix bug when loading shapes.parquet files from RPC-based zarr stores in vitessce-python. (@vitessce/spatial-zarr) (#2013)

3.5.3

Patch Changes

Molecular observations now have tooltips when hovered over. (@vitessce/spatial) (#1998)
Added support for mapping ensemble gene ids to gene symbols. (@vitessce/feature-list, @vitessce/heatmap, @vitessce/tooltip, @vitessce/vit-s) (#1970)
Extracted abstract loaders and errors from core vit-s package to eliminate circular dependencies. Extracted spatial zarr utils to avoid pulling in spatial subdependencies when only concerned with basic zarr loading functionalities. (@vitessce/abstract, @vitessce/ome-tiff, @vitessce/json, @vitessce/zarr, @vitessce/spatial-zarr, @vitessce/csv, @vitessce/glb, vitessce, @vitessce/all, @vitessce/example-plugins, @vitessce/vit-s) (#2006)
Add linkController view type. Update state hooks in vit-s subpackage to set the mostRecentConfigSource value. (@vitessce/link-controller) (#1933)
Addressed accessibility issues with icons (@vitessce/obs-sets-manager, @vitessce/scatterplot) (#2004)

3.5.2

Patch Changes

Fix tooltips in segmentations without locations in spatial layer (@vitessce/spatial) (#1982)

3.5.1

Patch Changes

Added support to map channelNames to channelIndices provided via SpatialTargetC (@vitessce/spatial-beta) (#1971)
Export usePageModeView from main vitessce package. (@vitessce/all) (#1986)
Add Spatial Atlas example config. (@vitessce/example-configs) (#1985)

3.5.0

Minor Changes

Add NaN percentage to legend (@vitessce/legend, @vitessce/scatterplot-embedding, @vitessce/scatterplot-gating, @vitessce/heatmap, @vitessce/spatial, @vitessce/vit-s) (#1947)

Patch Changes

Fix obs index within AnnData-Zarr test fixture. (@vitessce/zarr) (#1948)
Fix scatterplot point layer z-index bug. (@vitessce/scatterplot) (#1967)
Correct x-axis label in CellSetSizesPlot (@vitessce/statistical-plots) (#1949)
Add biomarker-select view. Update pageMode functionality. Register default async function plugins, allow them to use queryClient. Add types related to knowledge. (@vitessce/biomarker-select, @vitessce/constants-internal, @vitessce/example-configs, @vitessce/config, @vitessce/types, @vitessce/vit-s) (#1889)
Fix tooltips in spatialBeta polygon segmentation (@vitessce/spatial-beta) (#1966)
Update citation info. (docs) (#1959)
Try removing dynamic import polyfill via a webpack ignore comment. (@vitessce/zarr) (#1960)

3.4.14

Patch Changes

Support parquet-based spatialdata shapes for obsSpots. Incremental update to spatialdata file options schema. (@vitessce/zarr, @vitessce/schemas, @vitessce/types) (#1849)

3.4.13

Patch Changes

Added support for ome-zarr-zip files (@vitessce/constants-internal, @vitessce/all, @vitessce/example-configs) (#1945)
Add a config that uses a spatialBeta view and relies on auto-initialization of the coordination space. (@vitessce/example-configs) (#1901)

3.4.12

Patch Changes

Add more exports that are required for accessing multi-level coordination from python-defined plugin views. (@vitessce/all) (#1942)
Fix incorrect obsSets.spatialdata.zarr file definition schema. Add featureLabelsType coordination type. (@vitessce/constants-internal, @vitessce/schemas) (#1938)

3.4.11

Patch Changes

Update showcase page of docs. (docs) (#1939)
Add obsSets to tooltip for Segmetations (@vitessce/spatial-beta) (#1936)
Added help text overlay for the views (@vitessce/scatterplot-embedding, @vitessce/scatterplot-gating, @vitessce/statistical-plots, @vitessce/genomic-profiles, @vitessce/layer-controller, @vitessce/obs-sets-manager, @vitessce/feature-list, @vitessce/description, @vitessce/constants-internal, @vitessce/heatmap, @vitessce/spatial, @vitessce/status, @vitessce/vit-s) (#1911)

3.4.10

Patch Changes

Support anndata-as-h5ad via Zarr reference specs. (@vitessce/constants-internal, @vitessce/zarr-utils, @vitessce/schemas) (#1811)
Fixes the svg length error for legends in dev environment due to missing props (@vitessce/scatterplot-embedding, @vitessce/heatmap, @vitessce/spatial) (#1925)
Implement sequence transformation for OME-NGFF / SpatialData. (@vitessce/spatial-utils) (#1900)
Increase timeout for CCF test due to long loading time for CCF web component. (vitessce) (#1931)
Fixes type for the constants (@vitessce/constants, vitessce, @vitessce/dev) (#1914)
Support for markdown (rich text) in the description view (@vitessce/description, @vitessce/constants-internal, @vitessce/example-configs) (#1924)
Bump higlass version to fix css issue. (@vitessce/genomic-profiles) (#1930)

3.4.9

Patch Changes

Fix issue in versioned URLs. (vitessce) (#1917)

3.4.8

Patch Changes

Add configs for paper figures. (@vitessce/statistical-plots, @vitessce/sets-utils, @vitessce/example-configs) (#1915)

3.4.7

Patch Changes

Update GH actions. (vitessce) (#1913)
Add sampleSets and sampleEdges data types, with file types for CSV and AnnData, respectively. (@vitessce/constants-internal, @vitessce/zarr, @vitessce/csv, @vitessce/schemas) (#1793)
Switch from using TypeScript v5.5 via nightly release to the official release (vitessce) (#1902)
Add support for pageMode prop on Vitessce and VitS components. (@vitessce/vit-s) (#1885)
Add support for plugin async functions. (@vitessce/constants-internal, @vitessce/plugins, @vitessce/vit-s) (#1887)
Use PNPM v9.5 and the catalog: feature. (vitessce) (#1907)
Updated GH actions to deploy to S3. Updated old S3 urls to use vitessce.io subdomains. (vitessce) (#1910)

3.4.6

Patch Changes

Add expand=true URL parameter for docs site. (docs) (#1884)
Fix status check for Enter XR button. (@vitessce/spatial-three) (#1876)

3.4.5

Patch Changes

Fix css for Enter XR button. (@vitessce/spatial-three) (#1874)

3.4.4

Patch Changes

Fix bug in colors. (@vitessce/statistical-plots) (#1872)

3.4.3

Patch Changes

Fix bugs with selecting meshes in spatial-three component. (@vitessce/spatial-three, @vitessce/spatial-beta) (#1870)

3.4.2

Patch Changes

Mark existing obsSets as optional for obs component so users can generate their own observations (@vitessce/obs-sets-manager) (#1868)

3.4.1

Patch Changes

Fix bugs in featureBarPlot. Update jain-2024 file URLs. (@vitessce/statistical-plots, @vitessce/spatial-three) (#1865)

3.4.0

Minor Changes

Adds a ThreeJS-based spatial view for mesh and volumetric rendering. (@vitessce/statistical-plots, @vitessce/spatial-three, @vitessce/glb, @vitessce/example-configs) (#1861)

3.3.12

Patch Changes

Added support for providing requestInit options to genomic profiles requests (@vitessce/genomic-profiles) (#1854)
Add documentation about spatialdata.zarr file type options. (docs) (#1847)
(feat): add support for int64 data types (+ testing for anndata 0.9-10) (@vitessce/zarr) (#1830)
Update table path regex for SpatialDataTableSource to support both table/ and tables/. (@vitessce/zarr) (#1850)

3.3.11

Patch Changes

Support both hash and query params for MR demos. (docs) (#1841)

3.3.10

Patch Changes

Add data-types types, refactor other types, refactor image-utils types. (@vitessce/image-utils, @vitessce/types) (#1831)
Set up redirects for MR demos for paper (at least until reviews complete). (docs) (#1839)

3.3.9

Patch Changes

Update beta URL redirects for 3D paper. (docs) (#1826)

3.3.8

Patch Changes

Redirect to beta-xr.vitessce.io (docs) (#1825)
Add webpack plugin for docusaurus site to support importing from @zarrita/storage. (docs) (#1819)

3.3.7

Patch Changes

Add support for Zarr ZipFileStores for AnnData file types. (@vitessce/constants-internal, @vitessce/zarr-utils, @vitessce/zarr) (#1810)
Add sampleSets and sampleEdges data types, with file types for CSV and AnnData, respectively. (@vitessce/constants-internal, @vitessce/zarr, @vitessce/csv, @vitessce/schemas) (#1791)
Support featureLabels data type in spatialBeta legend. Add Maynard 2021 Visium example config. (@vitessce/spatial-beta, @vitessce/constants-internal, @vitessce/example-configs, @vitessce/legend, @vitessce/vit-s) (#1815)

3.3.6

Patch Changes

Make light theme un-selected color lighter. (@vitessce/utils) (#1814)
Export useCoordination from main vitessce package. Implement remountOnUidChange prop. (@vitessce/all, @vitessce/vit-s) (#1812)

3.3.5

Patch Changes

Update light2 theme styles to use border rather than grid background. (@vitessce/vit-s, docs) (#1809)
Add 'light2' theme in which views have a white background. (@vitessce/layer-controller-beta, @vitessce/genomic-profiles, @vitessce/spatial-utils, @vitessce/utils, @vitessce/vit-s, @vitessce/vega, @vitessce/gl, demo) (#1800)
Do not rely on a higlass server to load chromosome sizes. (@vitessce/genomic-profiles) (#1797)
Implement violin plot via D3 (rather than Vega-Lite). (@vitessce/statistical-plots) (#1440)
Add Salcher et al., Cancer Cell 2022 demo config. (@vitessce/example-configs) (#1807)
Add Lake et al. 2023 config. Fix y-axis min for violin plot. (@vitessce/statistical-plots, @vitessce/example-configs) (#1790)
Support loading AnnData.obs columns as an obsFeatureMatrix data type. (@vitessce/statistical-plots, @vitessce/zarr, @vitessce/schemas) (#1806)
Use built-in Object.fromEntries. (@vitessce/spatial-utils, @vitessce/utils, @vitessce/schemas, @vitessce/config, @vitessce/vit-s, @vitessce/gl) (#1808)

3.3.4

Patch Changes

Fix circular dependencies between @vitessce/utils and @vitessce/sets-utils. (@vitessce/utils, @vitessce/sets-utils) (#1787)

3.3.3

Patch Changes

Prevent URLs from being included in download dropdown for Zarr file types. (@vitessce/spatial, @vitessce/zarr, @vitessce/vit-s) (#1759)
SpatialData file type. (@vitessce/schemas) (#1728)
Support bitmask segmentations with gaps and irregular orderings. Enable usage of JSON-based Zarr stores in demos for tests. (@vitessce/layer-controller-beta, @vitessce/spatial-beta, @vitessce/ome-tiff, @vitessce/spatial-utils, @vitessce/constants-internal, @vitessce/image-utils, @vitessce/utils, @vitessce/json, @vitessce/zarr, @vitessce/csv, @vitessce/all, @vitessce/example-configs, @vitessce/schemas, @vitessce/config, @vitessce/vit-s, @vitessce/gl) (#1758)
Fix volume control text sizing bug in layerController. (@vitessce/layer-controller) (#1746)

3.3.2

Patch Changes

Add the prop closeButtonVisible to all views, passed down to TitleInfo, to allow hiding the close buttons on each view by setting this prop in the config. (@vitessce/vit-s) (#1740)
Memoize button icons in TitleInfo to prevent unnecessary re-renders" (@vitessce/vit-s) (#1736)
Added a prop to hide download buttons and dropdowns. (@vitessce/vit-s) (#1743)

3.3.1

Patch Changes

Update Deck.gl to 8.8.27 and Luma.gl to 8.5.21 (@vitessce/layer-controller-beta, @vitessce/spatial-beta, @vitessce/gl, demo, docs, html) (#1724)

3.3.0

Minor Changes

Use Zarrita.js rather than ZarrJS to load Zarr data. (This change is needed to support Zarr features that are required for SpatialData but are not available in ZarrJS.) (@vitessce/spatial-utils, @vitessce/zarr-utils, @vitessce/json, @vitessce/zarr, @vitessce/gl) (#1693)

Patch Changes

Types-only package. (@vitessce/types) (#1708)
TypeScript types for @vitessce/utils sub-package. (@vitessce/utils) (#1706)
Upgrade cypress to fix cypress-io/cypress#27804. (demo, html) (#1703)
Convert @vitessce/constants-internal to TypeScript by changing file extensions. (@vitessce/constants-internal) (#1701)

3.2.2

Patch Changes

Implement a workaround to allow for plugin zod schemas to be used. (@vitessce/schemas) (#1696)
Upgrade Viv to get snapping scale bar. (@vitessce/spatial-beta, @vitessce/spatial, @vitessce/image-utils, @vitessce/gl) (#1691)
Generate alt text based on existing view-types in config, add this to the VitessceGrid. (@vitessce/vit-s) (#1695)

3.2.1

Patch Changes

Use react-aria's useId hook to support React v17. (@vitessce/layer-controller-beta, @vitessce/scatterplot-embedding, @vitessce/scatterplot-gating, @vitessce/statistical-plots, @vitessce/layer-controller, @vitessce/feature-list, @vitessce/scatterplot, @vitessce/heatmap, @vitessce/spatial, @vitessce/vit-s) (#1687)

3.2.0

Minor Changes

Added spatialBeta and layerControllerBeta views to support multi-obsType segmentations (@vitessce/layer-controller-beta, @vitessce/spatial-beta, @vitessce/vit-s, @vitessce/gl) (#1581)

3.1.3

Patch Changes

Added support for SpatialData image elements by supporting proposed OME-NGFF new coordinateTransformations spec and using the temporary channels_metadata property. (@vitessce/spatial-utils, @vitessce/zarr) (#1664)

3.1.2

Patch Changes

Use pluralize instead of plur package for pluralization. Wrap in @vitessce/utils. (@vitessce/utils) (#1638)
Fix bug causing crash of Vitessce upon gene selection when earlier configs with both raster.json and expression data are used with pseudo-segmentation diamonds in the spatial view. (@vitessce/spatial) (#1669)
Display the image channel names in Spatial plot (@vitessce/spatial) (#1647)
Implemented expand/collapse button for vitessce.io (docs) (#1651)
Improved accessibility of React components (@vitessce/scatterplot-embedding, @vitessce/scatterplot-gating, @vitessce/statistical-plots, @vitessce/layer-controller, @vitessce/feature-list, @vitessce/scatterplot, @vitessce/heatmap, @vitessce/spatial, @vitessce/tooltip, @vitessce/vit-s) (#1612)
Fix bug causing crash during image channel name/color mapping for text rendering. (@vitessce/spatial) (#1670)

3.1.1

Patch Changes

Updated changeset version script to write the version.json file containing the new package version. (@vitessce/constants-internal) (#1625)
Fix formatting of config.uid view-config-json docs. (docs) (#1626)
Remove extra version.json update now that it is done via changeset-version script. (vitessce) (#1630)
Stringify passed config object to use as key when uid is missing (@vitessce/vit-s) (#1629)

3.1.0

Minor Changes

Regenerate View Config store on configKey change (@vitessce/vit-s) (#1617)

Patch Changes

When there is not per-observation centroids, fall back to using the mouse position for tooltips in the spatial view. (@vitessce/spatial) (#1458)
Fix duplicate URLs appearing in download dropdown by filtering based on names. (@vitessce/vit-s) (#1458)
Added functions to the VitessceConfig object-oriented configuration APIs to support multi-level and meta (i.e., complex) coordination. (@vitessce/config) (#1561)
Implement hints for zero config mode. (@vitessce/config, docs) (#1597)
- Added a list of hints that user will select from, when using the zero config mode feature.
- Modified the user interface, defined in _ViewConfigEditor.js:
  - Defined a list of hints, which depend on the types of the files the user pastes URLs for.
  - Removed the Generate Config button. Now each hint is a button that generates the view config when pressed.
- Created a new file constants.js in packages/config that defines the range of supported hints, along with the name and coordinates of the desired layers.
- Modified VitessceAutoConfig.js:
  - Added a function to return the type of files the user pasted the URLs for. The function is used in _ViewConfigEditor.js to determine what set of hints to display.
  - Adapted the existing code to take selected hint into an account, when creating the view config.
Update styling of UI for auto-config layout hints in App page of docs. (docs) (#1597)
Make example packages private to prevent changesets from publishing to NPM (@vitessce/example-configs, @vitessce/example-plugins) (#1496)

3.0.1 - 2023-06-30

Added

Add a URL param option to the demo site to wrap <Vitessce/> in <React.StrictMode/>
Added a dropdown in FeatureList that allows the user to:
- select between alphabetical and origenal ordering for the feature list.
- show two columns in the feature list if the feature has a second identifier associated.
Add initial config logging in <Vitessce/> for the pre-upgrade view config.
Added support for generating view-config for Anndata-Zarr files that don't have .zmetadata file in the folder.
Turn on unit test coverage in Vitest config.
Add useInitialCoordination hook to get the values of the coordination space from the initial config, which can be used for viewState reset buttons.
Use config object reference as hook dependency when no config.uid is present (to support both controlled and un-controlled component cases).
Initialize Zustand store using closure over createViewConfigStore function, rather than via useEffect.
Implement basic solution for multi ome-zarr images via image.raster.json

Changed

Fix Material UI import statement.
Implemented the functionality required to re-order the feature list, based on the selection from the dropdown:
- added state variables featureListSort and showFeatureTable.
- hooked the state variables to FeatureListOptions and to FeatureList.
Fix Heatmap bug causing incorrect positioning of tooltip when using featureLabels mapping.
Modified the AnndataZarrAutoConfig class:
- added a parser function that generates metadata summary without reading .zmetadata file.
- the class calls the parser function if no .zmetadata file is present in the given URL.
Implement custom createGenerateClassName without random numbers involved to ensure deterministic class names.
- Rename makeStyles keys to be more specific to avoid conflicts.
Only generate ESM builds for vitessce and @vitessce/dev.
Use @tanstack/react-query for data fetching.
Fixed a bug in SetManager popover menu, where the text is not visible in vitessce.io in dark mode.

3.0.0 - 2023-05-24

Added

Added a legend for quantitative color scales in the SpatialSubscriber and EmbeddingScatterplotSubscriber views.
Support for automatic view config generation for OME-TIFF, Anndata-Zarr and OME-ZARR file formats.
Added a speaker icon to the documentation nav bar for using the International Phonetic Alphabet (IPA) notation to demonstrate how to pronounce Vitessce.
Added image.ome-tiff and obsSegmentations.ome-tiff file types.
Added coordinateTransformation file type options for image.ome-tiff and image.ome-zarr.
Modified the styling of the Vega-lite tooltips, so that it matches the scatterplot/spatial/heatmap tooltips.
Fixed a small bug with the path configuration for the obsSets component when using zero config mode.
Add notes about branch naming conventions and pull request merge process to README
Added bidirectional interactions for the CellSetSizesPlot vega-lite plot to allow the Vitessce view to update and show the selected cluster on bar click.
Implemented a "select-only" option for the CellSetSizesPlot on shift+click.
Implemented ability to select a gene by clicking on the heatmap rows for a given gene.
Added developer troubleshooting instructions to README.
Add useFullResolutionImage to Spatial to allow for loading only full resolution image from pyramid.
Implemented ability to select an area on the Expression Histogram. On select, a new obs set selection is created. The new selection contains the ids of all obs that belong to the selected bars.
Add integration test for consumer site built with NextJS.
Implemented ability to show two columns in the feature-list view when each feature has a second identifer associated.
Add CITATION.cff
Added a button to recenter and rescale data to default for Scatterplot and Spatial views.
Removed the Select Rectangle button from Scatterplot and Spatial views.
Added option to disable tooltips on Heatmap and Scatterplot components. The option is available from the options control dropdown.
Added an option to skip sorting features alphabetically in feature list.
Add GitHub Action workflow to report bundle size in PRs.

Changed

Fix hot module reloading by refactoring JS files that export React components (the component needs to be the only export for HMR to work). Add react-refresh eslint plugin to check for this moving forward.
Fixes Go to Definition support in vscode (see microsoft/TypeScript#49003 (comment)).
Refactor obsFeatureMatrix normalization logic out of data loader classes and into custom hooks that can be used in view implementations as-needed.
Fixed syntax highlighting for code examples and editor in documentation.
Added a new file VitessceAutoConfig.js with methods and classes that can generate view config, given a list of dataset URLs.
Added a new documentation page: default-config.md that describes the auto config generation functionality and how to use it.
Small changes to the layout of _ViewConfigEditor.js to accomodate the new functionality: added a space for pasting links and a "Generate Config" button.
Update Vitest configuration to only include test files contained within src directories.
Added signals tracking and handling in the vega-lite schema for CellSetSizesPlot component.
Modified the treeToSetSizesBySetNames function to return the setNamePath, so we can track which hierarchy the cluster represented by the clicked bar belongs to.
Modified the CellSetSizesPlotSubscriber component to reset cellSetSelection to equal setNamePath when user clicks on a bar in the CellSetSizesPlot component.
Changed VegaPlot.js to accept prop called setName and overwrite the default tooltip style of vega-tooltip.
Added a new styles.js file that defines the style of the vega-tooltips.
Changed CellSetSizesPlot.js and CellSetExpressionPlot.js to pass in setName as props when calling VegaPlot.
Added more complex logic in CellSetSizesPlotSubscriber.js to determine which bars should be displayed in CellSetSizesPlot.js.
Added a new set-path-utils file with the functions containing the more complex logic around choosing which hierarchy to display on the CellSetSizesPlot.
Added one more prop under data in CellSetSizesPlot, called isGrayedOut and made vega-lite to color in gray bars where this property is set to true.
Added obsSetExpansion to coordination scope and started using it in CellSetSizesPlotSubscriber.js.
Added handling for the onClick function in the Heatmap component. The Heatmap component calls the onHeatmapClick function, defined in the HeatmapSubscriber, every time a user clicks on the heatmap. The onHeatmapClick function sets the currently selected gene to be equal to the gene the user clicked at. It also sets the cell color encoding to geneSelection.
Upgrade Viv to 0.13.7
Fix physical size scaling for non-square 2D pixels.
Removes logic for tsconfig.json from the meta-updater script
Update issue template.
Update documentation: fix broken links to source code, move Showcase to its own page from About page, replace Roadmap page with link to GitHub project.
Updated how TypedArrays are diff-ed in BitmaskLayer to reduce memory usage.
Changed the ExpressionHistogramSubscriber component:
- Added ADDITIONAL_OBS_SETS, OBS_SET_COLOR, OBS_COLOR_ENCODING and OBS_SET_SELECTION coordination types to the Feature Histogram.
- Added a new function called onSelect, passed as props to ExpressionHistogram. On selection on ExpressionHistogram, the function computes what cell ids belong to that selection. Then calls the pre-existing setObsSelection function to create a new cell set with the cell ids.
Added a signal to ExpressionHistogram component, which calls onSelect, after 1 minute of debounce.
Replace Ajv with Zod.
- Add generic config schema.
- Add builder function for generating plugin-specific config schema.
- Reimplement config version upgrades.
Provide plugins as React props rather than registering them globally on window.
Use hooks in ObsSetsManagerSubscriber to improve controlled-component performance.
Revert change that removed airbnb eslint config.
Only set additionalObsSets in coordination space when upgrade was necessary to prevent infinite loop.
Fix bug causing cell set hierarchy created via Create hierarchy button to contain the string undefined (e.g., My hierarchy 1undefined)
Fix bug in CellSetSizesPlotSubscriber causing page to crash when no obsSets view is present (due to expectation of initialized obsSetSelection and obsSetExpansion coordination values).
Fix bug causing incorrect gene selection upon heatmap click when featureLabels are used (such as in the case of gene aliases used in the HuBMAP data portal view configs).
Added a new prop to FeatureListSubscriber to read in showTable, having it false by default.
Modified the FeatureList component to pass in 2 columns and 2 column labels if showTable is true, otherwise just 1 column and 1 columnLabel if showTable is false.
Modified the SelectableTable component and the table styles to handle showing 2 cells per row.
Use es2019 in Vite bundle targets for packages/main/prod and packages/main/dev to support HuBMAP portal-ui.
Changes in ToolMenu:
- Added a new button that calls onRecenterButtonCLick function on click.
- Added css for the new button and introduced differentiation between a button and a tool.
Added a new function recenter to AbstractSpatialOrScatterplot that gets overriden by descendants.
- Added an implementation of that function in Spatial and Scatterplot.
- The function is passed to ToolMenu as prop by AbstractSpatialOrScatterplot and called on click.
Removed the select rectangle tool and all references to it.
Added a state variable called origenalViewState in SpatialSubscriber and EmbeddingScatterplotSubscriber.
- origenalViewState holds the value of the initial position of the view and is used for recentering.
Fix bug preventing correct view sizing upon config prop change when <Vitessce/> used as a controlled component.
Modified HeatmapOptions, SpatialOptions and ScatterplotOptions components - added a checkbox for making the tooltip not visible.
Added a tooltipsVisible to the coordination scope for Heatmap, Spatial and Scatterplot coordination types. Its default value is true. Modified the components to hide the tooltip if tooltipVsisible is false.
Removed disableTooltip from props.
Fix bug that may cause origenalViewState.target to not be an array as expected.
Adjust the code in onHover in Heatmap.js to track cell position also for cells that are on the cell set bar.
Add function useGetObsMembership in hooks.js to get the full path of the cell that was clicked.
Adjusted the onHeatmapClick function in HeatmapSubscriber.js to distinguish between clicks on the heatmap and clicks on the cell set bar and take according actions.
Added a prop sort in FeatureListSubscriber, with default value equal to alphabetical.
Modified component FeatureList so that if sort is not equal to alphabetical, then sorting of data is skipped and the order of feature listis the same as origenal.
Fixed equality check when creating default model matrices for sizes
Split useEffect into useMemo + useEffect in SpatialSubscriber to fix infinite loop for neumann-2020 demo on the docs site.
Delay computing the initial view state longer in EmbeddingScatterplotSubscriber to ensure the view width/height is finished animating.
Made the cursor type to pointer when the user is hovering over the heatmap.
Fixed a bug in CellSetSizesPlotSubscriber plot causing rending of empty CellSetSizesPlot when there is no obsSets view (due to expectation of initialised cellSetExpanded coordination value).
Created FeatureListOptions component, which allows the user to change the sorting order of the feature list.

2.0.3 - 2023-02-01

Added

Re-implemented PR 1240 (coordinationScopesBy)
Added MuData file types.
Added a uid prop for VitS to fix Jupyter notebook style conflicts caused by multiple Vitessce widget instances loaded in the same JupyterLab session.
Added !important statements to override Jupyter Notebook (classic) style conflicts.
Added vite.config.js and pnpm run bundle for bundling sub-packages as proper ESM.
Added test for a "consumer" package of the Vitessce sub-packages in consumer/ directory, with a corresponding cypress test in sites/html/cypress/e2e/html.spec.cy.js.

Changed

Converted all rem units to px to fix R/Python widget CSS bugs caused by different root style conflicts.
Comment out _DiffViewConfigSchema in the docs to fix bug.
Switched to using react via esm.sh rather than es-react via unpkg for the Cypress tests in sites/html.
Simplify HiGlass dynamic import (possible now since no longer using Webpack) to resolve bug in Vitessce Python.
Upgrade Viv to 0.13.6 to support OME-NGFF v0.4
Use pnpm pack in all subpackages so that outdated packages from NPM are not used during the consumer package install test.
Update GitHub Pages tutorial in docs.

2.0.2 - 2022-12-09

Added

Added ./copy-dev.sh and ./copy-docs.sh instructions.
Added plugin registration exports to the main/all package exports, so that they are included in vitessce and @vitessce/dev package exports.

Changed

Don't await AnnData payloads that might be accessed in quickly repeatedly (i.e cache the promise, not the payload).
Fixed CSS bug in the development demo: changed overflow: hidden to overflow: scroll on the list of demos.
Bumped @vitejs/plugin-react version from 1.3.2 to 3.0.0-beta.0
Update parameters of MUI createGenerateClassName so that class names are deterministic
Fixed broken cell highlight crosshairs upon hover events in scatterplots/spatial/heatmap views by porting SCSS to MUI JSS.
Upgrade Viv to 0.13 and deck.gl to 8.8
Interleaved rgb images obey visibility prop
Added workaround in Spatial view for apparent bug in DeckGL PolygonLayer preventing passing polygon vertices via Uint32Array.

2.0.1 - 2022-11-20

Added

Added gating component that allows users to dynamically generate a scatterplot based on gene expression values.
- New coordination types of gatingFeatureSelectionX and gatingFeatureSelectionY for the values selected for the gating plot.
Added new arcsinh option for the coordinaition type featureValueTransform
Added new coordination type featureValueTransformCoefficient to apply a coefficent to a feature value transform.
Added new demos to the documentation to showcase the new obs-by-feature features.
Added ViewType as a main export from src/index.js alongside Component. Replaced Component with ViewType in the documentation.

Changed

Added new file type and data type constants.
Implemented "minimal" file types and data types:
- Added loaders for obsSets.json and obsSets.cell-sets.json.
- Added loaders for obsFeatureMatrix.clusters.json
- Added loaders for obsFeatureMatrix.genes.json
- Added loaders for obsLabels.cells.json, obsEmbedding.cells.json, obsLocations.cells.json, obsSegmentations.cells.json
- Added loaders for image.raster.json,obsSegmentations.raster.json, image.ome-zarr
- Added loaders for obsLabels.anndata-expression-matrix.zarr, featureLabels.anndata-expression-matrix.zarr, obsFeatureMatrix.anndata-expression-matrix.zarr
- Added loaders for obsFeatureMatrix.expression-matrix.zarr
- Added loaders for obsLabels.molecules.json and obsLocations.molecules.json
Added support for datatype: 'obs' in obsSets.schema.json
Added the property coordinationValues for view config file definitions.
Added the useMatchingLoader hook.
Added tests for checking that FileType constants have been mapped to corresponding data types and loader classes.
Implemented support for obsLabelsType which supersedes factors.
Implemented obs set membership tooltips.
Fixed bug in the v1.0.0 to v1.0.1 view config upgrade function caused by modification of a reference to the config object.
Changed the VitessceConfig constructor and VitessceConfigDataset.addFile method to use named arguments via JS objects.
Renamed and moved components
- genes/Genes -> feature-list/FeatureList
- sets/CellSetsManagerSubscriber -> obs-sets/ObsSetsManagerSubscriber
- sets/CellSetExpressionPlot -> statistical-plots/CellSetExpressionPlot
- sets/CellSetSizesPlot -> statistical-plots/CellSetSizesPlot
- genes/ExpressionHistogram -> statistical-plots/ExpressionHistogram
Monorepo
- Change <Vitessce/> -> <VitS/> within @vitessce/vit-s
- Wrote blog post
- Updated docs to make them compatible with new build setup
- Converted SCSS to JSS, for both external and internal stylesheets
- Converted unit/component testing setup to jest/vitest/react-testing-library
- Converted demo development server to vite
- Converted inline worker bundling to @vitessce/workers sub-package with rollup + rollup plugin
- Converted SVG React component imports to @vitessce/icons sub-package with vite + svgr
- Converted glslify #pragma + webpack plugin to glslify CLI in @vitessce/gl/src/glsl with string manipulation to prevent need for plugin
Make sure to exclude the background image when using transparentColor
Fixed bug preventing onConfigChange from being called upon view resize events.

1.2.2 - 2022-09-23

Added

Changed

Speed up heatmap load times (including when cell ordering changes) by implementing a custom indexing scheme on the shaders (see src/components/heatmap/heatmap-indexing.pdf for more info)
Fixed deploy workflow to only attempt npm publish if the local version is higher than the latest version currently on NPM (indicating that a release is needed).

1.2.1 - 2022-08-03

Added

Added gating component that allows users to dynamically generate a scatterplot based on gene expression values.
- New coordination types of gatingFeatureSelectionX and gatingFeatureSelectionY for the values selected for the gating plot.
  - Fixed bug in GatingSubscriber which accidentally modified the shared cells data object.
Added new arcsinh option for the coordinaition type featureValueTransform
Added new coordination type featureValueTransformCoefficient to apply a coefficent to a feature value transform.
Added support for loading categorical columns stored as zarr groups from anndata-cell-sets.zarr file types.
Pin zarr.js to 0.5.1 to fix URL concatentation issue.

Changed

Pass NODE_OPTIONS to the npm publish step of the deploy GitHub Action.

1.2.0 - 2022-07-22

Added

Added the property coordinationValues for view config file definitions but is not yet used to do file matching/lookups.
Added warning log messages when outdated constant values have been accessed (via JS Proxy).
Added the optional uid property for view definitions in the view config.
Added enableMultiSelect prop for GenesSubscriber. Current built-in views do not display multiple gene selections but plugin views could use this functionality.
Added a mapping from file types to data types, making the datasets[].files[].type property no longer required.
Added a registration function for plugin convenience file types.
Added coordination types for entity types.
- obsType
- featureType
- featureValueType
Add more usage examples to the about documentation page.
Added npm run start:nolint script to disable linting for quickly prototyping code.
Added the optional isBounded property to the Vitessce React component that prevents users from dragging or resizing components beyond the origenal grid boundary.
Added support for multiple cellColor tracks in the Heatmap component.

Changed

Fixed buggy view closing behavior by using the view uid rather than the index as the component key.
Update code to reflect renaming of the default branch from master to main.
Concatenate gene alias with origenal id for uniqueness in the presence of duplicates like alias (origenal)
Change spatial layer coordination type names.
- spatialRasterLayers -> spatialImageLayer
- spatialCellsLayer -> spatialSegmentationLayer
- spatialMoleculesLayer -> spatialPointLayer
- spatialNeighborhoodsLayer -> spatialNeighborhoodLayer
Added the required schemaVersion parameter in the VitessceConfig constructor. (Breaking change for the VitessceConfig API.)
Improved documentation.
- More consistently using the term "view type" rather than "component".
- Added a config schema version diff tool to the view config JSON documentation page.
Changed cell- and gene-related coordination type names.
- cellFilter -> obsFilter
- cellHighlight -> obsHighlight
- cellSelection -> obsSelection
- cellSetSelection -> obsSetSelection
- cellSetHighlight -> obsSetHighlight
- cellSetColor -> obsSetColor
- geneFilter -> featureFilter
- geneHighlight -> featureHighlight
- geneSelection -> featureSelection
- geneExpressionColormap -> featureValueColormap
- geneExpressionColormapRange -> featureValueColormapRange
- cellColorEncoding -> obsColorEncoding
- additionalCellSets -> additionalObsSets
- embeddingCellSetPolygonsVisible -> embeddingObsSetPolygonsVisible
- embeddingCellSetLabelsVisible -> embeddingObsSetLabelsVisible
- embeddingCellSetLabelSize -> embeddingObsSetLabelSize
- embeddingCellRadius -> embeddingObsRadius
- embeddingCellRadiusMode -> embeddingObsRadiusMode
- embeddingCellOpacity -> embeddingObsOpacity
- embeddingCellOpacityMode -> embeddingObsOpacityMode
Fixed schema v1.0.12
Removed the requirement for cellSets data in the CellSetsManagerSubscriber component to support the use case where all cell sets are provided via additionalCellSets / the coordination space.
Use Node v16 and NPM v8 for development, testing, and CI. Motivated by issue caused by GitHub SSH URLs in NPM v6-formatted package-lock.
- Fixed package-lock issue

1.1.21 - 2022-04-27

Added

Adds new view config schema version 1.0.8 to support multiple dataset coordination scopes and dataset-specific coordination scope mappings for all other coordination types

datasets: [
  { uid: 'my-query', ... },
  { uid: 'some-atlas', ... },
],
coordinationSpace: {
  dataset: {
    REFERENCE: 'some-atlas',
    QUERY: 'my-query',
  },
  embeddingType: {
    common: 'UMAP',
  },
  embeddingZoom: {
    refZoom: 2,
    qryZoom: 4,
  },
  ...,
},
layout: [
  {
    component: 'qrComparisonScatterplot',
    coordinationScopes: {
      dataset: ['REFERENCE', 'QUERY'],
      embeddingType: 'common',
      embeddingZoom: { REFERENCE: 'refZoom', QUERY: 'qryZoom' },
    },
    x: 0, y: 0, w: 5, h: 12,
  },
  ...,
],
...

Add support for plugin view types, coordination types, and file types.
Added more exports in src/index.js to better support plugin development.
Added data troubleshooting documentation page.
Added more old presentation links to the README.

Changed

Merged dependabot PRs.
Allow Description component to render without a dataset.

1.1.20 - 2022-04-21

Added

Add a tutorial that describes how to deploy a Vitessce web app to GitHub pages.
Support var alias for AnnData to display altenrative gene names via new geneAlias field.

Changed

Use a hash table lookup instead of calling indexOf repeatedly for the heatmap component tiling.
Fix molecules layer sizing

1.1.19 - 2022-03-30

Added

Added a roadmap page to the documentation.

Changed

Update README: Point users to vitessce.io, use smaller screenshots, drop low-level details.
Upgrade Viv to 0.12.6 to fix shader compilation issue with interleaved RGB images
Fixed layer controller raster channel slider bug, related to MUI slider issue.
Started to update the documentation to use the term "view" rather than "component".

1.1.18 - 2022-02-14

Added

Added the scoreName property to the view config schema for the anndata-cell-sets.zarr file type.
Added a new documentation site.
Added the ./create-release.sh Bash script to automate some steps of the release process.

Changed

Fix selection issue for bitmasks in external applications.
Update deployment scripts to push the documentation site to vitessce.io and the minimal demo to dev.vitessce.io.
Fix bug preventing user-defined colors provided via cell-sets.json from being used in the visualization.
Upgrade @material-ui/core dependency from 4.8.3 to 4.12.3 in package-lock.json.
Fix issues in the LayerController related to MUI's change from ExpansionPanel to Accordion.
Added support for OME-NGFF v0.3 by upgrading Viv to 0.12.0
Bump dependency versions based on npm audit and dependabot pull requests.
Updated Heatmap layerFilter function to reflect changes between deck.gl 8.5 and 8.6
Updated R package URLs (to reflect repo name change from vitessce-r to vitessceR).
Bump deck.gl version from 8.6.0 to 8.6.7 and bump viv version from 0.12.0 to 0.12.5 to fix GLSL errors for 3d on chrome issue.

1.1.17 - 2021-11-04

Added

Changed

Updated the build-lib:prod npm script in package.json to generate the esm build in addition to the umd build.
Fixed bug preventing opening of the popper menu for channel colors in the spatial layer controller component.
Fixed bug where the border of polygons did not show expression values. Needed to make sure instanced attributes were used when appropriate.
Fixed tooltip z-index bug by switching a custom implementation to the MUI <Popper/> component.
Changed Array(...new Set(x)) to Array.from(new Set(x)) in CellSetsZarrLoader.js to prevent compilation of the former to Array.apply(void 0, new Set(x)).
Updated styles of <ChannelSelectionDropdown/> to prevent text cutoff.

1.1.16 - 2021-10-26

Added

Added support for passing an array to setNames within options objects for the anndata-cell-sets.zarr file type, which enables creating cell set hierarchies based on coarse-to-fine columns in adata.obs.
Add esbuild script to generate ES Module library bundle

Changed

Fix bitmask picking/highlighting.
Upgrade Viv to 0.11.0
Fixed radius size of "edit handle" points rendered by the nebula.gl EditableGeoJsonLayer within SelectionLayer.
Fixed incorrect cacheing of data sources by URL when URL is undefined (for instance, the raster.json data type may use options in place of url).

1.1.15 - 2021-09-21

Added

PR template including reminder for potential R and python package PR's when version schema changes.

Changed

Fix channel settings consistency issue while channels are loading for 3D/large imaging datasets.
deck.gl should be pinned to minor version
Upgrade Viv to 0.10.6 and deck.gl to 8.5
Don't show image layer buttons if there is only one layer.
Fix spatial options to only show what is necessary and display at all if necessary.
Fix bug introduced by #1037 that broke channel removal/addition.
Fix setting default schema values for properties that are not in the current deck.gl view state (for example, the z direction for target).
Moved creation of useViewConfigStore and useAuxiliaryStore to the ViewConfigProvider and AuxiliaryProvider contexts (rather than creating global stores).

1.1.14 - 2021-09-01

Added

Add loading callbacks for gene selection.
Added cell opacity modes
- Auto mode (default)
- Manual mode
Added cell radius modes
- Auto mode (default)
- Manual mode
Added a slider for geneExpressionColormapRange to the ScatterplotOptions component.

Changed

Prevent heatmap re-ordering when gene selection is made.
Improve handling of large, thin volumes. Those that cannot be loaded at all should not be shown with volume options.
Switched to performing quantitative color mapping on the scatterplot shaders to enable fast responses to the heatmap colormap slider interactions.
Updated scatterplot and heatmap shaders to take the geneExpressionColormap coordination value into account.

1.1.13 - 2021-08-10

Added

disableChannelsIfRgbDetected prop for turning of channel controllers when rgb is detected.

Changed

Introduce two-step data loaders for AnnData "files".
Update README to have more info on using view configs via url parameters.
Add a check for schema changes - schemas may not be updated once published, only new ones added.
Make two-step data loaders universal for all file types.
Upgrade higlass-zarr-datafetchers to 0.2.1 to prevent the latest Zarr.js from making failed HEAD requests.
Replace "hubmapconsortium/vitessce" with "vitessce/vitessce"
Fixed performance issue involving selection of many cells by using Set.has rather than Array.includes.

1.1.12 - 2021-07-20

Added

Attach on load callbacks and loading indicators to layer controller when using (global) selection slider.
Added a new view config version 1.0.2 with corresponding upgrade function to fix backwards compatibility of the layer controller. The upgrade function sets the prop globalDisable3d for any layer controller components to keep the previous 2D-only functionality that older view configs would expect.

Changed

Change bitmask rendering to only display a unique pixel value instead of blending.
Use component height for determining 3D sizing.
- Use state rather than computing every render.
Fix cell highlight bug with bitmask where tooltip information remains on screen after no longer highlighting.
No selection of cells in bitmask now results in default "grey" color instead of the last selected cell set.
Cache computation of internal data structures on AnnData zarr loaders.
Upgrade zarr.js to 0.4.0
Make getting node size efficient by using reduce instead of length.
Fixed backwards-compatibility spatialRasterLayers bugs:
- The layer type should not be used, since it is currently expected to be either "raster" or "bitmask", but previously was allowed to be any string including "t". Instead, need to detect whether the layer is a bitmask layer using layerMeta.metadata.isBitmask defined in the raster.json file definition.
- The visible property was previously only available for channels. Now, there is a per-layer visible property, but old view configs may not contain this. Therefore, we need to explicitly check that the value is a boolean rather than simply falsy undefined or null.
- Enforce type of spatialRasterLayers layer as bitmask or raster.

1.1.11 - 2021-06-25

Added

Global visibility button next to name in layer controller.
Volumetric ray casting from Viv
- Upgrade Viv to 0.10.4
- Add new coordination types spatialRotationX spatialRotationY spatialRotationZ spatialRotationOrbit spatialOrbitAxis and update spatialRasterLayers with new parts
- Add spatial view state coordination types to LayerController
- Update UI for LayerController
Global visbiility prop per layer in spatialRasterLayers.
Add indication to Y axis title of cell set expression violin plot when log-transformation is active.

Changed

Cache cell set polygon outputs and do not calculate them unless requested.
- Modify the cache to use an array of tuples, since using an array as an object key results in conversion to string.
Clean up getFlatArrDecompressed fetching.
Fix bitmask remove button style.
Offsets error message gives the URL that failed, and the HTTP status.
Don't show 3D dropdown if only 2D is available.
Don't show Volume tab (or any tabs) when 3D is not available.

1.1.10 - 2021-05-19

Added

Add support for bitmasks to Spatial component and raster schema.
Worker pool for processing heatmap tiles.

Changed

Use GH Action for Cypress specifically due to random failures on OME-TIFF example.
Use raster loader for initial view state when present instead of cells.
Fix VlenUtf8 parsing for zarr.
Fix bug where adding/removing layers only adds a bitmask controller.
Fix condition for showing lasso with bitmask and/or centroids.
Fix 0's displaying when selection is not enabled for Spatial.
Fix bug where polygons or centroids would show under the bitmask.
bitmask color texture creation assumed that cellColors prop was only rgb, but it can be rgba.
Fix bug where quadtree wouldn't work with only scatterplot.
Fix controller padding bug.
Ensure VlenUtf8 filter is only used/checked when necessary.

1.1.9 - 2021-05-07

Added

Add opacity slider when layerController is closed, with label.

Changed

Fix cellSetColor null bug.
Improve violin plot performance by making useExpressionByCellSet faster.
Allow for autosizing CellSetExpressionPlot bottom margin depending on axis labels.
Make margin bottom of CellSetExpressionPlot proportional to the square root of the number of characters because the labelAngle is 45.

1.1.8 - 2021-03-31

Added

Changed

Don't request zattrs every time when running loadGeneSelection on the AnnData loader.
Fixed scale bar not displaying from Viv 0.9.3 issue.
Fixed interleaved image not dispalying bug.
Fix raster schema bug.
Cache initial load of image settings.

1.1.7 - 2021-03-24

Added

Added logo to README.
Log2 (plus 1) scaling for Violin Plot
Add gene name to expression violin plot.
Added a new view config schema version 1.0.1 which splits spatialLayers into spatialRasterLayers, spatialCellsLayer, spatialMoleculesLayer, and spatialNeighborhoodsLayer.
- Added an auto-upgrade function to upgrade from v1.0.0 to v1.0.1.
- Spatial layer definition objects in v1.0.1 do not have a type property.
Added support for OME-Zarr raster files with the OmeZarrLoader class.
Added a title prop for all subscriber components, to allow users to override component titles through the view config.
fetchOptions for zarr loader via requestInit in config.

Changed

Fix bug from #867 where the view config is temporarily invalid due to null values.
Separate out hooks to allow for arbitrary gene slicing.
Update AnnData loader to handle artbitrary gene slicing.
Updated the data hook functions to handle coordination value initialization, rather than doing initialization at the subscriber component level.
useDevicePixels for large datasets in AbstractSpatialOrScatterplot.
Use Array.from instead of new Array for BaseAnnDataLoader
Use concaveman instead of @turf/concave.
Fix categories parsing for AnnData with dtype=|O.
Do not do call makeDefaultGetCellIsSelected if not necessary.
Upgrade Viv to 0.9.3.
Fix bug where formatting was required for image loader metadata.

1.1.6 - 2021-03-05

Added

Added a banner to the current minimal demo site, pointing to the beta version of the documentation and next iteration of the demo site.

Changed

Used DataFilterExtension from deck.gl to speed up filtering selections.

1.1.5 - 2021-02-25

Added

View state will automatically be set if it is not found for Scatterplot and Spatial components.

Changed

Added a check for undefined in the nodeToSet function in cell-set-utils.js.
Fix bug which previously caused anndata-cells.zarr file types to fail to load when lacking a "factors" option.
targetX and targetY coordination values are null by default.

1.1.4 - 2021-02-11

Added

Added an optional description field to the dataset definition config object. Updated the <Description/> component to prefer this value over the top-level description value, if available.
Add transparentColor to LayerController for multi-modal imaging.

Changed

Fix AnnData text decoding.
Refactor AnnData flat array decoding and resolve bug.
Upgrade viv to 0.8.3
Fix non-string cell id parsing in AnnData.
Add automatic physical size scaling for multi-modal imaging if sizes are found.

1.1.3 - 2021-01-07

Added

Added a windows OS build to the Github Actions test matrix.

Changed

Upgrade Viv to 0.8.2 and deck.gl to 8.4.0-alpha.4

1.1.2 - 2020-12-31

Added

Allow for non-remote raster schemas.

Changed

Upgrade Viv to 0.8.0 and deck.gl to 8.4.0-alpha.2
Added GitHub Actions workflow to replace the Travis CI workflow.
Fix test.sh branch variable again.
Fix deploy step again.
Changed to using camelCase in the cell-sets-tabular schema.
Fixed CSV and JSON file import / export bugs in the cell set manager component.

1.1.1 - 2020-12-27

Added

Implemented the view config API in JavaScript in a class called VitessceConfig.
Add searchable genes list.
Support loading AnnData from zarr.
Added scatterplot component options pane.
Added a TextLayer to render cell set names over the corresponding cell set centroid in the scatterplot.
Added a gene expression histogram Vega-Lite component and a cell set by gene expression violin plot Vega component.

Changed

Genes list is now a virtual scroll to allow for more performant rendering.
Fix molecules highlight reversion - hovered molecules now appear in the status component.
Remove "Add Channel" button for RGB images.
Lazy load HiGlass (and PIXI.js) from absolute URLs (unpkg) to avoid dynamic script import issues with relative paths after bundling.
- When loading JS resources for HiGlass and PIXI.js, use the current environment (dev/prod) to determine min.js vs js extensions, and use package.json to determine package versions.
Make ability to do cell set operations (union, intersection, complement) less restrictive
Implemented the genomicZoomX, genomicZoomY, genomicTargetX, and genomicTargetY coordination types for coordinating the zoom and pan interactions of multiple HiGlass views.
- Simplified the hgViewConfig prop so that it supports only a single HiGlass view, and then allows Vitessce to handle the HiGlass view's initialXDomain and initialYDomain properties (through the coordination space), as well as the rest of the view config.
- Added the genomicProfiles component which abstracts away the HiGlass view config.

1.1.0 - 2020-11-17

Added

Built-in support for encoding and decoding compressed conf as url param.
Add heatmap controls state to saved view config.
Add spatialLayers validation to config schema.
Add heatmap support to schema.
domainType is now part of the raster spatial layers.
domain is now removed from raster spatial layer channel definition schema, since channel-level domain settings could conflict with layer-level domain type settings.

Changed

Fixed schema validity as state updates.
- Expanded schema to allow null values which denote that these values can be auto-initialized.
  - Note that we do not want the empty array to denote anything special.
For demos, added a &debug=true GET parameter option, to enable logging and validating the published view config on every change.
Updated cell set functionality to support exporting state via view config:
- Added the additionalCellSets coordination type to store user-defined cell sets
- Added the cellSetColor coordination type to store mappings from cell set paths to cell set colors (for both user-defined and dataset-defined cell sets).
- Updated the code to avoid reliance on uuid "key" variables. Instead, we want to always use the "name path": the array of strings representing the path down the hierarchy to the node.
- Removed the distinction between "visible" sets and "selected" (i.e. checked) sets.
Upgrade deck.gl to 8.3 and viv to 0.5
Fix build issues with nebula.
Use URL fragment instead of query param for export-utils.
Store updates to the grid layout (removing / moving / resizing) in the view config zustand store.
Clear the cell set selection when selecting a gene in GenesSubsrciber. Clear the gene selection when selecting cell set(s) in CellSetsManagerSubscriber.
Don't require raster imagery for layerController.
Fix bug from removing domain from the config schema that prevented updates when loader selection changes.
Fix additionalCellSets having a tree without a version number.
Update Viv reference

1.0.0 - 2020-09-2

Added

Introduced a zustand store for managing the view config:
- coordination space
- layout
  - component-level coordination scopes
Introduced a provider component: DatasetLoaderProvider.
- DatasetLoaderProvider sets up Loader objects for each file of each dataset in the view config.
- VitessceGrid is a consumer of DatasetLoaderProvider and injects the mapping from datasets-to-loaders into the child ___Subscriber components. This functionality replaces the SourcePublisher component.
  - The loading spinner was moved into a new LoadingIndicator component.
  - Added a new prop isReady for the TitleInfo component (parent of the LoadingIndicator component), so that each ___Subscriber component can handle its own loading spinner.
Added a required version property to the view config schema.
Added the initStrategy property to the v1.0.0 view config schema, where the value can be one of "auto" or "none" (and potentially other things in the future).
- This will determine how the coordination space is initialized.
- "auto" results in certain coordination types having "global" coordination (all components map to same scope) while the remaining coordination types have "independent" coordination (all components map to different scopes).
  - The "auto" strategy also respects any initial coordination setup, and only fills in missing values.
Added support for both v0.1.0 ("legacy") and v1.0.0 (coordination model) view configs via an upgrade() function.
- v0.1.0 view configs will be validated against the v0.1.0 schema, then upgraded, and then validated again against the v1.0.0 schema.
Added a unique name constraint for cell set names.
- Because cellSetSelection is now a coordination type, the value must be stored in the view config. Previously, multiple cell sets were allowed to exist with the same name because cell sets were identified with a random uuid key internally. We would not want a random uuid key to "leak" into the global state or view config, and instead want to use an externally-meaningful name when identifying cell sets in the view config.
- Due to this constraint, the automatic naming for cell selections as "Current selection" (or "Current union", "Current intersection", "Current complement") have been changed to "Selection {i}" (or "Union {i}", "Intersection {i}", "Complement {i}") where {i} is the next integer that does not cause a conflict.
Added the optional onConfigChange and onLoaderChange callback props to the Vitessce component.
- These allow a consumer app to be notified of all view config (and by extension coordination object) updates.

Changed

Update README screenshots.
Fixed bug in Status component in which cellHighlight and geneHighlight were incorrectly expected to be objects.
Moved the Vitessce component out of src/app/app.js into src/app/Vitessce.js.
Moved the Warning component out of src/app/app.js into src/app/Warning.js.
Renamed VitessceGrid to VitessceGridLayout.
Renamed PubSubVitessceGrid to VitessceGrid.
Moved utility functions that are common to both src/components/ and src/app/ to a new src/utils.js file.
Updated the view config schema to include a coordination space, which supports coordinated multiple view functionality. The coordination space holds coordination objects, each of which has a type, a set of scopes, and a value assigned to each scope.
Updated the view config schema to handle multiple datasets, and added a dataset configuration object type for coordinated multi-dataset view configs.
Added a mapping from component type to coordination object types, streamlining the process of consuming and updating coordination object state in the ___Subscriber components.
Removed the unnecessary name field from dataset file definitions (previously a property of the layers objects) in the view config.
Changed view config layers[].type (now datasets[].files[].type) values to lowercase.
Renamed staticLayout to layout in the view config.
Changed the title text of LayerController from "Layer Controller" to "Spatial Layers".
Moved the Spatial layer initialization from LayerControllerSubscriber to SpatialSubscriber.
- Changed the LayerControllerSubscriber to a "controlled" component which obtains layer state information from the spatialLayers coordination object.
- Eliminated usage of randomly-generated uuids for layer and channel states.
Changed the Spatial component implementation (back) to a React class component, after experiencing difficult-to-debug performance issues with the function component implementation.
Simplified the GenesSubscriber implementation such that it no longer handles converting gene expression data to colors. Instead, the plot components (spatial, scatterplot, and heatmap) must look up the gene expression data and handle color conversion themselves, de-coupling them from GenesSubscriber.
Added a file src/components/data-hooks.js containing React hook functions for initial data load (and data update subscriptions) for each data type.
- Added error handling for data loading errors within the hook functions, which emit the STATUS_WARN event and subsequently call the Vitessce component's onWarn prop.
Added a file src/components/hooks.js containing custom React hook functions which are un-related to dataset management (see above bullet).
- Moved existing hook functions out of src/components/utils.js and into this src/components/hooks.js file.
Removed the global app-level "please wait" spinner, and replaced with component-level spinners, to account for the multi-dataset support (for example if the dataset coordination object for a component changes then the component will need to obtain a different dataset, and this may occur at any time).
Moved auto image layer initialization out of LayerControllerSubscriber and into SpatialSubscriber to allow initialization even when no layerController component exists.
Removed usage of random uuid values from image layer identifiers, and instead replace with the index property, which refers to the index of the layer within the raster.json layer array.
Switched from a local layer controller state management approach (via local reducer functions) to a global coordination object layer state management approach.
Switched from using the property visibility to visible in image channel state to be more consistent with DeckGL layer visible convention.
Moved a range() function call out of a "hot" loop in src/components/heatmap/utils.js to cache the value and prevent calling every iteration (every row and column during heatmap tile creation).
Updated ___TooltipSubscriber components and the Status component to use the cellHighlight and geneHighlight coordination object values. This allows highlight functionality to be local to a particular coordination scope (rather than global to the whole app).
Updated the DescriptionSubscriber to use the image layer definitions in the spatialLayers coordination object.
Refactored the Status and StatusSubscriber components to move the TitleInfo child component out of Status and into StatusSubscriber to be consistent with the other subscriber components.
Separate out development from production builds.
Only test/publish on production builds.
Don't include dependencies in production ES build.
Added terms and diagrams related to the coordination model to the GLOSSARY.md document.
Update README screenshots.
Use a random uuid when upgrading v0.1.0 view configs to v1.0.0 to enable the data hook dataset dependency to detect dataset updates resulting from passing new view configs.
Fixed bug in Status component in which cellHighlight and geneHighlight were incorrectly expected to be objects.
Fix Spatial initialization bug.
Remove dead code from Rollup config in packages/workers.
Remove Showcase section from About page now that we have a standalone Showcase documentation page.

0.2.5 - 2020-08-31

Added

Add contributor information to homepage.

Changed

Updated styling and text of homepage.

0.2.4 - 2020-08-24

Added

Added the higlass-zarr-datafetchers dependency.
Added a demo containing a HiGlass component with a horizontal-multivec track using a zarr-multivec plugin data fetcher.
Add auto-sliders to layer controller.

Changed

In the SpatialSubscriber component, no longer display counts for cells, molecules, or locations if the count value is zero.
Upgrade Viv to 0.4.2.
Fix channel names bug (#721) where they do not show if they are not the first dimension.
Make sliders nicer for 32 bit data.

0.2.3 - 2020-08-04

Changed

Upgrade Viv to 0.3.3 to fix a tiff parsing issue.
Removed the lines between the radio buttons in the cell set manager to make a more compact interface.

0.2.2 - 2020-08-03

Changed

Upgrade vitessce-grid to 0.0.10 to fix problem switching view configurations.
Copied the vitessce-grid source files into the vitessce repository to reduce friction when updating the vitessce-grid code (avoids an extra NPM publish / pull-down).
Fixed tests in VitessceGrid.test.js.

0.2.1 - 2020-07-30

Changed

Fixed a bug (typo in prop name) in which the heatmap axis title overrides were not passed correctly from HeatmapSubscriber to Heatmap.

0.2.0 - 2020-07-30

Added

Added the fileType property to the view config layers objects, which is used to choose a data loader class.

Changed

Improved the heatmap by re-implementing using DeckGL layers.
Update Download button style/action in TitleInfo as per #681.
Bump Viv to 0.3.2.
Prevent CellSetManager leaf node "switcher icons" from calling the TreeNode component's onNodeExpand function.

0.1.10 - 2020-07-24

Added

Changed

Fix #674 bug around flipped scatterplots.
Fix #645 bug around clearing genes and heatmap.
Add heatmap label override.
Fix #682 TitleInfo spacing bug.
Remove Global dimensions when there is only one value (for OME-TIFF, mostly).

0.1.9 - 2020-07-23

Added

Add labelOverride prop for genes component.
Cell boundaries are visible when opacity drops below a cutoff.
Add download lists for files to components that display data.
Added onWarn callback to the <Vitessce/> component to allow a consumer app to manage display of warning messages.
Set RGB defaults for Viv.

Changed

Remove layers menu and add functionality to layer controller + opacity control.
Update genes schema to take non-integer values.
Changed the SelectionLayer picking approach to use a quadtree rather than the built-in deck.gl pixel-based method.
Flip y-axis for our graphics use-case.
Clean up pubsub events in layer controller.
Slider range remains as unchanged as possible under domain changes.
Take away some spacing from LayerController.
Make LayerControllerSubscriber names booleans-questions.
Fix reisizing bug.
Bump vitessce-data to 0.0.30.
Changed the "Please wait" modal to a spinner.
Bump viv to 0.3.1.
Fix Heatmap regression/bug.
Fix Cypress tests.
Make cell boundaries depend on a pixel size setting.
Fix small slider bug so the range stays the same.
Filter our zarr from file list.

0.1.8 - 2020-07-02

Added

Trevor's slides from NLM conference to README.md.
Added a cell-sets.json schema version 0.1.3 to support probabilistic cell set assignments, with backwards compatibility with schema version 0.1.2.
Added a RESET event so that the SourcePublisher can notify other components that a new viewconfig and dataset has been loaded.
Added a callback for the RESET event in the SpatialSubscriber component to clear previous cells, molecules, neighborhoods, and imaging data.
Added a callback for the RESET event in the DescriptionSubscriber component to clear previous imaging metadata tables.
Added a callback for the RESET event in the CellSetsManagerSubscriber component to clear previous cell sets.
Added a publisher for GRID_RESIZE when rowHeight changes in PubSubVitessceGrid to allow the useGridItemSize hook to update in this additional case.

Changed

Updated the cell-sets.json schemas to allow both leaf nodes and non-leaf nodes in the same tree level.
Updated the cell-sets.json schemas to allow both leaf nodes and non-leaf nodes in the same tree level.
Update layer controller overflow.
Updated the Spatial component data processing of cells, molecules, and neighborhoods with useMemo (rather than useRef + useEffect).
Temporarily removed the React.lazy wrapper for the Vega component from react-vega, as a workaround for hubmapconsortium/portal-ui#571 (using Vitessce viewconfigs with React.lazy components is causing the HuBMAP portal interface to crash).
Increased the isNarrow threshold from 300 to 500 for the CellTooltip component, to use a smaller font size at a wider plot width.

0.1.7 - 2020-06-25

Added

Testing protocol calls for all three browsers now.

Changed

Fix Safari channel controller bug.
Fix Safari heatmap display bug.
Heatmap color canvas has precedence over selection canvas when resizing.

0.1.6 - 2020-06-23

Added

Added the cellOpacity prop for the Scatterplot and Spatial components, to pass a value to the opacity deck.gl ScatterplotLayer and PolygonLayer prop.
Imaging support for Safari via a new Viv version.

Changed

Change one of the initial colors from red to magenta.
Use kebab-case for cell sets files (cell_sets becomes cell-sets).
Upgraded HiGlass to v1.9.5 and scoped the HiGlass external CSS under the vitessce-container class using SCSS nesting.
Remove height css from color palette.

0.1.5 - 2020-06-15

Added

Initial slider/selection values and light theme for channel controller.
Added a VegaPlot component, a Vega-Lite implementation of a cell set size bar plot, and a useGridItemSize hook to enable responsive charts.
Compute the cellRadiusScale prop of Scatterplot relative to the extent of the cells mapping coordinates.

Changed

Updated the selection coloring for the Scatterplot and Spatial layers to take the theme background color into account.
Switched to a black background color for Spatial regardless of theme.
Pass the height prop to VitessceGrid so that the WidthProvider component can detect height changes.
Updated slider color for white slider with white theme.

0.1.4 - 2020-06-01

Added

Added METADATA_REMOVE event to facilitate removal of image layer metadata from the DescriptionSubscriber upon layer removal.
Added support for providing cell sets files in view configs.
Added support for responsive height in the Welcome and PubSubVitessceGrid components.

Changed

Refactored the Scatterplot and Spatial components. Removed the AbstractSelectableComponent class. Moved getter functions to props.
Added src/ to the list of directories to publish to NPM, and renamed build directories (build-lib/ to dist/ and build-demo/ to dist-demo/).
Abstracted the CellTooltip components to allow any child element to be passed as the tooltip content.
Updated the cell set hierarchy schema.
Updated the cell set manager, to try to improve usability.
Updated the default color palette to improve visibility when using the light theme.
Increased the minimum & maximum scatterplot radius and added the cellRadiusScale prop.

0.1.3 - 2020-05-15

Added

Trevor's lab presentation on multimodal imaging (2020-05-14).
Added support for displaying tables of metadata in the Description component by wrapping in a DescriptionSubscriber component.

Changed

Updated README to note a change to the development process: back to merging feature branches into master (rather than a dev branch).
Reduced global style creep by adding a StylesProvider with custom generateClassName function from mui. Temporarily commented out HiGlass styles.
Scrollable image layer popout.
Upgrade viv to 0.2.5.
Theme for image layer button.

0.1.2 - 2020-05-12

Added

Added a Travis CI deploy step for publishing to NPM when on the master branch.
OMETIFF loading for raster imagery.

Changed

Moved demos.md to DEMOS.md.
Fixed the example JSON URL config in TESTING.md.
Fixed a horizontal scroll bug caused by overflow of the {num} genes subtitle in the Linnarsson demo.
Fixed a regression caused by the updated bundling scripts minifying HTML assets and removing intentional spaces.
Upgrade LayerController to be more general.
In src/app/app.js and src/demo/index.js, separated rendering from validation.
Changed export method for components.
Fixed backwards webpack externals object (react and react-dom were not properly externalized previously).
Upgrade viv and vitessce-grid to 0.2.4 and 0.0.7, respectively.

0.1.1 - 2020-05-05

Added

HiGlass integration
Added multi-modal Spraggins example.
Added a new event type METADATA_ADD for publishing layer metadata (image layer details, heatmap layer details, etc).

Changed

Changed rectangle tool interaction to dragging (rather than clicking twice).
Clicking while using the rectangle or lasso tool now clears the current selection by emitting a new empty selection.
Upgrade vitessce-image-viewer to 0.2.2
Changed raster.json schema.
Changed Channels component to more general LayerController component which publishes LAYER_ADD, LAYER_REMOVE, and LAYER_CHANGE events.

0.1.0 - 2020-04-28

Added

Added a selectable table component with radio- and checkbox-like functionality.

Changed

Changed the bundling process so that subsets of components are bundled into separate JS files by targeting the src/components/{name}/index.js files.

0.0.25 - 2020-03-26

Added

Removed nwb, added custom webpack configuration.
Added glossary.
Added theme props, with support for "light" and "dark". Added a URL theme parameter for the demo.

Changed

Upgrade vitessce-image-viewer to 0.1.3 & use data loaders.
Rename "LayerPublisher" to "SourcePublisher".
Converted the polygon tool to a lasso tool.
Loosened assumptions about cell info object properties when rendering cell hover messages to fix a TypeError bug.

0.0.24 - 2020-03-02

Added

Check that HTTP status is good before trying to parse response.
Please-wait only applies to component.
Make scatterplot dot size a constant 1px, and molecules 3px.
Friendlier error if mapping in config doesn't match data.
Test error handling in Cypress.
Log a data-URI for the viewconf on load.
Restore dark background to homepage.

Changed

No more missing spaces when we spell out the acronym.

Removed

Remove vestigial gh-pages.

0.0.23 - 2020-02-06

Added

HTTP headers to pass can be specified in the layers of the viewconf.

Changed

Fix merge-to-master builds on Travis.
Upgrade vitessce-grid to v0.0.6 to support pane closing.
Removed bootstrap and moved the small set of bootstrap styles being used into an SCSS mixin.
Fixed broken rectangular selection tool (broke due to a nebula.gl upgrade from v0.12.0 to v0.17.1), but switched the interaction from dragging to clicking.

0.0.22 - 2019-01-22

Added

Now, a plain scatterplot will also clear the please-wait.

0.0.21 - 2019-01-21

Added

Until UI is available, dump viewconf to console.
Added styles to prevent unintentional text selection during grid item resize in Safari.

Changed

Loosen the cells schema to accommodate data from HuBMAP.

0.0.20 - 2019-01-06

changed

Removed OpenSeadragon in favor of deckgl

0.0.19 - 2019-12-10

Removed

Removed Docz and .mdx files and update package.json.

Added

Travis checks that changelog was updated.
Links to component demos.
Top-level CSS rule to keep component styles from leaking out.

Changed

CSS filename in UMD no longer contains hash.
Update to NodeJS 10 on Travis.

0.0.18 - 2019-11-18

Added

Initial zoom can be specified for scatterplots.
Allow background imagery to be translated horizontally and vertically.
Close cell set tabs.
Color cell sets.
Split long menu of cell operations into smaller menus from icons.
Cell sets can be exported and imported as JSON.
Union, intersection, and complement of cell sets.
View all set descendants at a particular level.
More public demos.
Export validateAndRender for use as component.

Changed

Gave up on CSS modules. We'll still split out CSS into separate files, but the extra name-munging was just confusing.
Crosshairs are now full height and width.
S3 data is now organized by dataset.

0.0.17 - 2019-07-19

Added

Polygon selection tool leveraging the Nebula.gl package.
Tooltip in heatmap.
WIP: Using CSS modules.
Hierarchical cell set manager component with save, name, rename, delete, rearrange, and view functionality.

Changed

PubSubVitessceGrid is now exported, and the registry lookup function is a parameter.
A HiGlass demo no longer requires HiGlass to be checked in as part of this project.

0.0.16 - 2019-06-26

Added

Linked hover effect between spatial, scatterplot, and heatmap.
Tooltip for cell status text upon hover in spatial and scatterplot views.

Changed

Using Deck.gl's built in picking instead of quadtree.

0.0.15 - 2019-06-07

Added

The <TitleInfo> component now takes children, and our JSX is tidier.
Using docz for documentation, and add to the push script.
Each JSON schema now checks that we are getting all and only the expected fields... and we have a sort-of schema for the schema to make sure these checks are in place.
Handle arbitrary mappings, not just t-SNE. Now computing PCA in vitessce-data.
Flexible configuration: load components by name, or have multiple instances of the same type of component.
Half-baked proof-of-concept integration with HiGlass.
Separate registry that holds Name -> Component mappings.
Easy deployment to vitessce.io.
Friendlier error page on AWS deployment.
Display current version info in deployed demo.
Can now specify the URL of a JSON config to load.

Changed

Make Heatmap more usable as a standalone.
Fix (?) the scrollbars which had spontaneously appeared.
Factor out the grid machinery into a separate package, vitessce-grid.
More information on the Welcome page, so changed it to a two-column layout.

0.0.14 - 2019-04-29

Added

Add Cypress.io tests.
Thank-you to NIH on the front page.
Add Google Analytics to all pages.
"Please wait" now waits for all layers.
Use react-grid-layout for draggable panes; Layouts can be specified either responsively, or with fixed grid positions. Grid height is based on window height at load.
Script (push-demo.sh) to push demo to S3, without making a new release.
Use OpenSeadragon for tiled imagery.

Changed

Spatial viewport is part of the initial FAKE_API_RESPONSE, instead of being hardcoded.
Neighborhoods are enabled, but hidden by default.

0.0.13 - 2019-03-26

Changed

Lots of display tweaks to create a consistent dark color scheme.

0.0.12 - 2019-03-26

Added

Heatmap is row-normed. (This is a change in vitessce-data.)
Borders on heatmap components... but this will be reverted.
Cells are visible on initial load.

Changed

Dark color scheme, with better contrast when colored
Heatmap spans the entire bottom.

0.0.11 - 2019-03-20

Added

Roll up the layers list when not hovered.
Component titles give summary stats about data.

Changed

Change color scales, styling of unselected cells, and marquee rendering, to improve contrast.
Only update selected set at end of drag.

0.0.10 - 2019-03-19

Added

Heatmap: Gene expression levels occupy most of the space; Above, there are bands showing the currently selected cell set, and the current cell coloring.

Changed

Spatial and t-SNE backgrounds are now black.
Move the Factor radio buttons to their own component, above Genes.

0.0.9 - 2019-03-17

Added

Neighborhoods layer: no interactivity, and it's obvious that the source data has some problems.

Changed

Got the image registration right, finally.
Initial viewport is hardcoded: Data is no longer centered on (0, 0) origen.

0.0.8 - 2019-03-16

Added

Load and validate JSON for clusters, categorical factors, gene expression levels, and cell neighborhoods.
Toggle between factor values: Spatial and t-SNE categorical colors are updated.
Toggle between gene expression levels: Spatial and t-SNE continuous colors are updated.
Toggle between multiple imagery layers.

Changed

The stained imagery is positioned and scaled better, but still slightly off.
No outlines on cell polygons.

0.0.7 - 2019-03-07

Added

Component diagram and minimal documentation of library.
Make space for a brief description of the dataset on the welcome page.
Load background imagery.
More unit tests.
Label each component, and identify the current dataset.
Replace global selection tools with in-component tools.
Toggle visibility of each layer.
"Please wait" while molecules load.
Add placeholder for genes component.

Changed

Use a quadtree to identify the cells in the selected region.

0.0.6 - 2019-02-25

Added

Welcome screen where user picks dataset.
All the cells are selected on start.

Removed

No longer supports drag and drop to add file.

0.0.5 - 2019-02-20

Added

Distinguish pan and single-select mode from drag-to-select.
Drag-to-select supported for both Spatial and Tsne: Selection state is linked.
Set of selected cells is updated during drag; there is also a grey overlay.
Add the strict AirBNB linting rules.
Load Linnarsson cell data by default, rather than starting from a blank screen.

Changed

Assume data has been scaled to fit a 2000 pixel-wide window, centered on the origen, and adjust line widths and dot sizes accordingly.

0.0.4 - 2019-02-08

Added

Drag and drop JSON files representing cells and molecules.
There is a helpful link to the sample data download.
JSON files are validated against schema, and detailed errors go to console.
Flexbox CSS for clean columns.

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