v4.1.0

Minor Changes

• Upgrade from Material UI (MUI) v7 to v9, and from MUI X Data Grid v8 to v9. Removed the unused @mui/lab dependency. (@vitessce/styles) (#2601)

Patch Changes

• Add annotation story editing to the annotation controller (frames, text, view state capture, and shapes drawn on spatial/scatterplot views via a new annotation editing store), and only re-apply annotation shapes when the active frame is edited in-place. (@vitessce/annotation-controller, @vitessce/vit-s, @vitessce/styles, @vitessce/scatterplot, @vitessce/scatterplot-embedding, @vitessce/spatial, @vitessce/spatial-beta) (#2628)

• Remove repeated validation of selection history after each lasso. Configs and imported files remain validated and upgraded on entry. (@vitessce/obs-sets-manager) (#2629)

• Fix a flash of the previous selection's colors after a lasso selection made while coloring by feature values. The switch to set-selection coloring is now deferred together with the new selection and colors, so the points change straight from feature values to the new selection. (@vitessce/scatterplot-embedding, @vitessce/scatterplot-gating) (#2629)

• Synced spatialBeta and Neuroglancer interactions and camera using OrbitControls from three.js. (@vitessce/neuroglancer, @vitessce/spatial-beta, @vitessce/scatterplot, @vitessce/example-configs) (#2617)

• Speed up lasso selection by pruning quadtree nodes against the selection's bounding box and testing candidate points against the exact polygon. Include observations at index zero. (@vitessce/gl) (#2629)

• Add requireShiftForMultiSelect prop to the feature list view to allow toggling multiple features with plain clicks (no shift key) when enableMultiSelect is true. (@vitessce/feature-list) (#2634)

• Only apply the Y-mirror to image layers in the spatialBeta view when synced with Neuroglancer (3D rendering mode with a camera snapshot), fixing misalignment between image and bitmask segmentation layers. (@vitessce/spatial-beta) (#2639)

• Fix the bottom-right tile of tiled points failing to load by clamping the row group bisection result to the final row group index. (@vitessce/spatial-zarr) (#2638)

• Fix tiled points not loading in the final row/column of tiles by clamping (rather than throwing on) Morton query rectangles that extend beyond the points bounding box. (@vitessce/spatial-zarr) (#2637)

• Resolve pathway and other non-gene selections in the biomarker selector to their member genes, so the feature selection receives gene labels instead of the pathway itself. (@vitessce/biomarker-select) (#2632)

• Adds per feature opacity when genes are added as feature for points (@vitessce/layer-controller-beta, @vitessce/neuroglancer, @vitessce/spatial-beta, @vitessce/all) (#2500)

• Add the spatialCameraSnapshot coordination type to sync cameras between the Neuroglancer and spatialBeta views, vendor the required three/three-stdlib code, and move Neuroglancer info fetching into the data loaders. (@vitessce/neuroglancer, @vitessce/spatial-beta) (#2617)

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