v2.0.0

cerebroAppLite 2.0.0

Spatial analysis and overlay improvements

• Multi-gene co-expression: a new "Co-expression (RGB)" plot type maps up to
  three genes onto the red / green / blue channels, so each cell's colour blends
  the genes it expresses and spatial co-localisation reads as a mixed hue.
• Spatial autocorrelation: ImageFeaturePlot now reports the displayed gene's
  Moran's I — how spatially clustered its expression is (large slides are
  down-sampled for a responsive, stable score).
• Region outlines: an opt-in toggle outlines each colour group's spatial
  region with its convex hull.
• Copy alignment as preset: after hand-aligning a histology overlay, a button
  emits the matching spatial_images_* Cerebro.options lines to paste into an
  app so the dataset ships pre-aligned.
• Honest single-source overlay scale: the background scale is now applied
  once (a squared-scale bug is fixed), the image is clipped to the plot area so
  it no longer covers the axes, and the default view is evenly framed.
• Overlay controls UX: interacting with any Additional-parameters control
  collapses the Main-parameters box, and the Additional panel scrolls internally
  (hidden scrollbar with soft top/bottom fades), so the plot stays visible while
  adjusting Move/Rotate.
• Fixes: switching from an image-bearing platform to a bead-only one
  (Slide-seq) no longer leaves a stale tissue image behind, and the embedded-image
  option is offered only for datasets that actually carry one.

Spatial transcriptomics (interactive tab + histology overlay)

• Spatial tab: the interactive Spatial projection is now wired into the app.
  It mounts conditionally (via insertConditionalTab()) whenever the loaded
  dataset carries spatial data, with plotly-based coloring, group filters, and
  box/lasso cell selection.
• Histology background overlay: createShinyApp() gains spatial_images
  plus per-dataset spatial_images_flip_x, spatial_images_flip_y,
  spatial_images_scale_x, spatial_images_scale_y, and spatial_plot_rotation
  parameters. Matched images are copied into the app bundle and shown behind the
  cells, controlled by a Background image dropdown and an Image opacity
  slider. Unmatched entries are ignored with a warning rather than an error.
• Bundled demo: the "Cortex - Spatial (synthetic)" demo pairs fully
  synthetic cortical-depth cell coordinates (illustrative cell-type labels such
  as Excitatory L2/3 … Oligodendrocyte) with a synthetic H&E cortex-section SVG
  whose layer bands align with the cells, so cell types visibly stratify across
  the cortex out of the box. Both the coordinates and the image are synthetic —
  no patient data.
• Documentation: added the vignette("spatial_analysis") guide.
• Bundled demo set: the app now opens on demo_full_tcr_bcr.crb (PBMC,
  TCR + BCR + trajectory) plus four real spatial sections (Visium, Slide-seq v2,
  MERFISH, Xenium), so the dataset switcher spans immune-repertoire, trajectory,
  and spatial content. The two narrower PBMC subsets (demo_healthy_t.crb,
  demo_bcell_rich.crb) are no longer shipped — the Full set is their superset;
  data-raw/build_ir_demos.R can still rebuild them for a multi-sample demo.

Spatial transcriptomics (backend)

• Spatial data layer: the Cerebro_v1.3 class gains a spatial field with
  addSpatialData(), getSpatialData(), and availableSpatial() accessors.
• Export support: exportFromSeurat() now extracts spatial coordinates and
  expression from Seurat v5 image slots (Visium / Xenium / FOV) via the internal
  .getSpatialData() helper, storing them per image in the exported .crb.
• Utility wrappers: added availableSpatial(), getSpatialData(), and
  serverSideGeneSelector() in the Shiny utility layer.
• Demo dataset: bundled a synthetic Xenium spatial demo
  (demo_spatial.crb, 1,000 cells) as a fifth demo dataset.

What's Changed

• feat: interactive Spatial transcriptomics tab by @duocang in #71

Full Changelog: v1.7.8...v2.0.0