Skip to content

Landscape

Landscape is Celldega's main spatial visualization: an interactive, deck.gl-powered view of a tissue section that scales to datasets with hundreds of millions of transcripts by loading data as vector tiles instead of all at once.

What it shows

  • Image: the underlying microscopy image (e.g. H&E, DAPI), rendered as a zoomable tile pyramid, with per-channel visibility/contrast controls.
  • CELL: cell segmentation boundaries, colored by cluster/category (e.g. a leiden column from an AnnData) or by gene expression, with a size slider.
  • TRX: individual transcript locations, colored by gene, with a size slider.
  • NBHD: tissue neighborhoods (alpha-shape or hextile regions), toggled on/off with their own opacity control.
  • A gene search box and a bar graph that summarizes the currently visible cells by category or gene, updated as you pan/zoom.
  • Support for multiple datasets via a dropdown selector.

For 3D, orbit-camera views of a dataset (thick tissue, multi-slice alignments, or precomputed neighborhoods), see CellCloud and NeighborhoodCloud, which replace Landscape's older technology="point-cloud" / "neighborhood-cloud" modes.

Usage

import celldega as dega

landscape = dega.viz.Landscape(
    base_url="https://your-landscape-files-url",
    adata=adata,
    ini_zoom=-5,
)
landscape

Landscape can also be linked to a Clustergram so that selections in one update the other — see dega.viz.spatial_clustergram.

For the full list of constructor arguments (multi-dataset support, point-cloud options, AnnData integration, etc.), see the Viz Module API reference.

Note

Screenshots and an example video are coming soon.