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NeighborhoodCloud

NeighborhoodCloud is a 3D, orbit-camera view of precomputed tissue neighborhoods — one alpha-shape polygon per cluster/slice, so it stays cheap to display regardless of dataset size. It replaces Landscape's older technology="neighborhood-cloud" mode.

What it shows

  • Neighborhood polygons: one alpha-shape region per (cluster, slice), rendered in 3D with the same orbit camera as CellCloud.
  • On-demand cell detail: real cell centroids load in only when a neighborhood is selected, instead of being loaded up front.
  • A slice control for stepping through multi-slice datasets.

Note: the 2D neighborhood drawing editor (used to hand-draw a region on a tissue section) is a Landscape feature and is intentionally not part of NeighborhoodCloud, which only visualizes neighborhoods that already exist.

Usage

import celldega as dega

nbhd_cloud = dega.viz.NeighborhoodCloud(
    base_url="https://your-landscape-files-url",
    adata=adata,
)
nbhd_cloud

Build the underlying neighborhood-cloud DegaFiles with celldega.align.write_nbhd_cloud (or celldega.pre.write_nbhd_cloud_dataset). NeighborhoodCloud can also be linked to a Clustergram, exactly like Landscape — see dega.viz.spatial_clustergram.

For the full list of constructor arguments, see the Viz Module API reference.

Note

Screenshots and an example video are coming soon.