Human craniocervical region

Data from: Integrated single-cell and spatial analysis reveals context-dependent myeloid-T cell interactions in the response to immune checkpoint blockade in head and neck squamous cell carcinoma (CosMx RNA TMA) (Run5607_TMAA)

SpatialData object
├── Points
│     └── 'points': DataFrame with shape: (39538393, 11) (2D points)
├── Shapes
│     ├── 'cells_polygons': GeoDataFrame shape: (87711, 9) (2D shapes)
│     ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (87711, 2) (2D shapes)
│     └── 'fov_boxes': GeoDataFrame shape: (25, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (87711, 979)
with coordinate systems:
    ▸ 'global', with elements:
        points (Points), cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes)
    ▸ 'microns', with elements:
        points (Points), cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes)

from sddb import Catalog

ds = Catalog().dataset("LMatNh0ELIstzZrp0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("LMatNh0ELIstzZrp")   # stem uid: Lamin resolves it to the latest version

sdata = artifact.load()   # cache, then load into memory
group = artifact.open()   # stream without downloading
path  = artifact.cache()  # sync into the local cache, returns the path

# sddb client: download the .zarr into data/
sddb-cli download LMatNh0ELIstzZrp0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/LMatNh0ELIstzZrp

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LMatNh0ELIstzZrp

Metadata

Technology

CosMx SMI

Vendor

Bruker

Organism

human

Tissue

craniocervical region

Condition

head and neck squamous cell carcinoma

Modality

RNA

Observations (cells)

87,711

Transcripts

39,538,393

Target genes

960

Tier

bronze

Size

1.4 GB

Sample ID

dryad.n2z34tn7x:Run5607_TMAA

License

CC0 1.0

Published

Mar 9, 2026

Review

TMA slide: cores of several patients; per-core annotation needed; tissue site within head and neck not stated

@article{dryad:dryad.n2z34tn7x,
  doi = {10.5061/dryad.n2z34tn7x},
  title = {Data from: Integrated single-cell and spatial analysis reveals context-dependent myeloid-T cell interactions in the response to immune checkpoint blockade in head and neck squamous cell carcinoma (CosMx RNA TMA) (Run5545_TMAB)},
  year = {2026}
}