Human lymph node

Spatial and Single Cell Mapping of Castleman Disease Reveals Key Stromal Cell Types and Cytokine Pathways, 20220311_Reactive_LN_R1

SpatialData object
├── Images
│     └── '20220311_Reactive_LN_R1_image': DataTree[cyx] (44, 7488, 30080), (44, 3744, 15040), (44, 1872, 7520), (44, 936, 3760), (44, 468, 1880)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (534514, 1) (2D shapes)
│     └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (534514, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (534514, 44)
with coordinate systems:
    ▸ 'global', with elements:
        20220311_Reactive_LN_R1_image (Images), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes)

from sddb import Catalog

ds = Catalog().dataset("PGtOAedCkUcqicKi0000")
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("PGtOAedCkUcqicKi")   # 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 PGtOAedCkUcqicKi0000 --dest data/

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

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

Metadata

Technology

PhenoCycler (CODEX)

Vendor

Quanterix

Organism

human

Tissue

lymph node

Modality

protein

Observations (cells)

534,514

Segmentation

Segmented by SpatialData-DB (Cellpose-SAM (cellpose 4.2.1.1, cpsam))

Tier

bronze

Chemistry

CODEX Instrument Manager

Staining

IF

Size

7.3 GB

Sample ID

28394915:20220311_Reactive_LN_R1

License

CC BY 4.0

Published

Jul 2, 2025

@article{figshare:28394915,
  doi = {10.1038/s41467-025-61214-1},
  title = {Spatial and Single Cell Mapping of Castleman Disease Reveals Key Stromal Cell Types and Cytokine Pathways, 20220518_Lung_LN_healthy_with_Castleman_Disease_Panel},
  year = {2025}
}