Xenium
Human liver
A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures: C95 (Liver – Caudate)
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 23911, 48299), (1, 11955, 24149), (1, 5977, 12074), (1, 2988, 6037), (1, 1494, 3018)
│ └── 'morphology_mip': DataTree[cyx] (1, 23911, 48299), (1, 11955, 24149), (1, 5977, 12074), (1, 2988, 6037), (1, 1494, 3018)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23911, 48299), (11955, 24149), (5977, 12074), (2988, 6037), (1494, 3018)
│ └── 'nucleus_labels': DataTree[yx] (23911, 48299), (11955, 24149), (5977, 12074), (2988, 6037), (1494, 3018)
├── Points
│ └── 'transcripts': DataFrame with shape: (62284243, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (142659, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (142659, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (142659, 1) (2D shapes)
└── Tables
└── 'table': AnnData (142659, 477)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("kAMpfNxWkvyw5Pcp0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("kAMpfNxWkvyw5Pcp") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download kAMpfNxWkvyw5Pcp0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kAMpfNxWkvyw5Pcp
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kAMpfNxWkvyw5PcpLicense: NCBI GEO policy
Metadata
- Technology
- Xenium
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- liver
- Modality
- RNA
- Observations (cells)
- 142,659
- Transcripts
- 62,284,243
- Target genes
- 477
- Tier
- bronze
- Size
- 5.2 GB
- Sample ID
- GSM8721782
- License
- NCBI GEO policy
- Published
- Jul 18, 2025
Cite this dataset
doi.org/10.1101/2025.04.16.649149 ↗ BibTeX
@article{geo:GSE286254,
doi = {10.1101/2025.04.16.649149},
title = {A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures: C101 (Liver – Caudate)},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB