Xenium
Human skin of back
Xenium spatial transcriptomics datasets from upper back skin of three healthy volunteers under UV-irradiated/non-disinfected, UV-irradiated/disinfected, non-irradiated/non-disinfected, and non-irradiated/disinfected conditions (0052569_001_no_uv_micro_positive)
bronze Under review Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 13709, 17126), (4, 6854, 8563), (4, 3427, 4281), (4, 1713, 2140), (4, 856, 1070)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13709, 17126), (6854, 8563), (3427, 4281), (1713, 2140), (856, 1070)
│ └── 'nucleus_labels': DataTree[yx] (13709, 17126), (6854, 8563), (3427, 4281), (1713, 2140), (856, 1070)
├── Points
│ └── 'transcripts': DataFrame with shape: (391121, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (5295, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (5295, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (5499, 2) (2D shapes)
└── Tables
└── 'table': AnnData (5295, 475)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("5GfYyu5Sp0Ynr0hI0000")
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("5GfYyu5Sp0Ynr0hI") # 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 5GfYyu5Sp0Ynr0hI0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5GfYyu5Sp0Ynr0hI
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5GfYyu5Sp0Ynr0hILicense: CC BY 4.0
Metadata
- Technology
- Xenium
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- skin of back
- Modality
- RNA
- Observations (cells)
- 5,295
- Transcripts
- 391,121
- Target genes
- 475
- Tier
- bronze
- Size
- 506 MB
- Sample ID
- 32190978:0052569_001_no_uv_micro_positive
- License
- CC BY 4.0
- Published
- May 7, 2026
- Review
- condition (UV / disinfection) from the bundle name
Cite this dataset
doi.org/10.48420/32190978.v1 ↗ BibTeX
@article{figshare:32190978,
doi = {10.48420/32190978.v1},
title = {Xenium spatial transcriptomics datasets from upper back skin of three healthy volunteers under UV-irradiated/non-disinfected, UV-irradiated/disinfected, non-irradiated/non-disinfected, and non-irradiated/disinfected conditions (0052858_002_no_uv_no_micro)},
year = {2026}
}Source: figshare.manchester.ac.uk ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB