Xenium
Human brain
IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-PeritumoralTissue-3 (Patient-derived peritumoral tissue, Normal Peritumoral tissue, 48 years)
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23931, 25617), (1, 11965, 12808), (1, 5982, 6404), (1, 2991, 3202), (1, 1495, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (19154, 23610), (9577, 11805), (4788, 5902), (2394, 2951), (1197, 1475)
│ └── 'nucleus_labels': DataTree[yx] (19109, 23565), (9554, 11782), (4777, 5891), (2388, 2945), (1194, 1472)
├── Points
│ └── 'transcripts': DataFrame with shape: (1279521, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (4411, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (4411, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (4411, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4411, 339)
with coordinate systems:
▸ 'global', with elements:
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("pfQ6LVPl9TMIDf9t0000")
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("pfQ6LVPl9TMIDf9t") # 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 pfQ6LVPl9TMIDf9t0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pfQ6LVPl9TMIDf9t
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pfQ6LVPl9TMIDf9tLicense: NCBI GEO policy
Metadata
- Technology
- Xenium
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 4,411
- Transcripts
- 1,279,521
- Target genes
- 339
- Tier
- bronze
- Size
- 245 MB
- Sample ID
- GSM9107842
- License
- NCBI GEO policy
- Published
- Jan 13, 2026
Cite this dataset
doi.org/10.1126/science.adt0559 ↗ BibTeX
@article{geo:GSE302642,
doi = {10.1126/science.adt0559},
title = {IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-Tumor-Astrocytoma (IDH-mutant glioma, 61 years)},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB