10x Xenium
Human hippocampal formation
GSM9822865
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34085, 34147), (1, 17042, 17073), (1, 8521, 8536), (1, 4260, 4268), (1, 2130, 2134)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (32209, 33087), (16104, 16543), (8052, 8271), (4026, 4135), (2013, 2067)
│ └── 'nucleus_labels': DataTree[yx] (31841, 33078), (15920, 16539), (7960, 8269), (3980, 4134), (1990, 2067)
├── Points
│ └── 'transcripts': DataFrame with shape: (10708127, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (22698, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (22698, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (22307, 2) (2D shapes)
└── Tables
└── 'table': AnnData (22698, 300)
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("SHu3Xi6QYZbnm2ja0000")
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("SHu3Xi6QYZbnm2ja") # 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 SHu3Xi6QYZbnm2ja0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/SHu3Xi6QYZbnm2ja
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid SHu3Xi6QYZbnm2jaLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- hippocampal formation
- Modality
- RNA
- Observations (cells)
- 22,698
- Transcripts
- 10,708,127
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM9822865
- License
- NCBI GEO policy
- Published
- Jul 31, 2026
Cite this dataset
doi.org/10.1016/j.cell.2026.07.007 ↗ BibTeX
@article{geo:GSM9822865,
doi = {10.1016/j.cell.2026.07.007},
title = {GSM9822865},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB