Atera
Human breast
Atera In Situ Gene Expression, Fresh Frozen Human Breast Cancer
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 52963, 33455), (3, 26481, 16727), (3, 13240, 8363), (3, 6620, 4181), (3, 3310, 2090)
│ └── 'morphology': DataTree[cyx] (4, 37930, 70735), (4, 18965, 35367), (4, 9482, 17683), (4, 4741, 8841), (4, 2370, 4420)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37930, 70735), (18965, 35367), (9482, 17683), (4741, 8841), (2370, 4420)
│ └── 'nucleus_labels': DataTree[yx] (37930, 70735), (18965, 35367), (9482, 17683), (4741, 8841), (2370, 4420)
├── Points
│ └── 'transcripts': DataFrame with shape: (4565138232, 7) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (485985, 1) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (489641, 2) (2D shapes)
└── Tables
└── 'table': AnnData (485985, 24677)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), morphology (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Oc0RVwT6WdZXOkAv0000")
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("Oc0RVwT6WdZXOkAv") # 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 Oc0RVwT6WdZXOkAv0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Oc0RVwT6WdZXOkAv
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Oc0RVwT6WdZXOkAvLicense: CC BY 4.0
Metadata
- Technology
- Atera
- Vendor
- 10x Genomics
- Panel
- Atera Human Whole Transcriptome Gene Expression
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (cells)
- 485,985
- Transcripts
- 4,565,138,232
- Tier
- silver
- Chemistry
- Atera v1
- Magnification
- 40x
- Resolution
- 33,455 × 52,963 px
- Size
- 87.8 GB
- Sample ID
- atera-wta-ff-human-breast-cancer
- License
- CC BY 4.0
- Published
- Nov 5, 2026
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB