Atera
Human breast
Preview Data: Atera In Situ Gene Expression, FFPE Human Breast Cancer
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 40024, 25893), (3, 20012, 12946), (3, 10006, 6473), (3, 5003, 3236), (3, 2501, 1618)
│ └── 'morphology_focus': DataTree[cyx] (4, 28048, 46543), (4, 14024, 23271), (4, 7012, 11635), (4, 3506, 5817), (4, 1753, 2908)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (28048, 46543), (14024, 23271), (7012, 11635), (3506, 5817), (1753, 2908)
│ └── 'nucleus_labels': DataTree[yx] (28048, 46543), (14024, 23271), (7012, 11635), (3506, 5817), (1753, 2908)
├── Points
│ └── 'transcripts': DataFrame with shape: (740442119, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (170057, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (170057, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (169293, 2) (2D shapes)
└── Tables
└── 'table': AnnData (170057, 18028)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), 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("jCLxdY1tWKmbfWOB0001")
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("jCLxdY1tWKmbfWOB") # 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 jCLxdY1tWKmbfWOB0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jCLxdY1tWKmbfWOB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jCLxdY1tWKmbfWOBLicense: CC BY 4.0
Metadata
- Technology
- Atera
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (cells)
- 170,057
- Transcripts
- 740,442,119
- Tier
- silver
- Chemistry
- Atera Preproduction
- Magnification
- 40x
- Resolution
- 25,893 × 40,024 px
- Size
- 27.0 GB
- Sample ID
- atera-wta-ffpe-human-breast-cancer
- License
- CC BY 4.0
- Published
- Jun 2, 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