10x Xenium
Human kidney
human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hkidney-cancer-section
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 27323, 8832), (3, 13661, 4416), (3, 6830, 2208), (3, 3415, 1104), (3, 1707, 552)
│ ├── 'morphology_focus': DataTree[cyx] (1, 10346, 36943), (1, 5173, 18471), (1, 2586, 9235), (1, 1293, 4617), (1, 646, 2308)
│ └── 'morphology_mip': DataTree[cyx] (1, 10346, 36943), (1, 5173, 18471), (1, 2586, 9235), (1, 1293, 4617), (1, 646, 2308)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (10346, 36943), (5173, 18471), (2586, 9235), (1293, 4617), (646, 2308)
│ └── 'nucleus_labels': DataTree[yx] (10346, 36943), (5173, 18471), (2586, 9235), (1293, 4617), (646, 2308)
├── Points
│ └── 'transcripts': DataFrame with shape: (5115684, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (56510, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (56510, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (56510, 1) (2D shapes)
└── Tables
└── 'table': AnnData (56510, 377)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), morphology_focus (Images), 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("USOaqAveOg9ScruM0001")
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("USOaqAveOg9ScruM") # 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 USOaqAveOg9ScruM0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/USOaqAveOg9ScruM
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid USOaqAveOg9ScruMLicense: CC BY 4.0
Part of collection
10x-human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard→ 2 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Modality
- RNA
- Observations (cells)
- 56,510
- Transcripts
- 5,115,684
- Tier
- silver
- Chemistry
- Xenium v1
- Resolution
- 8,832 × 27,323 px
- Size
- 1.8 GB
- Sample ID
- human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hkidney-cancer-section
- License
- CC BY 4.0
- Published
- Jul 17, 2023
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