10x Xenium
Mouse brain
xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard__ffpe-wildtype-13-4-months
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 24863, 31342), (1, 12431, 15671), (1, 6215, 7835), (1, 3107, 3917), (1, 1553, 1958)
│ └── 'morphology_mip': DataTree[cyx] (1, 24863, 31342), (1, 12431, 15671), (1, 6215, 7835), (1, 3107, 3917), (1, 1553, 1958)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (24863, 31342), (12431, 15671), (6215, 7835), (3107, 3917), (1553, 1958)
│ └── 'nucleus_labels': DataTree[yx] (24863, 31342), (12431, 15671), (6215, 7835), (3107, 3917), (1553, 1958)
├── Points
│ └── 'transcripts': DataFrame with shape: (16223926, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (59935, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (59935, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (59935, 1) (2D shapes)
└── Tables
└── 'table': AnnData (59935, 347)
with coordinate systems:
▸ 'global', with elements:
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("K8uQ1Ge2i9y8qDPI0000")
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("K8uQ1Ge2i9y8qDPI") # 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 K8uQ1Ge2i9y8qDPI0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/K8uQ1Ge2i9y8qDPI
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid K8uQ1Ge2i9y8qDPILicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 59,935
- Transcripts
- 16,223,926
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 2.4 GB
- Sample ID
- xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard__ffpe-wildtype-13-4-months
- License
- CC BY 4.0
- Published
- Jul 13, 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