10x Xenium
Human colon
human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-base-ffpe
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 77802, 53802), (3, 38901, 26901), (3, 19450, 13450), (3, 9725, 6725), (3, 4862, 3362)
│ ├── 'morphology_focus': DataTree[cyx] (1, 30725, 42851), (1, 15362, 21425), (1, 7681, 10712), (1, 3840, 5356), (1, 1920, 2678)
│ └── 'morphology_mip': DataTree[cyx] (1, 30725, 42851), (1, 15362, 21425), (1, 7681, 10712), (1, 3840, 5356), (1, 1920, 2678)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30725, 42851), (15362, 21425), (7681, 10712), (3840, 5356), (1920, 2678)
│ └── 'nucleus_labels': DataTree[yx] (30725, 42851), (15362, 21425), (7681, 10712), (3840, 5356), (1920, 2678)
├── Points
│ └── 'transcripts': DataFrame with shape: (29122611, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (270984, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (270984, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (270984, 1) (2D shapes)
└── Tables
└── 'table': AnnData (270984, 325)
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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ZcUlrf9ps0SifYJc") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZcUlrf9ps0SifYJc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZcUlrf9ps0SifYJc Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ZcUlrf9ps0SifYJc0001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard→ 2 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- colon
- Modality
- RNA
- Observations
- 270,984
- Transcripts
- 29,122,611
- Tier
- silver
- Chemistry
- Xenium v1
- Resolution
- 53,802 × 77,802 px
- Size
- 13 GB
- Sample ID
- human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-base-ffpe
- License
- CC BY 4.0
- Published
- Aug 29, 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