10x Xenium
Human colon
human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-cancer-add-on-ffpe
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 43090, 26909), (3, 21545, 13454), (3, 10772, 6727), (3, 5386, 3363), (3, 2693, 1681)
│ ├── 'morphology_focus': DataTree[cyx] (1, 34338, 42905), (1, 17169, 21452), (1, 8584, 10726), (1, 4292, 5363), (1, 2146, 2681)
│ └── 'morphology_mip': DataTree[cyx] (1, 34338, 42905), (1, 17169, 21452), (1, 8584, 10726), (1, 4292, 5363), (1, 2146, 2681)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34338, 42905), (17169, 21452), (8584, 10726), (4292, 5363), (2146, 2681)
│ └── 'nucleus_labels': DataTree[yx] (34338, 42905), (17169, 21452), (8584, 10726), (4292, 5363), (2146, 2681)
├── Points
│ └── 'transcripts': DataFrame with shape: (79447189, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (587115, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (587115, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (587115, 1) (2D shapes)
└── Tables
└── 'table': AnnData (587115, 425)
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("oJcc9qMT64W5g87P") # 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/oJcc9qMT64W5g87P
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid oJcc9qMT64W5g87P Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["oJcc9qMT64W5g87P0001"])[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
- 587,115
- Transcripts
- 79,447,189
- Tier
- silver
- Chemistry
- Xenium v1
- Resolution
- 26,909 × 43,090 px
- Size
- 9.6 GB
- Sample ID
- human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-cancer-add-on-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