10x Xenium
Human femur
human-bone-and-bone-marrow-data-with-custom-add-on-panel-1-standard__hbone-nondiseased-section
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 36158, 34751), (3, 18079, 17375), (3, 9039, 8687), (3, 4519, 4343), (3, 2259, 2171)
│ ├── 'morphology_focus': DataTree[cyx] (1, 44254, 48289), (1, 22127, 24144), (1, 11063, 12072), (1, 5531, 6036), (1, 2765, 3018)
│ └── 'morphology_mip': DataTree[cyx] (1, 44254, 48289), (1, 22127, 24144), (1, 11063, 12072), (1, 5531, 6036), (1, 2765, 3018)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (44254, 48289), (22127, 24144), (11063, 12072), (5531, 6036), (2765, 3018)
│ └── 'nucleus_labels': DataTree[yx] (44254, 48289), (22127, 24144), (11063, 12072), (5531, 6036), (2765, 3018)
├── Points
│ └── 'transcripts': DataFrame with shape: (1347715, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (33801, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (33801, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (33801, 1) (2D shapes)
└── Tables
└── 'table': AnnData (33801, 477)
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("y5TW6maEuPp519Hm") # 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/y5TW6maEuPp519Hm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid y5TW6maEuPp519Hm Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["y5TW6maEuPp519Hm0001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-human-bone-and-bone-marrow-data-with-custom-add-on-panel-1-standard→ 3 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- femur
- Modality
- RNA
- Observations
- 33,801
- Transcripts
- 1,347,715
- Tier
- silver
- Chemistry
- Xenium v1
- Resolution
- 34,751 × 36,158 px
- Size
- 6.4 GB
- Sample ID
- human-bone-and-bone-marrow-data-with-custom-add-on-panel-1-standard__hbone-nondiseased-section
- License
- CC BY 4.0
- Published
- Apr 3, 2024
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