10x Xenium
Human brain
ffpe-human-brain-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard
silver Interactive viewer H&E glioblastoma multiforme No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 58584, 38957), (3, 29292, 19478), (3, 14646, 9739), (3, 7323, 4869), (3, 3661, 2434)
│ └── 'morphology_focus': DataTree[cyx] (4, 51043, 53946), (4, 25521, 26973), (4, 12760, 13486), (4, 6380, 6743), (4, 3190, 3371)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (51043, 53946), (25521, 26973), (12760, 13486), (6380, 6743), (3190, 3371)
│ └── 'nucleus_labels': DataTree[yx] (51043, 53946), (25521, 26973), (12760, 13486), (6380, 6743), (3190, 3371)
├── Points
│ └── 'transcripts': DataFrame with shape: (178716169, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (816769, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (816769, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (818128, 2) (2D shapes)
└── Tables
└── 'table': AnnData (816769, 480)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), morphology_focus (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("iHSXYBFbeAMN3zxa0001")
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("iHSXYBFbeAMN3zxa") # 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 iHSXYBFbeAMN3zxa0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/iHSXYBFbeAMN3zxa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iHSXYBFbeAMN3zxaLicense: CC BY 4.0
Part of collection
10x-ffpe-human-brain-cancer-human-immuno-oncology-profiling-panel-custom-add-on→ 1 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioblastoma multiforme
- Modality
- RNA
- Observations (cells)
- 816,769
- Transcripts
- 178,716,169
- Tier
- silver
- Chemistry
- Xenium v1
- Resolution
- 38,957 × 58,584 px
- Size
- 30.1 GB
- Sample ID
- ffpe-human-brain-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard
- License
- CC BY 4.0
- Published
- Apr 15, 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