Visium
Human blood vessel
GSM6703213
bronze Interactive viewer H&E Loeys-Dietz syndrome Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM6703213_Replicate2_Patient_hires_image': DataArray[cyx] (3, 1864, 2000)
├── Shapes
│ └── 'GSM6703213_Replicate2_Patient': GeoDataFrame shape: (865, 2) (2D shapes)
└── Tables
└── 'table': AnnData (865, 17943)
with coordinate systems:
▸ 'GSM6703213_Replicate2_Patient', with elements:
GSM6703213_Replicate2_Patient_hires_image (Images), GSM6703213_Replicate2_Patient (Shapes)
▸ 'GSM6703213_Replicate2_Patient_downscaled_hires', with elements:
GSM6703213_Replicate2_Patient_hires_image (Images), GSM6703213_Replicate2_Patient (Shapes)
▸ 'GSM6703213_Replicate2_Patient_downscaled_lowres', with elements:
GSM6703213_Replicate2_Patient (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("tFr816qQjethDK8U0000")
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("tFr816qQjethDK8U") # 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 tFr816qQjethDK8U0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/tFr816qQjethDK8U
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid tFr816qQjethDK8ULicense: NCBI GEO policy
Part of collection
Spatial transcriptomic profiling of Patient and Patient-corrected bioengineered vascular grafts.→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- blood vessel
- Condition
- Loeys-Dietz syndrome
- Modality
- RNA
- Observations (spots)
- 865
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,864 px
- mpp
- 4.118 µm/px
- Size
- 6.5 MB
- Sample ID
- GSM6703213
- License
- NCBI GEO policy
- Published
- May 8, 2024
Cite this dataset
doi.org/10.1126/scitranslmed.adg6298 ↗ BibTeX
@article{geo:GSM6703213,
doi = {10.1126/scitranslmed.adg6298},
title = {GSM6703213},
year = {2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB