Visium
Human brain
NCBI635
silver Interactive viewer H&E ependymoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI635_full_image': DataTree[cyx] (3, 10152, 9913), (3, 5076, 4956), (3, 2538, 2478), (3, 1269, 1239)
├── Shapes
│ └── 'NCBI635_spots': GeoDataFrame shape: (3027, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3027, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI635_full_image (Images), NCBI635_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("pfST2RSwtkUvFYOK") # 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/pfST2RSwtkUvFYOK
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pfST2RSwtkUvFYOK Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["pfST2RSwtkUvFYOK0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression→ 14 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- ependymoma
- Modality
- RNA
- Observations
- 3,027
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 9,913 × 10,152 px
- mpp
- 0.798 µm/px
- Size
- 306 MB
- Sample ID
- NCBI635
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Oct 13, 2022
Cite this dataset
doi.org/10.1093/neuonc/noac079.165 ↗ BibTeX
@article{Donson_2022,
title = {EPEN-29. Spatial transcriptomic analysis of ependymoma implicates unresolved wound healing as a driver of tumor progression},
volume = {24},
ISSN = {1523-5866},
url = {http://dx.doi.org/10.1093/neuonc/noac079.165},
DOI = {10.1093/neuonc/noac079.165},
number = {Supplement_1},
journal = {Neuro-Oncology},
publisher = {Oxford University Press (OUP)},
author = {Donson, Andrew and Fu, Rui and Norris, gregory and Willard, Nicholas and Griesinger, Andrea and Riemondy, Kent and Amani, Vladimir and Grimaldo, Enrique and Harris, Faith and Hankinson, Todd and Mitra, Siddhartha and Ritzmann, timothy and Grundy, Richard and Foreman, Nicholas},
year = {2022},
month = June,
pages = {i45–i45}
}Source: academic.oup.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB