Visium
Human skeletal muscle tissue
GSM7782915
bronze Interactive viewer H&E sarcoidosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7782915_INMG3_hires_image': DataArray[cyx] (3, 2000, 1989)
│ └── 'GSM7782915_INMG3_lowres_image': DataArray[cyx] (3, 600, 597)
├── Shapes
│ └── 'GSM7782915_INMG3': GeoDataFrame shape: (2723, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2723, 17943)
with coordinate systems:
▸ 'GSM7782915_INMG3', with elements:
GSM7782915_INMG3_hires_image (Images), GSM7782915_INMG3_lowres_image (Images), GSM7782915_INMG3 (Shapes)
▸ 'GSM7782915_INMG3_downscaled_hires', with elements:
GSM7782915_INMG3_hires_image (Images), GSM7782915_INMG3 (Shapes)
▸ 'GSM7782915_INMG3_downscaled_lowres', with elements:
GSM7782915_INMG3_lowres_image (Images), GSM7782915_INMG3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("DvBLhBijzXZSL9qX0000")
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("DvBLhBijzXZSL9qX") # 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 DvBLhBijzXZSL9qX0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/DvBLhBijzXZSL9qX
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid DvBLhBijzXZSL9qXLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics reveal signatures of histopathological changes in muscular sarcoidosis→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skeletal muscle tissue
- Condition
- sarcoidosis
- Modality
- RNA
- Observations (spots)
- 2,723
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,989 × 2,000 px
- mpp
- 3.399 µm/px
- Size
- 44.4 MB
- Sample ID
- GSM7782915
- License
- NCBI GEO policy
- Published
- Nov 29, 2023
Cite this dataset
doi.org/10.3390/cells12232747 ↗ BibTeX
@article{geo:GSM7782915,
doi = {10.3390/cells12232747},
title = {GSM7782915},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB