Visium
Human skeletal muscle tissue
GSM7782914
bronze Interactive viewer H&E sarcoidosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7782914_INMG2_hires_image': DataArray[cyx] (3, 1990, 2000)
│ └── 'GSM7782914_INMG2_lowres_image': DataArray[cyx] (3, 597, 600)
├── Shapes
│ └── 'GSM7782914_INMG2': GeoDataFrame shape: (2299, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2299, 17943)
with coordinate systems:
▸ 'GSM7782914_INMG2', with elements:
GSM7782914_INMG2_hires_image (Images), GSM7782914_INMG2_lowres_image (Images), GSM7782914_INMG2 (Shapes)
▸ 'GSM7782914_INMG2_downscaled_hires', with elements:
GSM7782914_INMG2_hires_image (Images), GSM7782914_INMG2 (Shapes)
▸ 'GSM7782914_INMG2_downscaled_lowres', with elements:
GSM7782914_INMG2_lowres_image (Images), GSM7782914_INMG2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("7phWAsGZQIK0zT0m0000")
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("7phWAsGZQIK0zT0m") # 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 7phWAsGZQIK0zT0m0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7phWAsGZQIK0zT0m
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7phWAsGZQIK0zT0mLicense: 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)
- 2,299
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,990 px
- mpp
- 3.364 µm/px
- Size
- 40.7 MB
- Sample ID
- GSM7782914
- License
- NCBI GEO policy
- Published
- Nov 29, 2023
Cite this dataset
doi.org/10.3390/cells12232747 ↗ BibTeX
@article{geo:GSM7782914,
doi = {10.3390/cells12232747},
title = {GSM7782914},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB