Visium
Human synovial membrane of synovial joint
GSM7146860
bronze Interactive viewer H&E psoriatic arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7146860_A4_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM7146860_A4_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM7146860_A4': GeoDataFrame shape: (899, 2) (2D shapes)
└── Tables
└── 'table': AnnData (899, 36601)
with coordinate systems:
▸ 'GSM7146860_A4', with elements:
GSM7146860_A4_hires_image (Images), GSM7146860_A4_lowres_image (Images), GSM7146860_A4 (Shapes)
▸ 'GSM7146860_A4_downscaled_hires', with elements:
GSM7146860_A4_hires_image (Images), GSM7146860_A4 (Shapes)
▸ 'GSM7146860_A4_downscaled_lowres', with elements:
GSM7146860_A4_lowres_image (Images), GSM7146860_A4 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("AceXRGG3HiV0dy9Z0000")
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("AceXRGG3HiV0dy9Z") # 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 AceXRGG3HiV0dy9Z0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/AceXRGG3HiV0dy9Z
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AceXRGG3HiV0dy9ZLicense: NCBI GEO policy
Part of collection
Molecular reframing of fibroblasts during resolution of arthritis [Visium]→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- synovial membrane of synovial joint
- Condition
- psoriatic arthritis
- Modality
- RNA
- Observations (spots)
- 899
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.300 µm/px
- Size
- 10.3 MB
- Sample ID
- GSM7146860
- License
- NCBI GEO policy
- Published
- Jan 16, 2024
Cite this dataset
doi.org/10.1038/s41590-024-01774-4 ↗ BibTeX
@article{geo:GSM7146860,
doi = {10.1038/s41590-024-01774-4},
title = {GSM7146860},
year = {2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB