Visium
Human superior temporal gyrus
GSM8675581
silver Interactive viewer H&E Alzheimer disease ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8675581_Cohort8-A_A14-193-3_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8675581_Cohort8-A_A14-193-3_hires_image': DataArray[cyx] (3, 1861, 2000)
│ └── 'GSM8675581_Cohort8-A_A14-193-3_lowres_image': DataArray[cyx] (3, 558, 600)
├── Shapes
│ └── 'GSM8675581_Cohort8-A_A14-193-3': GeoDataFrame shape: (13670, 2) (2D shapes)
└── Tables
└── 'table': AnnData (13670, 18085)
with coordinate systems:
▸ 'GSM8675581_Cohort8-A_A14-193-3', with elements:
GSM8675581_Cohort8-A_A14-193-3_full_image (Images), GSM8675581_Cohort8-A_A14-193-3_hires_image (Images), GSM8675581_Cohort8-A_A14-193-3_lowres_image (Images), GSM8675581_Cohort8-A_A14-193-3 (Shapes)
▸ 'GSM8675581_Cohort8-A_A14-193-3_downscaled_hires', with elements:
GSM8675581_Cohort8-A_A14-193-3_hires_image (Images), GSM8675581_Cohort8-A_A14-193-3 (Shapes)
▸ 'GSM8675581_Cohort8-A_A14-193-3_downscaled_lowres', with elements:
GSM8675581_Cohort8-A_A14-193-3_lowres_image (Images), GSM8675581_Cohort8-A_A14-193-3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("APuzaGrWvk4jmz060000")
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("APuzaGrWvk4jmz06") # 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 APuzaGrWvk4jmz060000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/APuzaGrWvk4jmz06
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid APuzaGrWvk4jmz06License: CC BY 4.0
Part of collection
Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer’s disease [dataset3]→ 8 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- superior temporal gyrus
- Condition
- Alzheimer disease
- Modality
- RNA
- Observations (spots)
- 13,670
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 2,000 × 1,861 px
- mpp
- 7.084 µm/px
- Size
- 50.7 MB
- Sample ID
- GSM8675581
- License
- CC BY 4.0
- Published
- Mar 3, 2025
Cite this dataset
doi.org/10.1038/s41591-025-03574-1 ↗ BibTeX
@article{van_Olst_2025,
title = {Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer’s disease},
volume = {31},
ISSN = {1546-170X},
url = {http://dx.doi.org/10.1038/s41591-025-03574-1},
DOI = {10.1038/s41591-025-03574-1},
number = {5},
journal = {Nature Medicine},
publisher = {Springer Science and Business Media LLC},
author = {van Olst, Lynn and Simonton, Brooke and Edwards, Alex J. and Forsyth, Anne V. and Boles, Jake and Jamshidi, Pouya and Watson, Thomas and Shepard, Nate and Krainc, Talia and Argue, Benney MR and Zhang, Ziyang and Kuruvilla, Joshua and Camp, Lily and Li, Mengwei and Xu, Hang and Norman, Jeanette L. and Cahan, Joshua and Vassar, Robert and Chen, Jinmiao and Castellani, Rudolph J. and Nicoll, James AR and Boche, Delphine and Gate, David},
year = {2025},
month = Mar,
pages = {1604–1616}
}Source: NCBI GEO ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB