Visium
Human hippocampal formation
GSM8675583
silver Interactive viewer H&E Alzheimer disease ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8675583_Cohort8-A_A14-193-9_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8675583_Cohort8-A_A14-193-9_hires_image': DataArray[cyx] (3, 1978, 2000)
│ └── 'GSM8675583_Cohort8-A_A14-193-9_lowres_image': DataArray[cyx] (3, 594, 600)
├── Shapes
│ └── 'GSM8675583_Cohort8-A_A14-193-9': GeoDataFrame shape: (10003, 2) (2D shapes)
└── Tables
└── 'table': AnnData (10003, 18085)
with coordinate systems:
▸ 'GSM8675583_Cohort8-A_A14-193-9', with elements:
GSM8675583_Cohort8-A_A14-193-9_full_image (Images), GSM8675583_Cohort8-A_A14-193-9_hires_image (Images), GSM8675583_Cohort8-A_A14-193-9_lowres_image (Images), GSM8675583_Cohort8-A_A14-193-9 (Shapes)
▸ 'GSM8675583_Cohort8-A_A14-193-9_downscaled_hires', with elements:
GSM8675583_Cohort8-A_A14-193-9_hires_image (Images), GSM8675583_Cohort8-A_A14-193-9 (Shapes)
▸ 'GSM8675583_Cohort8-A_A14-193-9_downscaled_lowres', with elements:
GSM8675583_Cohort8-A_A14-193-9_lowres_image (Images), GSM8675583_Cohort8-A_A14-193-9 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("LAs9TAygmXG8lrbD") # 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/LAs9TAygmXG8lrbD
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LAs9TAygmXG8lrbD Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["LAs9TAygmXG8lrbD0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- hippocampal formation
- Condition
- Alzheimer disease
- Modality
- RNA
- Observations
- 10,003
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 2,000 × 1,978 px
- mpp
- 6.079 µm/px
- Size
- 59 MB
- Sample ID
- GSM8675583
- 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