Visium
Macaque colon
GSM9913884
bronze Interactive viewer H&E simian immunodeficiency virus infection Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9913884_08M236_IV_T_Colon1_hires_image': DataArray[cyx] (3, 2000, 1965)
│ └── 'GSM9913884_08M236_IV_T_Colon1_lowres_image': DataArray[cyx] (3, 600, 590)
├── Shapes
│ └── 'GSM9913884_08M236_IV_T_Colon1': GeoDataFrame shape: (2561, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2561, 35441)
with coordinate systems:
▸ 'GSM9913884_08M236_IV_T_Colon1', with elements:
GSM9913884_08M236_IV_T_Colon1_hires_image (Images), GSM9913884_08M236_IV_T_Colon1_lowres_image (Images), GSM9913884_08M236_IV_T_Colon1 (Shapes)
▸ 'GSM9913884_08M236_IV_T_Colon1_downscaled_hires', with elements:
GSM9913884_08M236_IV_T_Colon1_hires_image (Images), GSM9913884_08M236_IV_T_Colon1 (Shapes)
▸ 'GSM9913884_08M236_IV_T_Colon1_downscaled_lowres', with elements:
GSM9913884_08M236_IV_T_Colon1_lowres_image (Images), GSM9913884_08M236_IV_T_Colon1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("pvQ2KZPKLMYGNgJ40000")
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("pvQ2KZPKLMYGNgJ4") # 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 pvQ2KZPKLMYGNgJ40000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pvQ2KZPKLMYGNgJ4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pvQ2KZPKLMYGNgJ4License: NCBI GEO policy
Part of collection
A Tissue Virus Microenvironment with Activated Stress Responses Underlies Durable SIV Persistence [Visium]→ 18 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- macaque
- Tissue
- colon
- Condition
- simian immunodeficiency virus infection
- Modality
- RNA
- Observations (spots)
- 2,561
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,965 × 2,000 px
- mpp
- 3.666 µm/px
- Size
- 33.3 MB
- Sample ID
- GSM9913884
- License
- NCBI GEO policy
- Published
- Aug 26, 2026
Cite this dataset
doi.org/10.3389/fimmu.2026.1862864 ↗ BibTeX
@article{Crentsil_2026,
title = {A tissue microenvironment analogous to certain tumor microenvironments facilitates HIV persistence},
volume = {17},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2026.1862864},
DOI = {10.3389/fimmu.2026.1862864},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Crentsil, Eliana U. and Stegman, Natalie and Monette, Anne and Hope, Thomas J. and Lorenzo-Redondo, Ramon},
year = {2026},
month = Aug
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB