Visium
Mouse brain
GSM6171788
bronze Interactive viewer H&E Alzheimer disease Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6171788_PSAPP_CO2_hires_image': DataArray[cyx] (3, 2000, 1863)
│ └── 'GSM6171788_PSAPP_CO2_lowres_image': DataArray[cyx] (3, 600, 559)
├── Shapes
│ └── 'GSM6171788_PSAPP_CO2': GeoDataFrame shape: (2601, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2601, 32285)
with coordinate systems:
▸ 'GSM6171788_PSAPP_CO2', with elements:
GSM6171788_PSAPP_CO2_hires_image (Images), GSM6171788_PSAPP_CO2_lowres_image (Images), GSM6171788_PSAPP_CO2 (Shapes)
▸ 'GSM6171788_PSAPP_CO2_downscaled_hires', with elements:
GSM6171788_PSAPP_CO2_hires_image (Images), GSM6171788_PSAPP_CO2 (Shapes)
▸ 'GSM6171788_PSAPP_CO2_downscaled_lowres', with elements:
GSM6171788_PSAPP_CO2_lowres_image (Images), GSM6171788_PSAPP_CO2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("jse5UsJxCDfTnrSH0000")
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("jse5UsJxCDfTnrSH") # 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 jse5UsJxCDfTnrSH0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jse5UsJxCDfTnrSH
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jse5UsJxCDfTnrSHLicense: NCBI GEO policy
Part of collection
INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease→ 12 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Condition
- Alzheimer disease
- Modality
- RNA
- Observations (spots)
- 2,601
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,863 × 2,000 px
- mpp
- 3.533 µm/px
- Size
- 65.4 MB
- Sample ID
- GSM6171788
- License
- NCBI GEO policy
- Published
- Sep 26, 2022
Cite this dataset
doi.org/10.1002/alz.12821 ↗ BibTeX
@article{Castranio_2022,
title = {Microglial
<i>INPP5D</i>
limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer’s disease},
volume = {19},
ISSN = {1552-5279},
url = {http://dx.doi.org/10.1002/alz.12821},
DOI = {10.1002/alz.12821},
number = {6},
journal = {Alzheimer’s & Dementia},
publisher = {Wiley},
author = {Castranio, Emilie L. and Hasel, Philip and Haure‐Mirande, Jean‐Vianney and Ramirez Jimenez, Angie V. and Hamilton, B. Wade and Kim, Rachel D. and Glabe, Charles G. and Wang, Minghui and Zhang, Bin and Gandy, Sam and Liddelow, Shane A. and Ehrlich, Michelle E.},
year = {2022},
month = Nov,
pages = {2239–2252}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB