Visium
Mouse brain
GSM8341553
bronze Interactive viewer H&E Alzheimer disease Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8341553_sample3_hires_image': DataArray[cyx] (3, 1968, 2000)
│ └── 'GSM8341553_sample3_lowres_image': DataArray[cyx] (3, 590, 600)
├── Shapes
│ └── 'GSM8341553_sample3': GeoDataFrame shape: (2610, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2610, 31053)
with coordinate systems:
▸ 'GSM8341553_sample3', with elements:
GSM8341553_sample3_hires_image (Images), GSM8341553_sample3_lowres_image (Images), GSM8341553_sample3 (Shapes)
▸ 'GSM8341553_sample3_downscaled_hires', with elements:
GSM8341553_sample3_hires_image (Images), GSM8341553_sample3 (Shapes)
▸ 'GSM8341553_sample3_downscaled_lowres', with elements:
GSM8341553_sample3_lowres_image (Images), GSM8341553_sample3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("stUxkEhve4ETilcF0000")
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("stUxkEhve4ETilcF") # 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 stUxkEhve4ETilcF0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/stUxkEhve4ETilcF
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid stUxkEhve4ETilcFLicense: NCBI GEO policy
Part of collection
Tau accumulation induces microglial state alterations in Alzheimer’s disease model mice (Spatial Transcriptomics)→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Condition
- Alzheimer disease
- Modality
- RNA
- Observations (spots)
- 2,610
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,968 px
- mpp
- 3.685 µm/px
- Size
- 55.3 MB
- Sample ID
- GSM8341553
- License
- NCBI GEO policy
- Published
- Dec 15, 2024
Cite this dataset
doi.org/10.1523/eneuro.0260-24.2024 ↗ BibTeX
@article{Nagata_2024,
title = {Tau Accumulation Induces Microglial State Alterations in Alzheimer’s Disease Model Mice},
volume = {11},
ISSN = {2373-2822},
url = {http://dx.doi.org/10.1523/eneuro.0260-24.2024},
DOI = {10.1523/eneuro.0260-24.2024},
number = {12},
journal = {eneuro},
publisher = {Society for Neuroscience},
author = {Nagata, Kenichi and Hashimoto, Shoko and Joho, Daisuke and Fujioka, Ryo and Matsuba, Yukio and Sekiguchi, Misaki and Mihira, Naomi and Motooka, Daisuke and Liu, Yu-Chen and Okuzaki, Daisuke and Kikuchi, Masataka and Murayama, Shigeo and Saido, Takaomi C. and Kiyama, Hiroshi and Sasaguri, Hiroki},
year = {2024},
month = Nov,
pages = {ENEURO.0260–24.2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB