Visium
Mouse cerebral cortex
GSM8577746
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8577746_Cond3_hires_image': DataArray[cyx] (3, 2000, 1767)
│ └── 'GSM8577746_Cond3_lowres_image': DataArray[cyx] (3, 600, 530)
├── Shapes
│ └── 'GSM8577746_Cond3': GeoDataFrame shape: (2857, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2857, 21866)
with coordinate systems:
▸ 'GSM8577746_Cond3', with elements:
GSM8577746_Cond3_hires_image (Images), GSM8577746_Cond3_lowres_image (Images), GSM8577746_Cond3 (Shapes)
▸ 'GSM8577746_Cond3_downscaled_hires', with elements:
GSM8577746_Cond3_hires_image (Images), GSM8577746_Cond3 (Shapes)
▸ 'GSM8577746_Cond3_downscaled_lowres', with elements:
GSM8577746_Cond3_lowres_image (Images), GSM8577746_Cond3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("7IU72tR3UFO3JDq90001")
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("7IU72tR3UFO3JDq9") # 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 7IU72tR3UFO3JDq90001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7IU72tR3UFO3JDq9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7IU72tR3UFO3JDq9License: NCBI GEO policy
Part of collection
Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- cerebral cortex
- Modality
- RNA
- Observations (spots)
- 2,857
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,767 × 2,000 px
- mpp
- 3.803 µm/px
- Size
- 38.0 MB
- Sample ID
- GSM8577746
- License
- NCBI GEO policy
- Published
- Feb 10, 2025
Cite this dataset
doi.org/10.1002/glia.24645 ↗ BibTeX
@article{Natarajan_2024,
title = {Single Cell Deletion of the Transcription Factors Trps1 and Sox9 in Astrocytes Reveals Novel Functions in the Adult Cerebral Cortex},
volume = {73},
ISSN = {1098-1136},
url = {http://dx.doi.org/10.1002/glia.24645},
DOI = {10.1002/glia.24645},
number = {4},
journal = {Glia},
publisher = {Wiley},
author = {Natarajan, Poornemaa and Koupourtidou, Christina and de Resseguier, Thibault and Thorwirth, Manja and Bocchi, Riccardo and Fischer‐Sternjak, Judith and Gleiss, Sarah and Rodrigues, Diana and Myoga, Michael H. and Ninkovic, Jovica and Masserdotti, Giacomo and Götz, Magdalena},
year = {2024},
month = Nov,
pages = {737–758}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB