Visium
Mouse spinal cord
GSM8097058
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8097058_WT_sham_T_R2_1mm_hires_image': DataArray[cyx] (3, 1953, 2000)
│ └── 'GSM8097058_WT_sham_T_R2_1mm_lowres_image': DataArray[cyx] (3, 586, 600)
├── Shapes
│ └── 'GSM8097058_WT_sham_T_R2_1mm': GeoDataFrame shape: (1440, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1440, 32285)
with coordinate systems:
▸ 'GSM8097058_WT_sham_T_R2_1mm', with elements:
GSM8097058_WT_sham_T_R2_1mm_hires_image (Images), GSM8097058_WT_sham_T_R2_1mm_lowres_image (Images), GSM8097058_WT_sham_T_R2_1mm (Shapes)
▸ 'GSM8097058_WT_sham_T_R2_1mm_downscaled_hires', with elements:
GSM8097058_WT_sham_T_R2_1mm_hires_image (Images), GSM8097058_WT_sham_T_R2_1mm (Shapes)
▸ 'GSM8097058_WT_sham_T_R2_1mm_downscaled_lowres', with elements:
GSM8097058_WT_sham_T_R2_1mm_lowres_image (Images), GSM8097058_WT_sham_T_R2_1mm (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("w5AE7pNqcetocV650000")
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("w5AE7pNqcetocV65") # 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 w5AE7pNqcetocV650000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/w5AE7pNqcetocV65
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid w5AE7pNqcetocV65License: NCBI GEO policy
Part of collection
A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2→ 16 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- spinal cord
- Modality
- RNA
- Observations (spots)
- 1,440
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,953 px
- mpp
- 3.318 µm/px
- Size
- 26.3 MB
- Sample ID
- GSM8097058
- License
- NCBI GEO policy
- Published
- Jun 19, 2024
Cite this dataset
doi.org/10.1016/j.devcel.2024.06.016 ↗ BibTeX
@article{Wang_2024,
title = {A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2},
volume = {59},
ISSN = {1534-5807},
url = {http://dx.doi.org/10.1016/j.devcel.2024.06.016},
DOI = {10.1016/j.devcel.2024.06.016},
number = {20},
journal = {Developmental Cell},
publisher = {Elsevier BV},
author = {Wang, Zeqing and Li, Zhuxia and Luan, Tianle and Cui, Guizhong and Shu, Shunpan and Liang, Yiyao and Zhang, Kai and Xiao, Jingshu and Yu, Wei and Cui, Jihong and Li, Ang and Peng, Guangdun and Fang, Yanshan},
year = {2024},
month = Oct,
pages = {2787–2803.e8}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB