Visium
Mouse spinal cord
GSM8097070
bronze Interactive viewer H&E spinal cord injury Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8097070_WT_72h_T_R1_1mm_hires_image': DataArray[cyx] (3, 1975, 2000)
│ └── 'GSM8097070_WT_72h_T_R1_1mm_lowres_image': DataArray[cyx] (3, 593, 600)
├── Shapes
│ └── 'GSM8097070_WT_72h_T_R1_1mm': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 32285)
with coordinate systems:
▸ 'GSM8097070_WT_72h_T_R1_1mm', with elements:
GSM8097070_WT_72h_T_R1_1mm_hires_image (Images), GSM8097070_WT_72h_T_R1_1mm_lowres_image (Images), GSM8097070_WT_72h_T_R1_1mm (Shapes)
▸ 'GSM8097070_WT_72h_T_R1_1mm_downscaled_hires', with elements:
GSM8097070_WT_72h_T_R1_1mm_hires_image (Images), GSM8097070_WT_72h_T_R1_1mm (Shapes)
▸ 'GSM8097070_WT_72h_T_R1_1mm_downscaled_lowres', with elements:
GSM8097070_WT_72h_T_R1_1mm_lowres_image (Images), GSM8097070_WT_72h_T_R1_1mm (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("92azjqTNxut49GWu0000")
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("92azjqTNxut49GWu") # 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 92azjqTNxut49GWu0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/92azjqTNxut49GWu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 92azjqTNxut49GWuLicense: 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
- Condition
- spinal cord injury
- Modality
- RNA
- Observations (spots)
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,975 px
- mpp
- 3.297 µm/px
- Size
- 48.6 MB
- Sample ID
- GSM8097070
- 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