Visium
Human skin of body
GSM7983359
bronze Interactive viewer H&E melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7983359_sample4_hires_image': DataArray[cyx] (3, 2000, 1984)
│ └── 'GSM7983359_sample4_lowres_image': DataArray[cyx] (3, 600, 595)
├── Shapes
│ └── 'GSM7983359_sample4': GeoDataFrame shape: (1667, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1667, 36601)
with coordinate systems:
▸ 'GSM7983359_sample4', with elements:
GSM7983359_sample4_hires_image (Images), GSM7983359_sample4_lowres_image (Images), GSM7983359_sample4 (Shapes)
▸ 'GSM7983359_sample4_downscaled_hires', with elements:
GSM7983359_sample4_hires_image (Images), GSM7983359_sample4 (Shapes)
▸ 'GSM7983359_sample4_downscaled_lowres', with elements:
GSM7983359_sample4_lowres_image (Images), GSM7983359_sample4 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ghOyD8U0vp5Xwxjc0000")
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("ghOyD8U0vp5Xwxjc") # 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 ghOyD8U0vp5Xwxjc0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ghOyD8U0vp5Xwxjc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ghOyD8U0vp5XwxjcLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease.→ 9 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- melanoma
- Modality
- RNA
- Observations (spots)
- 1,667
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,984 × 2,000 px
- mpp
- 3.303 µm/px
- Size
- 21.1 MB
- Sample ID
- GSM7983359
- License
- NCBI GEO policy
- Published
- Jun 3, 2024
Cite this dataset
doi.org/10.1016/j.xcrm.2024.101606 ↗ BibTeX
@article{Alhaddad_2024,
title = {Spatial transcriptomics analysis identifies a tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease},
volume = {5},
ISSN = {2666-3791},
url = {http://dx.doi.org/10.1016/j.xcrm.2024.101606},
DOI = {10.1016/j.xcrm.2024.101606},
number = {6},
journal = {Cell Reports Medicine},
publisher = {Elsevier BV},
author = {Alhaddad, Hasan and Ospina, Oscar E. and Khaled, Mariam Lotfy and Ren, Yuan and Vallebuona, Ethan and Boozo, Mohammad Baraa and Forsyth, Peter A. and Pina, Yolanda and Macaulay, Robert and Law, Vincent and Tsai, Kenneth Y. and Cress, W. Douglas and Fridley, Brooke and Smalley, Inna},
year = {2024},
month = June,
pages = {101606}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB