Visium
Human brain
GSM8376639
bronze Interactive viewer H&E melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8376639_sample1_hires_image': DataArray[cyx] (3, 2000, 1587)
│ └── 'GSM8376639_sample1_lowres_image': DataArray[cyx] (3, 600, 476)
├── Shapes
│ └── 'GSM8376639_sample1': GeoDataFrame shape: (1732, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1732, 36601)
with coordinate systems:
▸ 'GSM8376639_sample1', with elements:
GSM8376639_sample1_hires_image (Images), GSM8376639_sample1_lowres_image (Images), GSM8376639_sample1 (Shapes)
▸ 'GSM8376639_sample1_downscaled_hires', with elements:
GSM8376639_sample1_hires_image (Images), GSM8376639_sample1 (Shapes)
▸ 'GSM8376639_sample1_downscaled_lowres', with elements:
GSM8376639_sample1_lowres_image (Images), GSM8376639_sample1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5AJLRM8SHjIJqlYq0000")
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("5AJLRM8SHjIJqlYq") # 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 5AJLRM8SHjIJqlYq0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5AJLRM8SHjIJqlYq
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5AJLRM8SHjIJqlYqLicense: NCBI GEO policy
Part of collection
spatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- melanoma
- Modality
- RNA
- Observations (spots)
- 1,732
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,587 × 2,000 px
- mpp
- 4.139 µm/px
- Size
- 13.6 MB
- Sample ID
- GSM8376639
- License
- NCBI GEO policy
- Published
- Nov 21, 2024
Cite this dataset
doi.org/10.1158/0008-5472.can-24-2346 ↗ BibTeX
@article{Ospina_2024,
title = {spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis},
volume = {85},
ISSN = {1538-7445},
url = {http://dx.doi.org/10.1158/0008-5472.can-24-2346},
DOI = {10.1158/0008-5472.can-24-2346},
number = {5},
journal = {Cancer Research},
publisher = {American Association for Cancer Research (AACR)},
author = {Ospina, Oscar E. and Manjarres-Betancur, Roberto and Gonzalez-Calderon, Guillermo and Soupir, Alex C. and Smalley, Inna and Tsai, Kenneth Y. and Markowitz, Joseph and Khaled, Mariam L. and Vallebuona, Ethan and Berglund, Anders E. and Eschrich, Steven A. and Yu, Xiaoqing and Fridley, Brooke L.},
year = {2024},
month = Dec,
pages = {848–858}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB