Visium
Human palatine tonsil
gene-protein-expression-library-of-human-tonsil-cytassist-ffpe-2-standard
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FFPE_Protein_Expression_Human_Tonsil_full_image': DataTree[cyx] (3, 31967, 39132), (3, 15983, 19566), (3, 7991, 9783), (3, 3995, 4891), (3, 1997, 2445)
│ ├── 'CytAssist_FFPE_Protein_Expression_Human_Tonsil_hires_image': DataArray[cyx] (3, 1634, 2000)
│ └── 'CytAssist_FFPE_Protein_Expression_Human_Tonsil_lowres_image': DataArray[cyx] (3, 490, 600)
├── Shapes
│ └── 'CytAssist_FFPE_Protein_Expression_Human_Tonsil': GeoDataFrame shape: (4194, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4194, 18085)
with coordinate systems:
▸ 'CytAssist_FFPE_Protein_Expression_Human_Tonsil', with elements:
CytAssist_FFPE_Protein_Expression_Human_Tonsil_full_image (Images), CytAssist_FFPE_Protein_Expression_Human_Tonsil_hires_image (Images), CytAssist_FFPE_Protein_Expression_Human_Tonsil_lowres_image (Images), CytAssist_FFPE_Protein_Expression_Human_Tonsil (Shapes)
▸ 'CytAssist_FFPE_Protein_Expression_Human_Tonsil_downscaled_hires', with elements:
CytAssist_FFPE_Protein_Expression_Human_Tonsil_hires_image (Images), CytAssist_FFPE_Protein_Expression_Human_Tonsil (Shapes)
▸ 'CytAssist_FFPE_Protein_Expression_Human_Tonsil_downscaled_lowres', with elements:
CytAssist_FFPE_Protein_Expression_Human_Tonsil_lowres_image (Images), CytAssist_FFPE_Protein_Expression_Human_Tonsil (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("3RYoRrsp7Zmx56H90000")
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("3RYoRrsp7Zmx56H9") # 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 3RYoRrsp7Zmx56H90000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3RYoRrsp7Zmx56H9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3RYoRrsp7Zmx56H9License: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- palatine tonsil
- Modality
- RNA
- Observations (spots)
- 4,194
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 39,132 × 31,967 px
- mpp
- 0.215 µm/px
- Size
- 3.5 GB
- Sample ID
- gene-protein-expression-library-of-human-tonsil-cytassist-ffpe-2-standard
- License
- CC BY 4.0
- Published
- May 15, 2023
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB