Visium
Human colon
visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard
silver Interactive viewer H&E colorectal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_full_image': DataTree[cyx] (3, 37434, 28731), (3, 18717, 14365), (3, 9358, 7182), (3, 4679, 3591), (3, 2339, 1795)
│ ├── 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_hires_image': DataArray[cyx] (3, 2000, 1535)
│ └── 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_lowres_image': DataArray[cyx] (3, 600, 461)
├── Shapes
│ └── 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1': GeoDataFrame shape: (6518, 2) (2D shapes)
└── Tables
└── 'table': AnnData (6518, 18085)
with coordinate systems:
▸ 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1', with elements:
CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_full_image (Images), CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_hires_image (Images), CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_lowres_image (Images), CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1 (Shapes)
▸ 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_downscaled_hires', with elements:
CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_hires_image (Images), CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1 (Shapes)
▸ 'CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_downscaled_lowres', with elements:
CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_lowres_image (Images), CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("r0hI7AaM1crJtqq60001")
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("r0hI7AaM1crJtqq6") # 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 r0hI7AaM1crJtqq60001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/r0hI7AaM1crJtqq6
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid r0hI7AaM1crJtqq6License: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- colon
- Condition
- colorectal adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 6,518
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 28,731 × 37,434 px
- mpp
- 0.251 µm/px
- Size
- 2.5 GB
- Sample ID
- visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard
- License
- CC BY 4.0
- Published
- Oct 5, 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