Visium
Mouse claustrum of brain
Claustrum/dorsal Endopiriform cortex complex cell identity is determined 1 by Nurr1 and regulates hallucinogenic-like states. (V12M09-008_B1)
bronze Under review Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'V12M09-008_B1_hires_image': DataArray[cyx] (3, 2000, 1892)
│ └── 'V12M09-008_B1_lowres_image': DataArray[cyx] (3, 600, 568)
├── Shapes
│ └── 'V12M09-008_B1': GeoDataFrame shape: (1863, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1863, 32285)
with coordinate systems:
▸ 'V12M09-008_B1', with elements:
V12M09-008_B1_hires_image (Images), V12M09-008_B1_lowres_image (Images), V12M09-008_B1 (Shapes)
▸ 'V12M09-008_B1_downscaled_hires', with elements:
V12M09-008_B1_hires_image (Images), V12M09-008_B1 (Shapes)
▸ 'V12M09-008_B1_downscaled_lowres', with elements:
V12M09-008_B1_lowres_image (Images), V12M09-008_B1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("YhXVanokVtFUQffl0000")
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("YhXVanokVtFUQffl") # 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 YhXVanokVtFUQffl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/YhXVanokVtFUQffl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YhXVanokVtFUQfflLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Vendor
- 10x Genomics
- Organism
- mouse
- Tissue
- claustrum of brain
- Modality
- RNA
- Observations (spots)
- 1,863
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,892 × 2,000 px
- mpp
- 3.432 µm/px
- Size
- 29.0 MB
- Sample ID
- wxcbdvrh2t:V12M09-008_B1
- License
- CC BY 4.0
- Published
- Aug 5, 2024
- Review
- organism inferred; sections are coronal brain sections containing the claustrum; tissue could also be "brain"
Cite this dataset
doi.org/10.17632/wxcbdvrh2t.1 ↗ BibTeX
@article{mendeley:wxcbdvrh2t,
doi = {10.17632/wxcbdvrh2t.1},
title = {Claustrum/dorsal Endopiriform cortex complex cell identity is determined 1 by Nurr1 and regulates hallucinogenic-like states. (V12M09-008_A1)},
year = {2024}
}Source: data.mendeley.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB