spatial transcriptomics

Mouse spinal cord

NCBI117

silver Interactive viewer H&E amyotrophic lateral sclerosis ✓ Verified publication

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI117_full_image': DataTree[cyx] (3, 9898, 9299), (3, 4949, 4649), (3, 2474, 2324), (3, 1237, 1162)
├── Shapes
│     └── 'NCBI117_spots': GeoDataFrame shape: (375, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (375, 15169)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI117_full_image (Images), NCBI117_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ZaKTJ7kpSKt8Mv2i")   # 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

Load from the CLI

# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZaKTJ7kpSKt8Mv2i

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZaKTJ7kpSKt8Mv2i

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["ZaKTJ7kpSKt8Mv2i0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis→

302 datasets · publication

Metadata

Technology: spatial transcriptomics
Organism: mouse
Tissue: spinal cord
Condition: amyotrophic lateral sclerosis
Modality: RNA
Observations: 375
Tier: silver
Chemistry: ST 1k
Resolution: 9,299 × 9,898 px
mpp: 0.691 µm/px
Size: 115 MB
Sample ID: NCBI117
License: CC BY-NC-SA 4.0 NonCommercial
Published: Apr 5, 2019

Cite this dataset

doi.org/10.1126/science.aav9776 ↗

BibTeX

@article{Maniatis_2019,
  title = {Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis},
  volume = {364},
  ISSN = {1095-9203},
  url = {http://dx.doi.org/10.1126/science.aav9776},
  DOI = {10.1126/science.aav9776},
  number = {6435},
  journal = {Science},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Maniatis, Silas and Äijö, Tarmo and Vickovic, Sanja and Braine, Catherine and Kang, Kristy and Mollbrink, Annelie and Fagegaltier, Delphine and Andrusivová, Žaneta and Saarenpää, Sami and Saiz-Castro, Gonzalo and Cuevas, Miguel and Watters, Aaron and Lundeberg, Joakim and Bonneau, Richard and Phatnani, Hemali},
  year = {2019},
  month = Apr,
  pages = {89–93}
}

Source: science.org ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB