spatial transcriptomics

Mouse spinal cord

NCBI179

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

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI179_full_image': DataTree[cyx] (3, 12344, 11596), (3, 6172, 5798), (3, 3086, 2899), (3, 1543, 1449)
├── Shapes
│     └── 'NCBI179_spots': GeoDataFrame shape: (270, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (270, 14033)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI179_full_image (Images), NCBI179_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("UjzKFAPAJsboKCuN0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("UjzKFAPAJsboKCuN")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download UjzKFAPAJsboKCuN0000 --dest data/

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

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

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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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 (spots): 270
Tier: silver
Chemistry: ST 1k
Magnification: 20x
Resolution: 11,596 × 12,344 px
mpp: 0.551 µm/px
Size: 120 MB
Sample ID: NCBI179
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