Imaging Mass Cytometry
Human breast
idr0076:MB0583_2_207
bronze breast cancer ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'img_MB0583_2_207_image': DataTree[cyx] (50, 608, 598), (50, 304, 299), (50, 152, 149), (50, 76, 74), (50, 38, 37)
├── Labels
│ └── 'img_MB0583_2_207_cells_labels': DataTree[yx] (608, 598), (304, 299), (152, 149), (76, 74), (38, 37)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1195, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (1195, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1195, 50)
with coordinate systems:
▸ 'global', with elements:
img_MB0583_2_207_image (Images), img_MB0583_2_207_cells_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5Em4xIk6HzNLkZfV0000")
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("5Em4xIk6HzNLkZfV") # 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 5Em4xIk6HzNLkZfV0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5Em4xIk6HzNLkZfV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5Em4xIk6HzNLkZfVLicense: CC BY 4.0
Metadata
- Technology
- Imaging Mass Cytometry
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- protein
- Observations (cells)
- 1,195
- Tier
- bronze
- Chemistry
- IMC
- Staining
- Antibodies
- Size
- 20.9 MB
- Sample ID
- idr0076:MB0583_2_207
- License
- CC BY 4.0
- Published
- Sep 29, 2020
Cite this dataset
doi.org/10.1038/s43018-020-0026-6 ↗ BibTeX
@article{idr:idr0076,
doi = {10.1038/s43018-020-0026-6},
title = {idr0076:MB0496_1_380},
year = {2020}
}Source: idr.openmicroscopy.org ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB