MIBIscope (MIBI-TOF)
Human breast
Risom et al., Cell 2022, "Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma" (pt1058)
bronze invasive ductal breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'Point4136_pt1058_31850_image': DataTree[cyx] (46, 1024, 1024), (46, 512, 512), (46, 256, 256), (46, 128, 128), (46, 64, 64)
├── Labels
│ └── 'Point4136_pt1058_31850_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│ └── 'Point4136_pt1058_31850_cell_boundaries': GeoDataFrame shape: (1016, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1016, 46)
with coordinate systems:
▸ 'global', with elements:
Point4136_pt1058_31850_image (Images), Point4136_pt1058_31850_whole_cell_labels (Labels), Point4136_pt1058_31850_cell_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("64VbGKTpbg1n6ncF0000")
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("64VbGKTpbg1n6ncF") # 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 64VbGKTpbg1n6ncF0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/64VbGKTpbg1n6ncF
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 64VbGKTpbg1n6ncFLicense: CC BY 4.0
Metadata
- Technology
- MIBIscope (MIBI-TOF)
- Vendor
- Ionpath
- Organism
- human
- Tissue
- breast
- Condition
- invasive ductal breast carcinoma
- Modality
- protein
- Observations (cells)
- 1,016
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 5.9 MB
- Sample ID
- d87vg86zd8:pt1058
- License
- CC BY 4.0
- Published
- Mar 17, 2022
Cite this dataset
doi.org/10.17632/d87vg86zd8.3 ↗ BibTeX
@article{mendeley:d87vg86zd8,
doi = {10.17632/d87vg86zd8.3},
title = {Risom et al., Cell 2022, "Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma" (pt1047)}
}Source: data.mendeley.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB