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" (Point4106_pt1162_30997)
bronze invasive ductal breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'Point4106_pt1162_30997_image': DataTree[cyx] (46, 1024, 1024), (46, 512, 512), (46, 256, 256), (46, 128, 128), (46, 64, 64)
├── Labels
│ └── 'Point4106_pt1162_30997_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│ └── 'Point4106_pt1162_30997_cell_boundaries': GeoDataFrame shape: (2079, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2079, 46)
with coordinate systems:
▸ 'global', with elements:
Point4106_pt1162_30997_image (Images), Point4106_pt1162_30997_whole_cell_labels (Labels), Point4106_pt1162_30997_cell_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("E8NSqYUcqSsXKAPE0000")
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("E8NSqYUcqSsXKAPE") # 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 E8NSqYUcqSsXKAPE0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/E8NSqYUcqSsXKAPE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid E8NSqYUcqSsXKAPELicense: CC BY 4.0
Metadata
- Technology
- MIBIscope (MIBI-TOF)
- Vendor
- Ionpath
- Organism
- human
- Tissue
- breast
- Condition
- invasive ductal breast carcinoma
- Modality
- protein
- Observations (cells)
- 2,079
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 8.1 MB
- Sample ID
- d87vg86zd8:Point4106_pt1162_30997
- 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