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MIBI-TOF

Mouse liver

S-BIAD2557:NL006:slide4-C2

bronze intrahepatic cholangiocarcinoma ✓ Verified publication
MIBI-TOF
print(sdata) 
SpatialData object
├── Images
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     └── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
├── Labels
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     └── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_cell_boundaries': GeoDataFrame shape: (943, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_cell_boundaries': GeoDataFrame shape: (876, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_cell_boundaries': GeoDataFrame shape: (851, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_cell_boundaries': GeoDataFrame shape: (829, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_cell_boundaries': GeoDataFrame shape: (916, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_cell_boundaries': GeoDataFrame shape: (1116, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_cell_boundaries': GeoDataFrame shape: (890, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_cell_boundaries': GeoDataFrame shape: (856, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_cell_boundaries': GeoDataFrame shape: (1140, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_cell_boundaries': GeoDataFrame shape: (896, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_cell_boundaries': GeoDataFrame shape: (718, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_cell_boundaries': GeoDataFrame shape: (950, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_cell_boundaries': GeoDataFrame shape: (1008, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_cell_boundaries': GeoDataFrame shape: (1035, 2) (2D shapes)
│     ├── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_cell_boundaries': GeoDataFrame shape: (922, 2) (2D shapes)
│     └── 'pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_cell_boundaries': GeoDataFrame shape: (1120, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (15066, 30)
with coordinate systems:
    ▸ 'global', with elements:
        pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_image (Images), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_whole_cell_labels (Labels), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_0_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_1_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_2_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_3_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_4_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_5_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_6_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_7_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_8_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_9_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_10_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_11_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_12_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_13_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_14_cell_boundaries (Shapes), pCSL005_NL006_Chol-PFfPt_MIBI_slide4-C2_0_15_cell_boundaries (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("eMGGe8HZIHr4acgJ0000")
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("eMGGe8HZIHr4acgJ")   # 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 eMGGe8HZIHr4acgJ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/eMGGe8HZIHr4acgJ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid eMGGe8HZIHr4acgJ
Install (Python 3.12+) Docs →

License: CC BY 4.0

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25 datasets · publication

Metadata

Technology
MIBI-TOF
Organism
mouse
Tissue
liver
Condition
intrahepatic cholangiocarcinoma
Modality
protein
Observations (cells)
15,066
Tier
bronze
Chemistry
MIBI
Staining
Antibodies
Size
2.0 GB
Sample ID
S-BIAD2557:NL006:slide4-C2
License
CC BY 4.0
Published
Jun 30, 2026

Cite this dataset

doi.org/10.64898/2026.03.24.711280 ↗
BibTeX 
@article{bia:S-BIAD2557,
  doi = {10.64898/2026.03.24.711280},
  title = {S-BIAD2557:CSL021:slide1-D1},
  year = {2026}
}

Source: BioImage Archive ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB