MIBI-TOF

Mouse liver

S-BIAD2557:CSL101:slide2-C2

bronze hepatocellular carcinoma ✓ Verified publication

MIBI-TOF

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SpatialData object
├── Images
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
│     └── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_image': DataTree[cyx] (30, 1024, 1024), (30, 512, 512), (30, 256, 256), (30, 128, 128), (30, 64, 64)
├── Labels
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│     └── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_cell_boundaries': GeoDataFrame shape: (722, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_cell_boundaries': GeoDataFrame shape: (865, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_cell_boundaries': GeoDataFrame shape: (1128, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_cell_boundaries': GeoDataFrame shape: (856, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_cell_boundaries': GeoDataFrame shape: (1197, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_cell_boundaries': GeoDataFrame shape: (974, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_cell_boundaries': GeoDataFrame shape: (969, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_cell_boundaries': GeoDataFrame shape: (1533, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_cell_boundaries': GeoDataFrame shape: (1410, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_cell_boundaries': GeoDataFrame shape: (1552, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_cell_boundaries': GeoDataFrame shape: (1391, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_cell_boundaries': GeoDataFrame shape: (1277, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_cell_boundaries': GeoDataFrame shape: (978, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_cell_boundaries': GeoDataFrame shape: (1437, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_cell_boundaries': GeoDataFrame shape: (1305, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_cell_boundaries': GeoDataFrame shape: (1330, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_cell_boundaries': GeoDataFrame shape: (866, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_cell_boundaries': GeoDataFrame shape: (1445, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_cell_boundaries': GeoDataFrame shape: (1231, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_cell_boundaries': GeoDataFrame shape: (1451, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_cell_boundaries': GeoDataFrame shape: (1180, 2) (2D shapes)
│     ├── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_cell_boundaries': GeoDataFrame shape: (1229, 2) (2D shapes)
│     └── 'pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_cell_boundaries': GeoDataFrame shape: (1411, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (27737, 30)
with coordinate systems:
    ▸ 'global', with elements:
        pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_image (Images), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_whole_cell_labels (Labels), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_0_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_1_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_2_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_3_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_4_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_5_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_6_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_7_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_8_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_9_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_10_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_11_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_12_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_13_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_14_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_15_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_16_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_17_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_18_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_19_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_20_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_21_cell_boundaries (Shapes), pCSL005_CSL101_Hep-PK_MIBI_slide2-C2_0_22_cell_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("WC30VI1FR4iVJpMX0000")
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("WC30VI1FR4iVJpMX")   # 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 WC30VI1FR4iVJpMX0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WC30VI1FR4iVJpMX

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WC30VI1FR4iVJpMX

Install (Python 3.12+) Docs →

License: CC BY 4.0

View on Lamin ↗ Flag a data issue

Part of collection

bia-s-biad2557→

25 datasets · publication

Metadata

Technology: MIBI-TOF
Organism: mouse
Tissue: liver
Condition: hepatocellular carcinoma
Modality: protein
Observations (cells): 27,737
Tier: bronze
Chemistry: MIBI
Staining: Antibodies
Size: 3.7 GB
Sample ID: S-BIAD2557:CSL101:slide2-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