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Stromal
DCIS_1
Myoepi_ACTA2+
Prolif_Invasive_Tumor
Macrophages_1
Macrophages_1
Stromal
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Stromal
Stromal
Invasive_Tumor
Invasive_Tumor
CD8+_T_Cells
Invasive_Tumor
Invasive_Tumor
Stromal
Invasive_Tumor
Macrophages_1
Stromal
Invasive_Tumor
Macrophages_1
Macrophages_1
CD8+_T_Cells
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Stromal
Macrophages_1
Endothelial
Macrophages_1
Invasive_Tumor
CD8+_T_Cells
Endothelial
Invasive_Tumor
Invasive_Tumor
Macrophages_1
Macrophages_1
Stromal
Stromal
Invasive_Tumor
Macrophages_1
Stromal
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
DCIS_2
Macrophages_1
Invasive_Tumor
Invasive_Tumor
Stromal
Macrophages_1
Invasive_Tumor
Stromal
Stromal
Invasive_Tumor
Myoepi_ACTA2+
Stromal
Invasive_Tumor
DCIS_1
Invasive_Tumor
Invasive_Tumor
Stromal
Stromal
Stromal
DCIS_1
DCIS_2
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Stromal
Stromal
Invasive_Tumor
Myoepi_ACTA2+
Invasive_Tumor
Invasive_Tumor
DCIS_1
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Endothelial
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Stromal
Invasive_Tumor
Stromal
Invasive_Tumor
Invasive_Tumor
Invasive_Tumor
Stromal
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MERFISH Breast Cancer Dataset — Representative Sample

This is a representative sample of the full dataset at: https://huggingface.co/datasets/kanand123/st-recon-merfish-breast-cancer

How the sample was created

  • test_sample.h5: First 5,000 cells from test.h5 (full test set: ~47K cells)
  • trainval_sample.h5: First 5,000 cells from trainval.h5 (full trainval set: ~430K cells)
  • All annotation and index files are included in full (they are small)
  • Sampling is sequential (first N rows), preserving the original data format and schema

Full dataset

The complete 218GB dataset is available at: https://huggingface.co/datasets/kanand123/st-recon-merfish-breast-cancer

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