{
  "dataset": "10x Genomics Xenium human breast cancer FFPE, replicate 1 (public)",
  "cells_raw": 167780,
  "panel_genes": 313,
  "control_features": {
    "Blank Codeword": 159,
    "Negative Control Codeword": 41,
    "Negative Control Probe": 28
  },
  "metadata_join_matched": 167780,
  "median_transcripts_per_cell": 164.0,
  "control_share_pct": 0.095,
  "cells_with_any_control": 23007,
  "cells_with_any_control_pct": 13.7,
  "signal_to_background_ratio": 766.5,
  "median_cell_area_um2": 140.3,
  "median_nucleus_fraction": 0.294,
  "nucleus_only_cells_pct": 0.0,
  "oversized_cells_pct": 0.5,
  "empty_cells": 1417,
  "min_transcripts_threshold": 10,
  "cells_after_qc": 164000,
  "removed_pct": 2.3,
  "clusters": 11,
  "marker_coverage": {
    "Epithelial / luminal": {
      "asked": 4,
      "in_panel": 3,
      "present": [
        "EPCAM",
        "KRT8",
        "ESR1"
      ]
    },
    "Basal / myoepithelial": {
      "asked": 4,
      "in_panel": 3,
      "present": [
        "KRT14",
        "KRT5",
        "ACTA2"
      ]
    },
    "T cells": {
      "asked": 4,
      "in_panel": 4,
      "present": [
        "CD3D",
        "CD3E",
        "CD8A",
        "IL7R"
      ]
    },
    "B / plasma": {
      "asked": 3,
      "in_panel": 2,
      "present": [
        "MS4A1",
        "CD79A"
      ]
    },
    "Myeloid": {
      "asked": 4,
      "in_panel": 4,
      "present": [
        "ITGAX",
        "CD68",
        "LYZ",
        "CD14"
      ]
    },
    "Endothelial": {
      "asked": 3,
      "in_panel": 2,
      "present": [
        "PECAM1",
        "VWF"
      ]
    },
    "Fibroblast": {
      "asked": 4,
      "in_panel": 3,
      "present": [
        "PDGFRA",
        "PDGFRB",
        "LUM"
      ]
    }
  },
  "lineages_fully_missing": [],
  "lineages_partially_covered": [
    "Epithelial / luminal",
    "Basal / myoepithelial",
    "B / plasma",
    "Endothelial",
    "Fibroblast"
  ],
  "top_markers_per_cluster": {
    "0": [
      "KRT8",
      "ERBB2",
      "TACSTD2",
      "S100A14",
      "CEACAM6"
    ],
    "1": [
      "EPCAM",
      "FASN",
      "FOXA1",
      "KRT7",
      "MLPH"
    ],
    "2": [
      "CEACAM6",
      "GATA3",
      "TACSTD2",
      "CD9",
      "MLPH"
    ],
    "3": [
      "FCER1G",
      "LYZ",
      "FGL2",
      "CD4",
      "CD68"
    ],
    "4": [
      "LUM",
      "POSTN",
      "CCDC80",
      "MMP2",
      "PDGFRB"
    ],
    "5": [
      "MYLK",
      "KRT14",
      "DST",
      "KRT5",
      "SERPINA3"
    ],
    "6": [
      "CAV1",
      "PECAM1",
      "CD93",
      "AQP1",
      "VWF"
    ],
    "7": [
      "MS4A1",
      "BANK1",
      "CXCR4",
      "SELL",
      "PTPRC"
    ],
    "8": [
      "CD3E",
      "TRAC",
      "PTPRC",
      "IL7R",
      "CXCR4"
    ],
    "9": [
      "KRT15",
      "SFRP1",
      "TACSTD2",
      "KRT23",
      "KRT6B"
    ],
    "10": [
      "ITM2C",
      "TENT5C",
      "SLAMF7",
      "MZB1",
      "SEC11C"
    ]
  },
  "lineages_recovered_in_clusters": 7,
  "lineages_checked": 7,
  "sanity_check_passed": true
}