{
  "categories": [
    {
      "name": "Sample QC",
      "key": "sample_summary_stats",
      "additionalAxes": false,
      "defaultFilters": []
    },
    {
      "name": "Cell RNA QC",
      "key": "cell_rna_stats",
      "additionalAxes": true,
      "defaultFilters": [
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "total_counts",
          "label": "Total UMI per cell",
          "description": "Total number of RNA molecules detected per cell. Low values typically indicate empty droplets or low-quality cells that should be filtered out.",
          "cutoffMin": null,
          "cutoffMax": null,
          "zoomMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "num_nonzero_vars",
          "label": "Number of non-zero genes per cell",
          "description": "Count of unique genes detected in each cell. Low gene counts often indicate poor-quality cells.",
          "cutoffMin": null,
          "cutoffMax": null,
          "zoomMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "fraction_mitochondrial",
          "label": "Fraction UMI of mitochondrial genes per cell",
          "description": "Proportion of cell's RNA from mitochondrial genes.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "fraction_ribosomal",
          "label": "Fraction UMI of ribosomal genes per cell",
          "description": "Proportion of cell's RNA from ribosomal protein genes. Extreme values may indicate stress responses or cell cycle abnormalities.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Area",
          "label": "Cell Area",
          "description": "Area of the segmented cells.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "AspectRatio",
          "label": "Aspect Ratio",
          "description": "Aspect ratio of the segmented cells.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Mean.DAPI",
          "label": "Mean DAPI Intensity",
          "description": "Mean intensity of DAPI stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Mean.MembraneStain",
          "label": "Mean Membrane Stain Intensity",
          "description": "Mean intensity of Membrane stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Mean.PanCK",
          "label": "Mean PanCK Intensity",
          "description": "Mean intensity of PanCK stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Mean.CD45",
          "label": "Mean CD45 Intensity",
          "description": "Mean intensity of CD45 stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Mean.CD3",
          "label": "Mean CD3 Intensity",
          "description": "Mean intensity of CD3 stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Max.DAPI",
          "label": "Max DAPI Intensity",
          "description": "Maximum intensity of DAPI stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Max.MembraneStain",
          "label": "Max Membrane Stain Intensity",
          "description": "Maximum intensity of Membrane stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Max.PanCK",
          "label": "Max PanCK Intensity",
          "description": "Maximum intensity of PanCK stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Max.CD45",
          "label": "Max CD45 Intensity",
          "description": "Maximum intensity of CD45 stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "visualizationType": "histogram",
          "field": "Max.CD3",
          "label": "Max CD3 Intensity",
          "description": "Maximum intensity of CD3 stain.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        }
      ]
    }
  ]
}
