Configuration file: config.json

The config.json file defines all parameters required by CellViability to run an analysis, including plate layout, control wells, filtering thresholds, preprocessing settings, and data paths. This configuration ensures reproducibility and allows the protocol to be adapted to different experimental designs.

Example:

{
  "screen": {
    "controls": {
      "negative": [
        "A01", "B01", "C01", "D01", "E01", "F01", "G01", "H01",
        "I01", "J01", "K01", "L01", "M01", "N01", "O01", "P01",
        "A24", "B24", "C24", "D24", "E24", "F24", "G24", "H24",
        "I24", "J24", "K24", "L24", "M24", "N24", "O24", "P24"
      ],
      "positive": [
        "A02", "B02", "C02", "D02", "E02", "F02", "G02", "H02",
        "I02", "J02", "K02", "L02", "M02", "N02", "O02", "P02",
        "A23", "B23", "C23", "D23", "E23", "F23", "G23", "H23",
        "I23", "J23", "K23", "L23", "M23", "O23", "N23", "P23"
      ]
    },
    "datadir": "screen",
    "fields": 1,
    "filter": {
      "Z": 0.5,
      "inCPE": 0.3
    },
    "parameters": {
      "channel": 0,
      "max_size": 500,
      "merge": "sum",
      "min_size": 0,
      "sigma": 1.0
    },
    "plates": [
      "P1",
      "P2"
    ],
    "wells": 64
  }
}

JSON fields

Field Description
controls Well identifiers (e.g., "A01", "B01") for negative controls (uninfected, untreated) and positive controls (infected, untreated), used for normalization and quality control.
datadir Root directory containing the image data for the screening experiment.
fields Number of image fields acquired per well (typically 1).
filter Quality and hit-selection thresholds: Z defines the minimum Z'-factor required for plate acceptance (default: 0.5), and inCPE defines the minimum inhibition of cytopathic effect for hit selection (default: 0.3).
parameters Image preprocessing and segmentation settings, including fluorescence channel index, Gaussian smoothing parameter (sigma), acceptable nucleus size range (min_size, max_size, in pixels), and the aggregation method (merge) for multi-field data.
plates List of plate identifiers included in the analysis.
wells Total number of wells per plate.