channels.json

{
  "view": "CD",
  "view_description": "density-augmented cell crop",
  "files": {
    "cell.bin": {
      "channels": [
        "DNA",
        "AGP",
        "ER",
        "Mito",
        "RNA"
      ],
      "stains": {
        "DNA": "Hoechst 33342",
        "AGP": "Phalloidin + WGA",
        "ER": "Concanavalin A",
        "Mito": "MitoTracker Deep Red",
        "RNA": "SYTO 14"
      },
      "shape": [
        5,
        224,
        224
      ],
      "dtype": "uint8",
      "layout": "channel-first (C, H, W)",
      "encoding": "raw bytes; np.frombuffer(blob, dtype=np.uint8).reshape(5, 224, 224)"
    },
    "mask.bin": {
      "channels": [
        "nucleus",
        "cell"
      ],
      "shape": [
        2,
        224,
        224
      ],
      "dtype": "uint8",
      "layout": "channel-first (C, H, W)",
      "encoding": "raw bytes; np.frombuffer(blob, dtype=np.uint8).reshape(2, 224, 224)"
    }
  },
  "notes": [
    "On-disk channel order [DNA, AGP, ER, Mito, RNA] differs from the JUMP-CP v2 publication order [DNA, ER, RNA, AGP, Mito] and from the Recursion RxRx order [DNA, ER, AGP, RNA, Mito, ...].",
    "Loaders must remap by name, not by index, when combining JUMP with other Cell Painting datasets.",
    "Mask channels are [nucleus, cell] \u2014 both binary uint8."
  ]
}