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   "source": [
    "# How To: Manual Grid Detection When Automatic Fails\n",
    "\n",
    "When automatic grid detection does not find the correct grid layout,\n",
    "use `ManualGridDetector` to specify colony positions explicitly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from phenotypic.data import load_yeast_plate\n",
    "from phenotypic.detect import ManualGridDetector"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plate = load_yeast_plate()\n",
    "plate.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Identify Anchor Points\n",
    "\n",
    "Use the interactive Plotly figure above to find the pixel coordinates of\n",
    "the top-left colony center (`coord1`) and optionally the adjacent colony\n",
    "at row 1, column 1 (`coord2`). Hover over the colonies to read coordinates.\n",
    "\n",
    "`ManualGridDetector` places a footprint of specified `shape` and `width`\n",
    "at each grid position, using the anchor points to infer the grid spacing."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Replace these coordinates with values from your plate\n",
    "detector = ManualGridDetector(\n",
    "    coord1=(50, 50),      # (y, x) of top-left colony center\n",
    "    coord2=(120, 120),    # (y, x) of colony at row 1, col 1\n",
    "    shape=\"disk\",\n",
    "    width=15,\n",
    ")\n",
    "plate = detector.apply(plate)\n",
    "plate.dash(overlay=True, show_grid=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Adjust `coord1`, `coord2`, and `width` until the footprints align with\n",
    "your colonies. Increase `width` for larger colonies."
   ]
  }
 ],
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