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   "source": [
    "# How To: Correct Edge Effects in Plate Assays\n",
    "\n",
    "Colonies on the outer rows and columns of an agar plate often grow\n",
    "differently due to temperature gradients and humidity effects. Use\n",
    "`EdgeCorrector` to statistically identify and correct these biases."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from phenotypic.data import load_meas\n",
    "from phenotypic.analysis import EdgeCorrector"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load Measurement Data\n",
    "\n",
    "`EdgeCorrector` operates on measurement DataFrames, not on images\n",
    "directly. Start with a DataFrame containing colony measurements and\n",
    "grid position information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = load_meas()\n",
    "print(f\"Shape: {df.shape}\")\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Apply Edge Correction\n",
    "\n",
    "Specify the measurement column to correct (`on`), the grouping columns\n",
    "(`groupby`), and the grid dimensions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "corrector = EdgeCorrector(\n",
    "    on=\"Shape_Area\",\n",
    "    groupby=[\"Metadata_Strain\"],\n",
    "    nrows=8,\n",
    "    ncols=12,\n",
    "    top_n=3,\n",
    "    pvalue=0.05,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "corrected = corrector.analyze(df)\n",
    "corrected.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The corrected DataFrame contains adjusted values for edge-affected\n",
    "colonies. The `top_n` parameter controls how many interior colonies\n",
    "are used as the reference baseline."
   ]
  }
 ],
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