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   "source": [
    "# How To: Measure Colony Size and Intensity\n",
    "\n",
    "Extract area, perimeter, circularity, and intensity statistics from\n",
    "detected colonies using `MeasureSize`, `MeasureShape`, and\n",
    "`MeasureIntensity`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import phenotypic as pht\n",
    "from phenotypic.data import load_yeast_plate\n",
    "from phenotypic.enhance import GaussianBlur, CLAHE\n",
    "from phenotypic.detect import OtsuDetector\n",
    "from phenotypic.measure import MeasureSize, MeasureShape, MeasureIntensity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pipeline = pht.ImagePipeline(\n",
    "    ops=[GaussianBlur(sigma=2.0), CLAHE(clip_limit=0.01), OtsuDetector()],\n",
    "    meas=[MeasureSize(), MeasureShape(), MeasureIntensity()],\n",
    ")\n",
    "df = pipeline.apply_and_measure(load_yeast_plate())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Size Metrics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "df[[\"Size_Area\", \"Size_IntegratedIntensity\"]].describe()"
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Shape Metrics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "df[[\"Shape_Circularity\", \"Shape_Solidity\", \"Shape_Eccentricity\"]].describe()"
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Intensity Metrics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "df[[\"Intensity_MeanIntensity\", \"Intensity_MedianIntensity\", \"Intensity_StandardDeviationIntensity\"]].describe()"
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The DataFrame has one row per colony. Filter, sort, and group using\n",
    "standard pandas operations to answer biological questions."
   ]
  }
 ],
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