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   "source": [
    "# How To: Denoise Low-Light Images\n",
    "\n",
    "Low-light or high-ISO plate images contain noise that confuses detectors.\n",
    "PhenoTypic offers several denoising approaches, each with different\n",
    "tradeoffs between speed and quality."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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     "end_time": "2026-04-21T02:48:31.962620Z",
     "start_time": "2026-04-21T02:48:29.957604Z"
    }
   },
   "outputs": [],
   "source": [
    "from phenotypic.data import load_fungi_plate\n",
    "from phenotypic.enhance import GaussianBlur, MedianFilter, VisuShrinkEnhancer\n",
    "from phenotypic.correction import StableDenoise"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-21T02:48:32.689774Z",
     "start_time": "2026-04-21T02:48:31.966699Z"
    }
   },
   "outputs": [],
   "source": [
    "plate = load_fungi_plate()\n",
    "plate.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 1: GaussianBlur (fastest)\n",
    "\n",
    "Simple and fast. Blurs noise but also softens colony edges."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-21T02:48:32.792218Z",
     "start_time": "2026-04-21T02:48:32.705123Z"
    }
   },
   "outputs": [],
   "source": [
    "result1 = GaussianBlur(sigma=2.0).apply(plate.copy())\n",
    "result1.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 2: MedianFilter (edge-preserving)\n",
    "\n",
    "Removes salt-and-pepper noise while keeping colony boundaries sharp."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-21T02:48:32.983868Z",
     "start_time": "2026-04-21T02:48:32.793013Z"
    }
   },
   "outputs": [],
   "source": [
    "result2 = MedianFilter(width=5).apply(plate.copy())\n",
    "result2.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 3: VisuShrinkEnhancer (wavelet)\n",
    "\n",
    "Wavelet-based denoising. Preserves fine details better than spatial\n",
    "filters at the cost of speed."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-21T02:48:33.071784Z",
     "start_time": "2026-04-21T02:48:32.987789Z"
    }
   },
   "outputs": [],
   "source": [
    "result3 = VisuShrinkEnhancer(wavelet=\"db2\", mode=\"soft\").apply(plate.copy())\n",
    "result3.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Option 4: StableDenoise (BM3D, highest quality)\n",
    "\n",
    "Variance-stabilized BM3D denoising. Best quality but slowest. Use for\n",
    "critical experiments where accuracy matters more than speed."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-21T02:48:36.315657Z",
     "start_time": "2026-04-21T02:48:33.073624Z"
    }
   },
   "outputs": [],
   "source": [
    "result4 = StableDenoise(stage_arg=\"hard_thresholding\").apply(plate.copy())\n",
    "result4.detect_mat.dash()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Choosing a Method\n",
    "\n",
    "| Method | Speed | Edge preservation | Best for |\n",
    "|--------|-------|-------------------|----------|\n",
    "| `GaussianBlur` | Fastest | Low | Quick preprocessing |\n",
    "| `MedianFilter` | Fast | High | Salt-and-pepper noise |\n",
    "| `VisuShrinkEnhancer` | Moderate | High | General noise, fine details |\n",
    "| `StableDenoise` | Slow | Highest | Critical experiments |"
   ]
  }
 ],
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