{
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  {
   "cell_type": "markdown",
   "id": "8ce6b74e-54af-48ba-abf2-7ce2caa573bf",
   "metadata": {},
   "source": [
    "# Xenium Pre-process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b81ab32e",
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "%env ANYWIDGET_HMR=1\n",
    "\n",
    "import celldega as dega"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b47f611d",
   "metadata": {},
   "source": [
    "## Xenium pre processing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "52602e61-45e7-45a2-83a0-9a1b364d6619",
   "metadata": {},
   "outputs": [],
   "source": [
    "sample = 'Xenium_V1_humanLung_Cancer_FFPE_outs'\n",
    "data_dir = f'../data/instrument_data'\n",
    "path_landscape_files=f'../data/processed_data/DegaFiles/{sample}'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13350680",
   "metadata": {},
   "outputs": [],
   "source": [
    "tile_size=250\n",
    "\n",
    "dega.pre.main(\n",
    "    sample=sample,\n",
    "    data_root_dir=data_dir,\n",
    "    tile_size=tile_size,\n",
    "    path_landscape_files=path_landscape_files,\n",
    "    use_int_index=True,\n",
    "    image_tile_layer=\"all\"\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2fd7f196-c6cc-4321-8481-6249ed0b96a7",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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   "title_cell": "Table of Contents",
   "title_sidebar": "Contents",
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