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"cells": [
{
"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": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.1"
},
"toc": {
"base_numbering": 1,
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": false,
"toc_position": {},
"toc_section_display": true,
"toc_window_display": false
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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