{
  "nbformat": 4,
  "nbformat_minor": 5,
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "language": "python",
      "name": "python3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "id": "intro",
      "metadata": {},
      "source": [
        "# HESRT: one verified sample\n",
        "Run beside hesrt_io.py after installing requirements.txt. No token is needed. The default package is about 3.2 MB.\n"
      ]
    },
    {
      "cell_type": "code",
      "id": "catalog",
      "metadata": {},
      "execution_count": null,
      "outputs": [],
      "source": [
        "from pathlib import Path\n",
        "from hesrt_io import load_catalog, download_sample\n",
        "catalog, revision = load_catalog()\n",
        "catalog[['gsm_id', 'tissue', 'technology', 'archive_bytes']].head()\n"
      ]
    },
    {
      "cell_type": "code",
      "id": "download",
      "metadata": {},
      "execution_count": null,
      "outputs": [],
      "source": [
        "row = catalog.loc[catalog.gsm_id.eq('GSM8915497')].iloc[0]\n",
        "folder = download_sample(row, Path('hesrt_demo'), revision)\n",
        "folder\n"
      ]
    },
    {
      "cell_type": "code",
      "id": "matrix",
      "metadata": {},
      "execution_count": null,
      "outputs": [],
      "source": [
        "import anndata as ad\n",
        "adata = ad.read_h5ad(folder / 'spatial.h5ad', backed='r')\n",
        "print(adata.shape, adata.obsm['spatial'].shape)\n",
        "adata.file.close()\n"
      ]
    },
    {
      "cell_type": "code",
      "id": "qc",
      "metadata": {},
      "execution_count": null,
      "outputs": [],
      "source": [
        "from PIL import Image\n",
        "with Image.open(folder / 'alignment_qc.png') as im:\n",
        "    display(im.copy())\n"
      ]
    }
  ]
}