PathoPatch.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GA0VTVQzkmEJ"
      },
      "source": [
        "# PathoPatch Example\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "chE1_Uyxk4Lt"
      },
      "source": [
        "### 1. Installation (OpenSlide, CuCIM, PathoPatch)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "syrpNbj1jYDH",
        "outputId": "00b06be6-5d1f-4fcd-a997-edeab2d0e88c"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "\u001b[33m\r0% [Working]\u001b[0m\r            \rGet:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3,626 B]\n",
            "\u001b[33m\r0% [Connecting to archive.ubuntu.com] [Waiting for headers] [1 InRelease 3,626 B/3,626 B 100%] [Conn\u001b[0m\r                                                                                                    \rGet:2 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]\n",
            "Hit:3 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64  InRelease\n",
            "Hit:4 http://archive.ubuntu.com/ubuntu jammy InRelease\n",
            "Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB]\n",
            "Hit:6 http://archive.ubuntu.com/ubuntu jammy-backports InRelease\n",
            "Hit:7 https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu jammy InRelease\n",
            "Hit:8 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy InRelease\n",
            "Hit:9 https://ppa.launchpadcontent.net/graphics-drivers/ppa/ubuntu jammy InRelease\n",
            "Hit:10 https://ppa.launchpadcontent.net/ubuntugis/ppa/ubuntu jammy InRelease\n",
            "Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1,920 kB]\n",
            "Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [2,104 kB]\n",
            "Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1,358 kB]\n",
            "Fetched 5,615 kB in 2s (2,454 kB/s)\n",
            "Reading package lists... Done\n",
            "Building dependency tree... Done\n",
            "Reading state information... Done\n",
            "45 packages can be upgraded. Run 'apt list --upgradable' to see them.\n",
            "Reading package lists... Done\n",
            "Building dependency tree... Done\n",
            "Reading state information... Done\n",
            "The following additional packages will be installed:\n",
            "  libopenslide0\n",
            "Suggested packages:\n",
            "  libtiff-tools\n",
            "The following NEW packages will be installed:\n",
            "  libopenslide0 openslide-tools\n",
            "0 upgraded, 2 newly installed, 0 to remove and 45 not upgraded.\n",
            "Need to get 104 kB of archives.\n",
            "After this operation, 297 kB of additional disk space will be used.\n",
            "Get:1 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libopenslide0 amd64 3.4.1+dfsg-5build1 [89.8 kB]\n",
            "Get:2 http://archive.ubuntu.com/ubuntu jammy/universe amd64 openslide-tools amd64 3.4.1+dfsg-5build1 [13.8 kB]\n",
            "Fetched 104 kB in 0s (416 kB/s)\n",
            "Selecting previously unselected package libopenslide0.\n",
            "(Reading database ... 121753 files and directories currently installed.)\n",
            "Preparing to unpack .../libopenslide0_3.4.1+dfsg-5build1_amd64.deb ...\n",
            "Unpacking libopenslide0 (3.4.1+dfsg-5build1) ...\n",
            "Selecting previously unselected package openslide-tools.\n",
            "Preparing to unpack .../openslide-tools_3.4.1+dfsg-5build1_amd64.deb ...\n",
            "Unpacking openslide-tools (3.4.1+dfsg-5build1) ...\n",
            "Setting up libopenslide0 (3.4.1+dfsg-5build1) ...\n",
            "Setting up openslide-tools (3.4.1+dfsg-5build1) ...\n",
            "Processing triggers for man-db (2.10.2-1) ...\n",
            "Processing triggers for libc-bin (2.35-0ubuntu3.4) ...\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbbbind.so.3 is not a symbolic link\n",
            "\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc_proxy.so.2 is not a symbolic link\n",
            "\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbb.so.12 is not a symbolic link\n",
            "\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_5.so.3 is not a symbolic link\n",
            "\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc.so.2 is not a symbolic link\n",
            "\n",
            "/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_0.so.3 is not a symbolic link\n",
            "\n"
          ]
        }
      ],
      "source": [
        "!apt update && apt install -y openslide-tools"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "WkCsLuQAj41e",
        "outputId": "a8fed62a-3989-44a8-c20b-f1a757f32c92"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Collecting openslide-python\n",
            "  Downloading openslide-python-1.3.1.tar.gz (358 kB)\n",
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            "\u001b[?25h  Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "Collecting pathopatch\n",
            "  Downloading pathopatch-1.0.0b0-py3-none-any.whl (83 kB)\n",
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            "\u001b[?25hRequirement already satisfied: Pillow in /usr/local/lib/python3.10/dist-packages (from openslide-python) (9.4.0)\n",
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            "\u001b[?25hCollecting colorama (from pathopatch)\n",
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            "\u001b[?25hCollecting rasterio==1.3.5.post1 (from pathopatch)\n",
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            "\u001b[2K     \u001b[91m━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m\u001b[90m╺\u001b[0m\u001b[90m━━━━━━━━━━━━\u001b[0m \u001b[32m84.9/124.2 MB\u001b[0m \u001b[31m1.3 MB/s\u001b[0m eta \u001b[36m0:00:30\u001b[0m"
          ]
        }
      ],
      "source": [
        "!pip install openslide-python pathopatch"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "xdsM1hLnkC1D"
      },
      "outputs": [],
      "source": [
        "!pip install cucim"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "MNTTsbCblo-Q"
      },
      "source": [
        "## 2. Download files"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ldwjSWvYmbic"
      },
      "outputs": [],
      "source": [
        "!mkdir wsi_data\n",
        "!wget --directory-prefix ./wsi_data https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs\n",
        "!wget --directory-prefix ./wsi_data https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3p86K0Qv0h80"
      },
      "source": [
        "## 3. Simple Patch-Extraction\n",
        "\n",
        "Simple patch extraction"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "6smBlRYcmgPQ"
      },
      "outputs": [],
      "source": [
        "!wsi_extraction \\\n",
        "  --wsi_paths \\\n",
        "  --output_path \\\n",
        "  --wsi_extension svs \\\n",
        "  --downsample 1 \\\n",
        "  --processes 8 \\\n",
        "  --log_level debug \\\n",
        "  --overwrite True"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_5_FnB560qtz"
      },
      "source": [
        "## 4. DICOM-Files"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "is9CORMn0CWy"
      },
      "source": [
        "DICOM-Files:\n",
        "\n",
        "whole folder must be provided, please use the wsi_extension .dcm for loading wsi, or provide a .csv file as a filelist with path to the dicom folder. Files can be converted using `wsidicomizer` (https://github.com/imi-bigpicture/wsidicomizer)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "wrQq4WpW0vD6"
      },
      "outputs": [],
      "source": [
        "!pip install wsidicomizer"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "UFVhoBet1OWc"
      },
      "outputs": [],
      "source": [
        "!wsidicomizer -i -o"
      ]
    }
  ],
  "metadata": {
    "colab": {
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}