Skip to content

Instantly share code, notes, and snippets.

@andreped

andreped/cellsens-read-magnification-python-bioformats.ipynb

Created March 6, 2023 19:49
Show Gist options
  • Save andreped/82a749f29d30f7e0f046fb43b8f3865a to your computer and use it in GitHub Desktop.
Save andreped/82a749f29d30f7e0f046fb43b8f3865a to your computer and use it in GitHub Desktop.
Download ZIP
cellsens-read-magnification-python-bioformats.ipynb
Display the source blob
Display the rendered blob
Raw
cellsens-read-magnification-python-bioformats.ipynb
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"toc_visible": true,
"authorship_tag": "ABX9TyPRKBChEJozowpVTJt7TrMh",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/andreped/82a749f29d30f7e0f046fb43b8f3865a/cellsens-read-magnification-python-bioformats.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "VZNUceysGbXf",
"outputId": "1331f4b8-4de9-45f5-db94-a10955b68796"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Collecting python-bioformats\n",
" Downloading python_bioformats-4.0.7-py3-none-any.whl (40.6 MB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m40.6/40.6 MB\u001b[0m \u001b[31m34.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hCollecting xmltodict\n",
" Downloading xmltodict-0.13.0-py2.py3-none-any.whl (10.0 kB)\n",
"Collecting boto3>=1.14.23\n",
" Downloading boto3-1.26.84-py3-none-any.whl (134 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m134.7/134.7 KB\u001b[0m \u001b[31m18.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hCollecting future>=0.18.2\n",
" Downloading future-0.18.3.tar.gz (840 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m840.9/840.9 KB\u001b[0m \u001b[31m42.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25h Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
"Collecting python-javabridge==4.0.3\n",
" Downloading python-javabridge-4.0.3.tar.gz (1.3 MB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.3/1.3 MB\u001b[0m \u001b[31m33.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25h Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
"Requirement already satisfied: numpy>=1.20.1 in /usr/local/lib/python3.8/dist-packages (from python-javabridge==4.0.3->python-bioformats) (1.22.4)\n",
"Collecting jmespath<2.0.0,>=0.7.1\n",
" Downloading jmespath-1.0.1-py3-none-any.whl (20 kB)\n",
"Collecting s3transfer<0.7.0,>=0.6.0\n",
" Downloading s3transfer-0.6.0-py3-none-any.whl (79 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m79.6/79.6 KB\u001b[0m \u001b[31m10.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hCollecting botocore<1.30.0,>=1.29.84\n",
" Downloading botocore-1.29.84-py3-none-any.whl (10.5 MB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m10.5/10.5 MB\u001b[0m \u001b[31m92.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hRequirement already satisfied: python-dateutil<3.0.0,>=2.1 in /usr/local/lib/python3.8/dist-packages (from botocore<1.30.0,>=1.29.84->boto3>=1.14.23->python-bioformats) (2.8.2)\n",
"Requirement already satisfied: urllib3<1.27,>=1.25.4 in /usr/local/lib/python3.8/dist-packages (from botocore<1.30.0,>=1.29.84->boto3>=1.14.23->python-bioformats) (1.26.14)\n",
"Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.8/dist-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.30.0,>=1.29.84->boto3>=1.14.23->python-bioformats) (1.15.0)\n",
"Building wheels for collected packages: python-javabridge, future\n",
" Building wheel for python-javabridge (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for python-javabridge: filename=python_javabridge-4.0.3-cp38-cp38-linux_x86_64.whl size=1895959 sha256=4bfa0abff7ae4c838762f510b851d2db7e12423310529029c31c4713b90a476c\n",
" Stored in directory: /root/.cache/pip/wheels/ce/f3/d8/389d390e98d568ea1dbcbd36398e73360038c289d29e78c462\n",
" Building wheel for future (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492036 sha256=1d7cc417ccf2d2d22f27fb813857e3a97b9c5856400c77fa8f57de681c4df19f\n",
" Stored in directory: /root/.cache/pip/wheels/a0/0b/ee/e6994fadb42c1354dcccb139b0bf2795271bddfe6253ccdf11\n",
"Successfully built python-javabridge future\n",
"Installing collected packages: xmltodict, python-javabridge, jmespath, future, botocore, s3transfer, boto3, python-bioformats\n",
" Attempting uninstall: future\n",
" Found existing installation: future 0.16.0\n",
" Uninstalling future-0.16.0:\n",
" Successfully uninstalled future-0.16.0\n",
"Successfully installed boto3-1.26.84 botocore-1.29.84 future-0.18.3 jmespath-1.0.1 python-bioformats-4.0.7 python-javabridge-4.0.3 s3transfer-0.6.0 xmltodict-0.13.0\n"
]
}
],
"source": [
"!pip install python-bioformats xmltodict"
]
},
{
"cell_type": "code",
"source": [
"# download test WSI in the cellSens VSI format and uncompress\n",
"!wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-2.zip\n",
"!unzip OS-2.zip"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "iKObWWw4GtV5",
"outputId": "53b8d489-e1d5-4ddb-f9fd-a5c4b2580568"
},
"execution_count": 2,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"--2023-03-06 19:42:59-- https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-2.zip\n",
"Resolving openslide.cs.cmu.edu (openslide.cs.cmu.edu)... 128.2.209.93\n",
"Connecting to openslide.cs.cmu.edu (openslide.cs.cmu.edu)|128.2.209.93|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 309552104 (295M) [application/zip]\n",
"Saving to: ‘OS-2.zip’\n",
"\n",
"OS-2.zip 100%[===================>] 295.21M 2.37MB/s in 96s \n",
"\n",
"2023-03-06 19:44:36 (3.07 MB/s) - ‘OS-2.zip’ saved [309552104/309552104]\n",
"\n",
"Archive: OS-2.zip\n",
" inflating: OS-2.vsi \n",
" creating: _OS-2_/\n",
" creating: _OS-2_/stack10001/\n",
" inflating: _OS-2_/stack10001/frame_t.ets \n",
" creating: _OS-2_/stack1/\n",
" inflating: _OS-2_/stack1/frame_t.ets \n"
]
}
]
},
{
"cell_type": "code",
"source": [
"import javabridge as jb\n",
"import bioformats as bf\n",
"import xmltodict\n",
"\n",
"\n",
"def get_vsi_magnification(wsi_path):\n",
"\n",
" # get OME XML from VSI format\n",
" ome_xml = bf.get_omexml_metadata(wsi_path)\n",
"\n",
" # convert XML to human readable format (dict)\n",
" metadata = dict(xmltodict.parse(ome_xml))\n",
"\n",
" # extract objective information (can be more than one lens/objective)\n",
" curr = metadata[\"OME\"][\"Instrument\"][\"Objective\"]\n",
"\n",
" # extract magnification for each objective\n",
" magnifications = [eval(obj[\"@NominalMagnification\"]) for obj in curr]\n",
"\n",
" # assumption: the highest magnification value is the total magnification\n",
" return max(magnifications)\n",
"\n",
"\n",
"if __name__ == \"__main__\":\n",
"\n",
" # start virtual machine\n",
" jb.start_vm(class_path=bf.JARS, max_heap_size=\"4G\")\n",
"\n",
" magn = get_vsi_magnification(\"./OS-2.vsi\")\n",
" print(magn)\n",
"\n",
" # kill virtual machine\n",
" #jb.kill_vm()"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "51RXGOdMHESE",
"outputId": "4ecf020a-05dd-4589-e278-3cc67547eee0"
},
"execution_count": 3,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"20.0\n"
]
}
]
}
]
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment