Aslide

This is an integrated Pathology Image (a.k.a. Whole-slide image) reading library.

Current support format:

• .svs
• .tif
• .ndpi
• .vms
• .vmu
• .scn
• .mrxs
• .tiff
• .kfb
• .svslide
• .sdpc
• .TMAP
• .bif

This package currently tested and worked on:
Ubuntu 22.04 LTS

Pre-requisite

Installing these pre-requisites need a super user privilege on a workstation/server. If you do not have this, please contact your administrator. You should have opencv 3.4.2 (you need to build it from source code, please make sure the version number is 3.4.2) and ffmpeg. If you don't have it, you can install it by the following commands:

OpenCV

Before installing opencv, a super user privilege is required to install the following pacakges:

sudo apt update && sudo apt full-upgrade -y
sudo apt install gcc cmake git pkg-config libavcodec-dev libavformat-dev libswscale-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libgstreamer1.0-dev libgstreamer-plugins-base1.0-dev libgstreamer-plugins-bad1.0-dev gstreamer1.0-plugins-base gstreamer1.0-plugins-good gstreamer1.0-plugins-bad gstreamer1.0-plugins-ugly gstreamer1.0-libav gstreamer1.0-tools gstreamer1.0-x gstreamer1.0-alsa gstreamer1.0-gl gstreamer1.0-gtk3 gstreamer1.0-qt5 gstreamer1.0-pulseaudio libgtk-3-dev

Then you can proceed to download and complie OpenCV 3.4.2 by the following code snippet:

wget https://github.com/opencv/opencv/archive/3.4.2.zip
unzip ./3.4.2.zip
cd ./opencv3.4.2  
mkdir build
cd build 

# Complie
cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D WITH_TBB=OFF -D BUILD_NEW_PYTHON_SUPPORT=ON -D WITH_V4L=ON -D WITH_QT=OFF -D WITH_OPENGL=ON .. 

# Install (use -j option to enable multi-core processing)
sudo make install

Please refer to this for more details.

ffmpeg

sudo apt-get install ffmpeg

Installation

Since the package is not uploaded to PyPI, you need to install it from source code.

python setup.py install

After installation, you may check the detail installation path, for instance, if you use conda, it would be put in the following path (denoted as Aslide-path from hereon):

/home/username/anaconda3/lib/python3.x/site-packages/Aslide

Make sure the following files are in the folder:

Aslide-path/sdpc/so
Aslide-path/tmap/lib
Aslide-path/kfb/lib

After checking, open your the config file of your python environment (e.g. ~/.bashrc), add the following lines to the environment variable:

export LD_LIBRARY_PATH=Aslide-path/sdpc/so/:Aslide-path/sdpc/so/ffmpeg/:Aslide-path/kfb/lib/:Aslide-path/tmap/lib:$LD_LIBRARY_PATH

Then, you need to source the config file, and you are good to go:

source ~/.bashrc

Usage

Just import the package and use it as follows:

from Aslide.aslide import Slide

slide = Slide('path/to/your/slide')

For more details, please refer to the example_test_case.py file.

Credits

This package is based on the following projects:
Openslide
sdpc-python
tct
WSI-SDK

Many thanks to the authors of these projects.