How To Install python-openslide on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-openslide on Ubuntu 18.04.
What is python-openslide
python-openslide is:
OpenSlide is a C library that provides a simple interface to read whole-slide images also known as virtual slides.
Whole-slide images, also known as virtual slides, are large, high resolution images used in digital pathology. Reading these images using standard image tools or libraries is a challenge because these tools are typically designed for images that can comfortably be uncompressed into RAM or a swap file. Whole-slide images routinely exceed RAM sizes, often occupying tens of gigabytes when uncompressed. Additionally, whole-slide images are typically multi-resolution, and only a small amount of image data might be needed at a particular resolution.
This library currently supports:
- Aperio (.svs, .tif)
- Hamamatsu (.vms, .vmu, .ndpi)
- Leica (.scn)
- MIRAX (.mrxs)
- Sakura (.svslide)
- Trestle (.tif)
- Generic tiled TIFF (.tif)
This package contains the Python 2 module needed to run OpenSlide applications.
There are three methods to install python-openslide on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python-openslide Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python-openslide using apt-get by running the following command:
sudo apt-get -y install python-openslide
Install python-openslide Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-openslide using apt by running the following command:
sudo apt -y install python-openslide
Install python-openslide Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python-openslide using aptitude by running the following command:
sudo aptitude -y install python-openslide
How To Uninstall python-openslide on Ubuntu 18.04
To uninstall only the python-openslide package we can use the following command:
sudo apt-get remove python-openslide
Uninstall python-openslide And Its Dependencies
To uninstall python-openslide and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-openslide
Remove python-openslide Configurations and Data
To remove python-openslide configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-openslide
Remove python-openslide configuration, data, and all of its dependencies
We can use the following command to remove python-openslide configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-openslide
References
Summary
In this tutorial we learn how to install python-openslide package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
