Installation¶

histolab has only one system-wide dependency: OpenSlide.

You can download and install it from https://openslide.org/download/ according to your operating system.

Warning

There is a known bug in Pixman versions 0.38.* that causes OpenSlide to produce images with black boxes for large images. See issue https://github.com/openslide/openslide/issues/291 for reference. Install version 0.40 (latest) depending on your operating system.

Install Pixman 0.40 on Ubuntu¶

Ubuntu 21.04¶

If you are running histolab on Ubuntu 21.04 you probably already have Pixman 0.40 and you are all set, go have fun 😎

Ubuntu 20.04 LTS¶

If you are using a conda environment, it is sufficient to run:

conda install -c anaconda pixman==0.40

Otherwise, to force a working version of libpixman to be loaded before a bad version, you need to exploit the LD_PRELOAD mechanism on Linux. Make sure you have that file installed first.

export LD_PRELOAD=/path/of/libpixman-1.so.0.40.0:$LD_PRELOAD

If necessary, build libpixman from source. It’s an easy build since it doesn’t have any dependencies:

wget https://cairographics.org/releases/pixman-0.40.0.tar.gz
tar -xvf pixman-0.40.0.tar.gz
cd pixman-0.40.0
./configure
make
sudo make install

Install Pixman 0.40 on macOS¶

If OpenSlide is installed via brew, pixman 0.40 will be automatically installed ✔️

Install Pixman 0.40 on Windows¶

OpenSlide builds are the same for all Windows versions and they include pixman 0.34.

Pixman 0.40 can be retrieved using pacman (the package manager of Arch Linux, see https://www.msys2.org/ for more info):

pacman -S mingw-w64-x86_64-pixman

Once pixman 0.40 is installed you have to link the current version of the dll to the OpenSlide installation. The only thing to do is overwrite libpixman-1-0.dll in the bin directory of OpenSlide with the one installed with pixman 0.40 that should be placed in /mingw64/bin/libpixman-1-0.dll.

For example if OpenSlide is installed in C:\ you should replace C:\OpenSlide\bin\libpixman-1-0.dll with /mingw64/bin/libpixman-1-0.dll.

Verify Correct Pixman installation¶

Ubuntu¶

ldconfig -v | grep libpixman

macOS¶

brew list --versions pixman

Windows (PowerShell)¶

(Get-Item "C:\OpenSlide\bin\libpixman-1-0.dll").VersionInfo | format-list