histolab has only one system-wide dependency:
You can download and install it from https://openslide.org/download/ according to your operating system.
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¶
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.
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¶
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
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
For example if
OpenSlide is installed in
C:\ you should replace
Verify Correct Pixman installation¶
ldconfig -v | grep libpixman
brew list --versions pixman
(Get-Item "C:\OpenSlide\bin\libpixman-1-0.dll").VersionInfo | format-list