The pamly-lib originates from the initial pamly project for whole slide image conversion, upload and viewing. The pamly-lib contains the source code for the pamly rust crate which contains the converter tool of pamly as a CLI.
It builds upon the C-library Openslide in order to convert the main propietary scanner formats to an accessible sqlite database. Thus, follow the installation and compilation instructions for Openslide as the pamly-lib depends on openslide to be properly installed. Mac users can also install via brew.
NOTE: If openslide is not found during cargo install it might be caused by your PATH, e.g. if you brew install on Mac run
export LIBRARY_PATH="/opt/homebrew/lib"
If you've installed and compiled via the git repo, add the path to the .dylib, so something like
export DYLD_LIBRARY_PATH="$HOME/.../openslide/builddir/src"
We also provide a dockerfile building upon rust:alpine-linux.
In order to install the pamly CLI, including the converter tool, run
cargo install pamly --features convert
Without the flag --features convert you still get other features of pamly which do not depend on openslide, such as generating the types file (containing diagnoses, stains, labels, ...).
In order to convert a raw WSI scan into an .sqlite databse run
pamly convert <Slide Path>