pamly 0.3.5

Command line interface for digital pathology tools.

pamly-lib

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.

Installing and Compiling Openslide locally

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"

Using the provided DOCKERFILE

We also provide a dockerfile building upon rust:alpine-linux.

Installing the Converter Tool

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, ...).

Run the Converter Tool

In order to convert a raw WSI scan into an .sqlite databse run

pamly convert <Slide Path>